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The Bone Marrow Microenvironment is Essential for the Function of Connective Tissue Growth Factor (CTGF/CCN2) in Childhood Acute Lymphoblastic Leukaemia Julia Wells, B.A, B.Sc (Hons) This thesis is presented for the degree of Doctor of Philosophy The University of Western Australia School of Paediatrics and Child Health Telethon Institute for Child Health Research Faculty of Medicine and Dentistry -2014-

Transcript of The Bone Marrow Microenvironment is Essential for the ... · iv! ! overexpressing cell lines 2.3.5...

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The Bone Marrow Microenvironment is Essential for the Function of

Connective Tissue Growth Factor (CTGF/CCN2) in Childhood

Acute Lymphoblastic Leukaemia

Julia Wells, B.A, B.Sc (Hons)

This thesis is presented for the degree of Doctor of PhilosophyThe University of Western Australia

School of Paediatrics and Child HealthTelethon Institute for Child Health Research

Faculty of Medicine and Dentistry-2014-

2015
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Abstract

Acute lymphoblastic leukaemia (ALL) is the most commonly diagnosed cancer

in children. Successive chemotherapy treatment protocols have been

successful in increasing overall survival rates to 90%. However, further

improvement is achievable only through a better understanding of the

pathogenesis of ALL and the mechanisms of drug resistance. Connective tissue

growth factor (CTGF/CCN2) has previously been reported as the most

deregulated gene in childhood B-cell precursor (BCP) ALL, existing in

approximately 75% of cases (Boag et al., 2007) and has been associated with a

poor prognosis in both children and adults (Kang et al., 2010, Sala-Torra et al.,

2005). A functional role for CTGF has yet to be determined in ALL, though in

other cancers it’s deregulation contributes positively to tumour progression and

survival.

In this thesis the functional role of CTGF in childhood BCP ALL was explored in

three ways. Firstly, two BCP ALL cell lines (PER-278 and PER-371, established

from primary patient specimens) where engineered to stably express human

CTGF and a GFP reporter coding sequence. Overexpression of CTGF in PER-

278 and PER-371 was confirmed by qRT-PCR (2.6 and 3.4 fold, respectively)

and by western blot, for both cellular protein and conditioned media. In culture

conditions, high levels of CTGF did not alter proliferation, drug sensitivity (to

cytarabine and vincristine) or the gene expression profile of PER-278 or PER-

371. A marked difference was seen between the gene expression profiles of the

two BCP ALL cell lines, resulting in different genes being co-expressed with

CTGF and foreshadowing the cell line-specific interactions seen in the mouse

bone marrow microenvironment.

Secondly, in culture conditions recombinant human CTGF was found to

significantly alter gene expression in a human bone marrow stromal cell line

(HS5) after 8, 16 and 48 hours in culture. Microarray analyses revealed the

greatest number of genes were deregulated at 8 hours (787 upregulated and

622 downregulated) determined by LIMMA significance and a greater than 2-

fold change compared with controls. A large number were associated with

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secreted proteins functioning in extracellular matrix, lipid metabolism, adhesion

and cytokine signalling.

Lastly, xenograft models of leukaemia were established using non-obese

diabetic/ severe combined immunodeficiency (NOD/SCID) mice injected via the

tail-vein with either 2x105 PER-278 or 1x106 PER-371 CTGF-High and Low

cells. Within the murine microenvironment, a divergent response was observed

due to CTGF overexpression in these cell lines, attributable to their distinct

gene expression profiles. PER-371 xenografts showed reduced survival in

CTGF High compared with Low groups (median survival 62 versus 71 days

post-injection, p=0.01). This difference was attributed to increased engraftment

of PER-371 High cells in the bone marrow, and associated with an increased

deposition of reticulin fibres in the surrounding extracellular matrix (Ag+ stain for

reticulin). No difference in survival was observed between PER-278 High and

PER-278 Low xenografted mice, with both groups having a median survival of

49 days post-injection. However, increased resistance to low dose cytarabine, a

chemotherapeutic drug, occurred exclusively in PER-278 xenografted mice due

to CTGF overexpression, though a clear mechanism of action was not

distinguished. Both cell lines responded to high dose cytarabine in vivo, with

differing levels of drug toxicity. This indicates that CTGF can contribute to

cytarabine resistance in some subtypes of BCP ALL, but the drug overcomes

these effects at increased doses, that are more clinically relevant.

The results presented in this thesis suggest a complex role for CTGF in BCP

ALL, with functions being sub-type and context specific. New understanding of

the role of CTGF in the disease emphasised the requirement for interaction with

stromal elements from the bone marrow to accelerate tumour growth or

contribute to drug resistance. This thesis outlines an extracellular matrix-

dependent molecular mechanism by which CTGF confers a growth advantage

to BCP ALL cells. Contributing to the list of known genotype changes that lead

to phenotypic differences in BCP ALL cells, with the goal of providing new

treatment strategies for children with the disease.

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Table of Contents Abstract i Table of Contents iii Figure List vi Table List ix

Abbreviations x

Acknowledgments xii Publications arising xiii Presentations related to this thesis xiv

Statement of Candidature Contribution xvii

Chapter 1 Introduction 1

1.1 ⏐ Acute Lymphoblastic leukaemia 3

1.2 ⏐ The bone marrow microenvironment 10

1.3 ⏐ Connective tissue growth factor (CTGF) 20

1.4 ⏐ Aims and outline of the thesis 37

Chapter 2 Materials and Methods 39

2.1⏐ Cell lines and tissue culture 41

2.1.1 Suspension cell lines

2.1.2 Adherent cell lines

2.2⏐ Cell transfections 42

2.2.1.1 Plasmids used in cell transfection

2.2.2 Standard electroporation of B-cell precursor ALL cells

2.2.3 Neon electroporation of B-cell precursor ALL cells

2.2.4 Selection of stable cells transfected with pcDNA3.1 vector

2.2.5 Lentiviral production

2.2.6 Lentiviral infection

2.2.7 selection of stable cells onfected with pCDH vector

2.3⏐ RNA analyses 49

2.3.1 RNA extraction

2.3.2 cDNA synthesis

2.3.3 Quantitation of CTGF gene expression

2.3.4 Global gene expression to determine effect of CTGF on stable CTGF-

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overexpressing cell lines

2.3.5 Global gene expression to determine effect of recombinant human CTGF

on stromal cells

2.4⏐ Protein Analyses 53

2.4.1 Cellular protein extraction

2.4.2 Secreted protein purification

2.4.3 Western blot

2.4.4 Enzyme linked immunosorbent assay

2.4.5 Protein array

2.5⏐ Proliferation assays 58

2.6⏐ Drug sensitivity assays 59

2.6.1 Optimisation of antibiotics for stable cell line selection

2.6.2 Sensitivity to chemotherapy drugs in CTGF-High and CTGF-Low cell lines

2.6.3 Nucleoside transporter activity in PER-278 High or Low cells

2.7⏐ NOD/SCID mouse xenografts 62

2.7.1 Mice

2.7.2 Generation of NOD/SCID mice

2.7.3 Chemotherapy regimen

2.7.4 Mouse dissection and tissue preparation

2.7.5 Tissue analysis by flow cytometry

2.7.6 Histochemical and immunohistochemical (IHC) staining

2.8⏐ Statistical analyses 72

Chapter 3 Stable overexpression of CTGF in B-cell precursor ALL cell lines

does not alter function 73

3.1⏐ Abstract 75

3.2⏐ Introduction 76

3.3⏐ Results 76

3.4⏐ Discussion 94

Chapter 4 Recombinant human CTGF has the capacity to alter the gene

expression profile of human BM stromal cells 99

4.1⏐ Abstract 101

4.2⏐ Introduction 101

4.3⏐ Results 102

4.4⏐ Discussion 114

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Chapter 5 CTGF contributes to drug sensitivity in PER-278

B-cell precursor ALL

5.1⏐ Abstract

5.2⏐ Introduction

5.3⏐ Results

5.4⏐ Discussion

Chapter 6 CTGF confers a growth advantage to PER-371 B-cell

precursor ALL cells in the BM microenvironment

6.1⏐ Abstract

6.2⏐ Introduction

6.3⏐ Results

6.4⏐ Discussion

Chapter 7 General Discussion

7.1⏐ Introduction

7.2⏐ Limitations of the current research

7.3⏐ Critical findings

7.4⏐ Proposed mechanism of CTGF action

7.5⏐ Future directions

7.4⏐ Final conclusions

Chapter 8 References Appendix: Supplementary Figures

117 119 120 121 134

137 139 140 141 174 179

181

183

184

189

189 191 193 217

 

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Figure List No. Figure Title Page Number

1.1 1.2 1.3 1.4 2.1 2.2 2.3 2.4 3.1 3.2 3.3 3.4 3.5 3.6 3.7 3.8 3.9 3.10 4.1 4.2  

B-precursor acute lymphoblastic leukaemia (ALL) originates in the bone marrow . Mesenchymal stem cells (MSC) have the potential to differentiate into divergent cell lineages Human long bone as a model for the bone marrow niche Conserved structure of the CCN family members Leukaemia engraftment was determined by GFP+ cell detection using flow cytometry Immunohistochemical staining was scored by the Nuance FX multispectral imaging system and InForm software (Perkin Elmer) Reticulin stain scoring Sample size required per treatment group (x axis) to detect a difference in population means (y axis) Transfection of B-precursor ALL cell lines by electroporation was not successful in producing stable clones Transduction efficiency of B-precursor ALL cell lines by lentiviral infection Verification of stable overexpression of CTGF mRNA in B-precursor ALL cell lines PER-278 and PER-371 Overexpression of CTGF cellular and secreted protein in B-precursor ALL cell lines PER-278 and PER-371 PER-278 and PER-371 CTGF overexpression did not effect proliferation PER-278 and PER-371 representative drug sensitivity curves for vincristine (VCR) and cytarabine (ARAC) PER-278 and PER-371 CTGF overexpression did not affect sensitivity to chemotherapeutic drugs RNA integrity analysis for PER-278 and PER-371 cell line sample CTGF RNA and protein was overexpressed in the PER-278 and PER-371 cell line samples collected for microarray analysis PER-278 and PER-371 CTGF High cells did not affect global gene expression patterns compared to CTGF Low cells Changes to global gene expression in BM stromal cells (HS5) caused by treatment with rhCTGF compared to control buffer CTGF deregulates HS5 genes involved in the IGF1 signalling pathway

5 13 15 23 67 69 71 71 79 81 83 85 87 89 90 92 93 95 103 107

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No. Figure Title Page Number

4.3 4.4 4.5 5.1 5.2 5.3 5.4 5.5 5.6 5.7 6.1 6.2 6.3 6.4 6.5 6.6 6.7 6.8 6.9

CTGF deregulates HS5 genes involved in the PI3K/AKT signalling pathway CTGF deregulates HS5 genes involved in TGFβ networks. Validation of two ECM-associated genes upregulated in HS5 cells after treatment with CTGF CTGF protein expression levels for PER-278 High and Low NOD/SCID xenografts PER-278 NOD/SCID xenografts showed no difference in survival or BM engraftment between High and Low injected cell lines Rapid engraftment of leukaemia at end stage disease for PER-278 NOD/SCID xenografts Kaplan Meier survival curve of PER-278 High and Low engrafted NOD/SCID xenografts treated with single agent chemotherapy Snapshot of proliferation in PER-278 NOD/SCID xenografts 24 hours post ARAC dose Snapshot of apoptosis in PER-278 NOD/SCID xenografts 24 hours post ARAC injection Reduced drug sensitivity to ARAC by PER-278 High cells was not replicated in presence of secreted proteins from stromal-leukaemia cell interactions CTGF secreted protein expression levels for PER-371 High and Low cells intended for NOD/SCID inoculation Kaplan-Meier survival curve of PER-371 High and Low engrafted NOD/SCID xenografts treated with chemotherapy drugs or saline PER-371 NOD/SCID xenografts showed increased BM engraftment in CTGF High compared to Low cells at late stage disease Rapid engraftment of leukaemia cells at end stage disease for PER-371 NOD/SCID xenografts Snapshot of proliferation and apoptosis in PER-371 cells at late stage disease Leukemic-burden in diaphysis of PER-371 engrafted bone marrow Leukemic-burden in epiphysis/ metaphysisof PER-371 engrafted bone marrow Proliferating cells in diaphysis of PER-371 leukaemia-burdened bone marrow Proliferating cells in depiphysis/ metaphysis of PER-371 leukaemia-burdened bone marrow

108 109 113 122 124 125 127 129 131 133 142 144 146 147 149 153 155 157 159

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No. Figure Title Page Number

6.10 6.11 6.12 6.13 6.14

Megakaryocyte count in diaphysis of PER-371 leukaemia-burdened bone marrow Reticulin connective tissue density in diaphysis of PER-371 leukaemia-burdened bone marrow Reticulin connective tissue density in epiphysis/ metaphysis Invading Leukaemia front depicts immunostaining associations significant by Pearson’s correlation coefficient of PER-371 leukaemia-burdened bone marrow Decreased survival of PER-371 High xenografts was not replicated in vitro

161 164 165 167 169

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Table List No. Table Title Page Number

1.1 1.2 2.1 3.1 3.2 3.3 3.4 4.1 4.2 5.1 6.1 6.2 6.3

A topography of CTGF-associated neoplasms in humans Pattern of CTGF deregulation compared to normal tissue and its association with clinical outcome and cellular mechanism of action List of primary, secondary and tertiary antibodies Patient details for derived cell lines PER-278 and PER-371 Patient-derived B-precursor ALL cell lines maintain patient DNA profile RNA integrity number for PER-278 and PER-371 cell line samples Fold change of CTGF High or Intermediate compared to Low for RNA and cellular protein samples Ingenuity Pathway Analysis (IPA) for differentially regulated genes between stromal cells (HS5) treated with rhCTGF (100ng/ml) or control buffer for 8 hours Top functions of secreted HS5 genes differentially regulated after treatment with rhCTGF (100ng/ml) or control buffer for 8 hours. Fold change difference between PER-278 High and Low cells before tail-vein injection into NOD/SCID mice Fold change difference between PER-371 High and Low cells before injection of 1x106 cells into the tail-vein of NOD/SCID mice Leukaemia cells alter secreted proteins from HS5 stromal cells after co-culture CTGF alters secreted proteins from stromal-leukaemia cell co-cultures

25 29 55 77 77 92 93 105 111 122 142 171 173

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Abbreviations ABI3BP - ABI gene family member 3 binding protein ADAMTS1 - A disintegrin and metalloproteinase with thrombospondin motifs 1 ALL - Acute lymphoid leukaemia ARAC - Cytarabine ASNS - Asparagine synthetase ATCC - American Type Culture Collection BCA - Bicinchoninic acid BCR - B-cell receptor BM - Bone marrow BSA - Bovine serum albumin CAR - CXCL12-abundant reticular CMV - Cytomegalovirus CNT - Cumulative nucleoside transporters COG - Childrenís Oncology Group COL3A1 - Collagen, type 3, alpha 1 CSF3/GCSF - Colony stimulating factor 3 CTGF - Connective tissue growth factor CXCL1 - Chemokine (C-X-C motif) ligand 1 CXCL12 - CXC-chemokine ligand 12 CXCL6 - Chemokine (C-X-C motif) ligand 6 CXCR4 - C-X-C chemokine receptor type 4 DMEM - Dulbeccoís Modified Eagleís Medium ECM - Extracellular matrix EDTA - Ethylenediaminetetraacetic acid EF1 - Elongation factor 1 EGTA - Ethylene glycol tetraacetic acid ELISA - Enzyme-linked immunosorbent assay ENT - Equilibrative nucleoside transporters ERK1/2 - Extracellular signal-regulating kinases FCS - Fetal calf serum FN - Fibronectin

FSC vs SSC - Forward and side scatter plot GFP - Green fluorescent protein HIV-1 - Human immunodeficiency virus HSC - Haematopoietic stem cell IGF - Insulin-like growth factor IHC - Immunohistochemical IL11 - Interleukin 11 IL6 - Interleukin 6 IL7 - Interleukin 7 IL8 - Interleukin 8 ILK - Integrin-linked kinase IPA - Ingenuity Pathway Analysis IRF4 - Interferon regulatory factor 4 ITGAV - Integrin, alpha V IVC - Individually ventilated cages LOX - Lysyl oxidase MHCI - Major histocompatability complex class I MLL - mixed lineage leukaemia MMN/CD10 - Membrane metallo-endopeptidase MMP1 - Matrix metalloproteinase 1 MSC - Mesenchymal stem cells MSCV - Murine stem cell virus NFKB - Nuclear factor kappa-B NMBPR - Nitrobenzylmercaptopurine ribonucleoside NOD/SCID - Non-obese diabetic/ severe-combined immunodeficient NSG - NOD scid gamma OPN - Osteopontin PCA - Principle component analysis PCR - Polymerase chain reaction PI3K/AKT - Phosphoinositide 3-kinase/protein kinase C PP2A - Protein phosphatase 2 PSMB4 - Proteasome subunit beta, type 4 PURO - Puromycin resistance gene RANKL - Receptor activator of nuclear factor-?B ligand SCF - Stem cell factor SPDI - Secreted protein database initiative SSC-A vs SSC-W – Side scatter area and width plot STR - Short tandem repeat TE - Tris-EDTA TGFβ - Transforming growth factor beta

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TMB - Tetramethylbenzidine TMSB10 - Thymosin beta 10 TRIM22 - Tripartite motif containing 22 U - Units VCAM1 - Vascular cell adhesion molecule 1 VCR - Vincristine XIAP - X-linked inhibitor of apoptosis protein

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Acknowledgements

Apparently it takes a pit crew to drive a race car and it takes a village to

raise a child... and I now know these sums mean nothing compared to what it

takes to earn a doctorate. My thanks go out to all who helped me on my way.

To my supervisors Prof. Ursula Kees, Prof. Cathy Cole, Dr Amy Samuels

and Dr Meegan Howlett, the league of extraordinary ladies, who have each at

particular moments throughout my candidature been beacons of skill, logic and

hope. Thanks for everything you amazing women!

To my scholarship funding bodies, I consider myself fortunate indeed to

be a recipient of your monetary support, the Richard Walter Gibbon Medical

Research Scholarship, Stan and Jean Perron Top-Up Scholarship, TICHR

Completion Scholarship, Children’s Leukaemia and Cancer Research

Foundation Travel Award, Friends of the Institute Travel Award, UWA Graduate

Research Centre Travel Grant and UWA School of Paediatrics and Child Health

Travel Grant.

To our collaborators Prof. David Brigstock, Dr Makiko Fujii and Prof.

Richard Lock, who shared resources and essential knowledge of the field.

To the histology department at PMH, especially Dr Adrian Charles,

pathologist to all needy scientists, and Maxine Crook, who generously saved

the day by teaching me some old school stains.

To my biostatistician and bioinformatician friends, Denise Anderson, Dr.

Kim Carter and Richard Francis, who always helped me with a smile.

To everyone in LCR and BTRP for the great friendships and lab

expertise. To Jasmin, who was my Virgil through the Inferno for the first two

years. To Ursula, Meegan, Jasmin, Jette, Heloise, Laurence, Sajzla, Patrizja,

Mat and Jo who have all been team CTGF, there is a reward waiting for us in

the afterlife for working with this promiscuous and tricky protein.

To my family and friends, even in your bafflement of the mysterious world

of academia you never wavered in your support. Putting up with my lame

excuses, cooking me meals and buying me drinks. (Except Matt, you told me

from the start that I should instead get a job, then helped me the most looking

for typos and abbreviations at 4AM.)

To Mubby, because no matter what we’re doing, so long as it’s together it

will turn out to be the good old days.

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Publications arising from this thesis Wells, J.E., Cole, C.H., Kees, U.R., Deregulated expression of connective tissue growth factor (CTGF/CCN2) is linked to poor outcome in human cancer, Int J Cancer, 2015;137(3):504-11 (Review Article)

Wells, J.E., Howlett, M, Cheung, LC, Kees, UR, The role of CCN family genes in haematological malignancies, J Cell Commun Signal., 2015; E-pub DOI: 10.1007/s12079-015-0296-4 (Review Article)

Wells, JE, Howlett, M, Halse, H, Heng, J, Ford, J, Cheung, LC, Samuels, AL, Crook, M, Charles, AK, Cole, CH, Kees, UR, High expression of connective tissue growth factor (CTGF) accelerates dissemination of leukaemia (Experimental article, for submission)

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Presentations arising from this thesis

Presentations (Oral) Wells, J.E. How Connective Tissue Growth Factor Mediates Communication between Pre-B Acute Lymphoblastic Leukaemia and the Bone Marrow Microenvironment, Telethon Institute for Child Health Research 4th Annual Postgraduate Student Forum, TICHR Seminar Room, Perth, Western Australia, August, 2010. Wells, J.E. Role of Microenvironment Interactions in Childhood Leukaemia, Child and Adolescent Health Research Symposium, Princess Margaret Hospital, Perth, Western Australia, October, 2010. Wells, J.E. Role of Connective Tissue Growth Factor in in vitro Models of Childhood Leukaemia, 7th State Cancer Conference, Perth Convention and Exhibition Centre, Perth, Western Australia, March, 2011. Wells, J.E., Ford, J., Samuels, A.L., Cole, C.H., Kees, U.R., Determining the role of connective tissue growth factor in childhood acute lymphoblastic leukaemia, Australian Society for Medical Research Scientific Symposium, Perth, Western Australia, June 2011. Wells, J.E., Microenvironment Interactions in Childhood Leukaemia, UWA Three Minute Thesis Semi-Finals, Perth, Western Australia, July 2011. Wells, J.E., Ford, J., Samuels, A.L., Cole, C.H., Kees, U.R., Connective tissue growth factor contributes to microenvironment interactions in childhood leukaemia, Telethon Institute for Child Health Research 5th Annual Postgraduate Student Forum, Perth, Western Australia, August 2011. Wells, J.E., Ford, J., Samuels, A.L., Cole, C.H., Kees, U.R., How connective tissue growth factor is involved in childhood leukaemia and the bone marrow microenvironment, Princess Margaret Hospital Child and Adolescent Health Research Symposium, Perth, Western Australia, October 2011.   Wells, JE, Heng, J, Ford, J, Howlett, M, Brigstock, DR, Samuels, AL, Cole, CH, Kees, UR, In vivo model to determine the role of connective tissue growth factor (CTGF) in childhood leukaemia, Telethon Institute for Child Health Research 6th Annual Postgraduate Student Forum, Perth, Western Australia, August 2012. Wells, JE, Heng, J, Ford, J, Howlett, M, Brigstock, DR, Samuels, AL, Cole, CH, Kees, UR, Love thy neighbour: an in vivo model to determine the role of the bone marrow microenvironment in childhood leukaemia, Perth Cancer Club, Perth, Western Australia, September 2012. Wells, JE, Heng, J, Ford, J, Howlett, M, Brigstock, DR, Samuels, AL, Cole, CH, Kees, UR, Neighbours from hell: leukaemia cells and the bone marrow microenvironment, TICHR Child Health Research Seminar, Perth, Western Australia, September 2012.

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Wells, JE, Heng, J, Ford, J, Howlett, M, Brigstock, DR, Samuels, AL, Cole, CH, Kees, UR, The role of connective tissue growth factor (CTGF) in an in vivo model of childhood leukaemia, Child and Adolescent Health Research Symposium, Perth, Western Australia, October 2012. Wells, JE, Heng, J, Ford, J, Howlett, M, Brigstock, DR, Samuels, AL, Cole, CH, Kees, UR, Connective tissue growth factor (CTGF) affects microenvironment interactions in a mouse xenograft model of acute lymphoblastic leukaemia, Australian Society for Medical Research Scientific Symposium, Perth, Western Australia, June 2013. Wells, J.E., Finding the genetic differences that matter in childhood leukaemia, UWA Three Minute Thesis Semi-Finals, Perth, Western Australia, July 2013. Wells, JE, Heng, J, Ford, J, Halse, H, Samuels, AL, Howlett, M, Cole, CH, Kees, UR, Connective tissue growth factor (ctgf/ccn2) alters progression of leukaemia in a xenograft mouse model, Child and Adolescent Health Research Symposium, Perth, Western Australia, October 2013. Wells, JE, Howlett, M, Halse, HM, Ford, J, Heng, J, Cheung LC, Kees, UR, Connective tissue growth factor is increased in acute lymphoblastic leukaemia and confers a growth advantage within the bone marrow niche, 8th State Cancer Conference, Perth Convention and Exhibition Centre, Perth, Western Australia, October 2013.

Wells, JE, Howlett, M, Cheung, LC Halse, H, Heng, J, Cole, CH, Kees, UR, Targeting the microenvironment in childhood acute lymphoblastic leukaemia: Identifying key players in the spread of disease, Australian and New Zealand Children's Haematology/Oncology Group (ANZCHOG) Annual Scientific Meeting, Perth, Western Australia, June 2015.

Presentations (Poster) Wells, J.E., Ford, J., Samuels, A.L., Cole, C., Kees, U.R., Role of Microenvironment Interactions in Childhood Leukaemia, 23rd Lorne Cancer Conference, Mantra Erskine, Lorne, Victoria, February, 2011. Wells, J.E., Ford, J., Samuels, A.L., Cole, C.H., Kees, U.R., The role of connective tissue growth factor in microenvironment interactions of childhood leukaemia, Students in Health and Medical Research Conference, Perth, Western Australia, August 2011.   Wells, J.E., Ford, J., Samuels, A.L., Cole, C.H., Kees, U.R., Connective tissue growth factor (CTGF) contributes to microenvironment interactions in childhood leukaemia, AACR Tumor microenvironment complexity: Emerging roles in cancer therapy, Orlando, Florida, November 2011. Wells, JE, Heng, J, Ford, J, Howlett, M, Brigstock, DR, Samuels, AL, Cole, CH, Kees, UR, In vivo model to determine the role of connective tissue growth factor (CTGF) in childhood leukaemia, Cold Spring Harbor Asia- International Cancer Microenvironment Society Joint International Conference, Suzhou, China, November 2012.    

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 Wells, JE, Howlett, M, Halse, M, Ford, J, Heng, J, Samuels, AL, Cole, CH, Kees, UR, Connective tissue growth factor (CTGF) is increased in pre-B acute lymphoblastic leukaemia and confers a growth advantage within the bone marrow niche, AACR conference on cellular heterogeneity in the tumor microenvironment, San Diego, USA, February 2014. Wells, JE, Howlett, M, Halse, M, Ford, J, Heng, J, Samuels, AL, Cole, CH, Kees, UR, Connective tissue growth factor (CTGF) is increased in pre-B acute lymphoblastic leukaemia and confers a growth advantage within the bone marrow niche, GTC4th International Conference on Tumor Progression and Therapeutic Resistance, Boston, USA, March 2014.

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Statement of Candidate Contribution

The experiments detailed in this thesis have been conducted at the Telethon

Institute for Child Health Research, Perth, Western Australia. All work presented

was performed solely by the author under the supervision of Prof Ursula Kees,

Dr Amy Samuels and Dr Meegan Howlett, except were contributions from

others have been acknowledged.

This thesis contains no material, which has previously been submitted for any

other degree or diploma.

In instances were work has been performed by other parties, permission has

been granted from these parties to include this work in the thesis.

………………….. …………………….

Julia E. Wells Prof Ursula R Kees

July 2015

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111111111Introduction

There's no limit to how complicated things can get, on account of one thing always

leading to another.

E.B. White

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Chapter 1 Introduction

Acute lymphoblastic leukaemia (ALL) is a significant disease in childhood. To

improve therapy and cure rates for patients, it is vital to understand the tumour

biology. This will increase our chances of finding novel selective agents that are

less toxic to normal cells and more effective than currently used cytotoxic

agents. At present, there is much we don’t know about the development and

propagation of ALL. This literature review will first cover our current knowledge

of ALL tumour biology and then expand on the role of the surrounding cells in

the bone marrow microenvironment. The third section will discuss the

significance of a deregulated protein, connective tissue growth factor (CTGF),

and the evidence supporting a possible functional role of this protein in ALL.

Finally, the aims and outline of this thesis will be addressed.

1.1 Acute lymphoblastic leukaemia

Cancer is the second most common cause of death, after accidents, in

Australian children under 15 years of age. The most prevalent form of childhood

cancer, accounting for 25.7 percent of total cases, is acute lymphoid leukaemia

(ALL) (Baade, 2010). Australian figures reflect world trends in cancer statistics

with ALL being the most prominent form of cancer in children (Jemal, 2008;

Kaatsch, et al., 2006; Pritchard-Jones, et al., 2006). Due to modern multimodal

chemotherapy regimes treatment of ALL has been a major success story with

overall event-free survival rates reaching approximately 90 percent (Inaba, et

al.; Pui, et al., 2010).

Leukaemias are malignant disorders of the haematopoietic system and are

characterised by alterations in aberrant lymphoid and myeloid progenitor cell. .

In ALL, lymphoid progenitor cells that normally differentiate into mature B, T and

natural killer cells, instead undergo unlimited self-renewal and clonal expansion.

ALL comprises several subtypes, broadly differentiated into B or T cell origin.

Leukaemogenesis involves the induction, development and progression of the

disease and is associated with changes to cellular proliferation, differentiation

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and apoptosis (cell death). The successive transformative steps required for

malignancy are not fully understood. However, leukemia induction in many

childhood cases begins in-utero and requires other “promotional” exposures for

emergence of disease (Inaba, et al., 2013). An exception to this is infant ALL

with a rearrangement of the mixed lineage leukaemia (MLL) gene, where the

disease is established by birth (Greaves, et al., 2003). After a precursor

lymphoid cell becomes malignant, accumulation of these clonal or oligoclonal

malignant cells continues unabated. The high numbers of malignant cells

overwhelm the immunocompetent cells of haematopoietic origin and affect

normal function. Childhood leukaemia is often not clinically diagnosed until

normal physiological function is affected caused by bone marrow failure,

presenting as neutropenia, thrombocytopenia, anemia or bone pain.

B-cell ALL Normal B-cell lymphopoiesis in humans initially occurs in the fetal liver and then

shifts to the bone marrow from mid-gestation and until death of the individual.

Haematopoietic stem cells commit to a lymphoid progenitor cell fate and further

differentiate into T-cell progenitors, which migrate to the thymus to before

differentiation into mature cells, and B-cell progenitors, which differentiate

entirely within the bone marrow in close association with stromal cells.

Immature-B cells migrate into the peripheral blood to reach spleen and

lymphoid organs where they differentiate into mature-B and plasma cells.

Normal mammalian B-cell development is highly ordered, comprises many

stages, involves sequential immunoglobulin gene recombination and expression

of transcription factors specific to the B-cell lineage (Clark, et al., 2014; Reya &

Rudolf, 1998). B-cells lymphopoiesis begins with the committed lymphoid

progenitor cells and progresses sequentially from early-B, pro-B, pre-B,

immature-B, mature-B, memory-B to plasma cells (Figure 1.1).

Human precursor B-cell ALLs similarly originate in the bone marrow and are the

most common form of acute leukaemia. They have a better overall prognosis

than T-cell ALLs, but due to their high incidence account for substantial

mortality (Armstrong, 2005). Human B-cell ALLs are classified by tumour

phenotype, which involves characterisation of antigen surface markers, nuclear

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tumourigenesis

Figure 1.1. B-precursor acute lymphoblastic leukaemia (ALL) originates in the bone marrow. B-precursor ALL occurs after initial genetic mutations in early B-lineage progenitor cells receive secondary ‘hits’ creating malignant cells with undeterred proliferation. B-cell leukaemia subtypes, such as B-precursor ALL, arise from similar transformations taking place along the various stages of the normal B cell maturation pathway. Haematopoietic stem cells (HSCs) become more lineage specific as they differentiate into immature B-cells in the bone marrow, which escape into peripheral blood vessels for subsequent maturation at external sites.

Early-B cell

B-precursor ALL

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gene expression and immunoglobulin gene rearrangements. The findings from

these tests identify at which stage of B-cell lineage-commitment the tumour is

formed and any chromosomal rearrangements they contain. Assigning B-

lineage ALL subtypes by stage of lineage-commitment does not necessarily

identify the cell of origin, but it can point to features of the cancer stem cell

(defined as a tumour cell that can proliferate and differentiate into daughter cells

that recapitulate the heterogeneity of the disease). It has been found that

experimentally-modified expression of transcription factors essential to normal

B-cell development can reverse differentiation all the way back to a common

lymphoid progenitor state (Cobaleda, et al., 2007). This high plasticity in B-cell

development leaves identifying the cell of origin within the B-cell lineage difficult

to ascertain. The cell where the first genetic lesion occurred may have been an

earlier stage of B-cell maturation, and differentiated further before being

arrested. Similarly the cell where the first genetic lesion occurred may have

been a later stage of B-cell development, after which it dedifferentiated

(Cobaleda & Sánchez-García, 2009). We must consider this limitation when

discussing specific B-lineage ALL subtypes such as precursor-B ALL, with the

knowledge that the origin of the disease may have been at one of many stages

of B-cell maturation (Figure 1.1).

Risk stratification of B-cell ALL

B-lineage ALL can be risk stratified to ascertain the most suitable treatment

protocol for the patient. The main risk factors include initial white blood cell

count, gender, rapidity of initial treatment response and cytogenetics. Recurrent

chromosomal alterations (cytogenetics) include changes to chromosome copy

number; where hyperdiploidy (greater than 50 chromosomes) predicts a good

prognosis and is found in approximately 24% of B-cell ALL cases in children.

Hypodiploidy (less than 44 chromosomes) is associated with a poor prognosis

and is rare, found in 1% of cases. Cytogenetic translocations, which create

fusion genes, are also prognostic in childhood B-lineage ALL. The most

common genetic lesion, named ETV6-RUNX1, occurs in 26% of cases and is

identified by a t(12;21)(p13;q22) chromosomal translocation. ETV6-RUNX1 has

been found to be a prenatal translocation and denotes a favourable outcome for

patients. The E2A-PBX1 (also known as TCF3-PBX1) fusion gene present at

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t(1;19)(q23;p13) is found in 5% of cases but has no association with outcome in

children receiving contemporary therapy. The BCR-ABL1 translocation at

t(9;22)(q34;q11), also called the Philadelphia chromosome, is found in 5% of B-

lineage cases. This translocation has been implicated in various downstream

pathways and is associated with a poor response to treatment. The MLL gene

forms translocations at 11q23 with several partner genes and forms many

distinct fusions. MLL translocations are found in 7% of cases and are

associated with a poor prognosis, particularly in infants (Armstrong, 2005;

Inaba, et al., 2013; O'Brien & Lacayo, 2008; Teitell & Pandolfi, 2009).

Consequently, B-lineage ALL can be separated into several distinct subtypes,

which are associated with distinct disease progression and response to

treatment. However, many B-lineage ALL cases have no gross chromosomal

alterations and no cytogenetic alterations to predict risk of relapse. For these

patients risk of relapse is determined by response to first phase treatment. This

suggests that many other genetic structural changes and mutations are

necessary for leukaemogenesis.

Treatment regimen

The large success in overall survival of paediatric patients with B-lineage ALL,

now reaching 90% event-free survival, can largely be attributed to the

successive clinical trials carried out by international study groups such as the

Children’s Oncology Group (COG), Berlin-Frankfurt-Munster and St Jude

Children’s Research Hospital. Half a century of clinical trials has tailored

treatment protocols for drug combinations, concentrations, administration

methods and timing. These modifications were made possible by the

concurrent advancements in supportive care, allowing patients to better tolerate

highly intensive treatment regimens (Pui, 2006, 2009). The response to

treatment is a consequence of four facets; the regimen administered and its

effectiveness, treatment adherence by the oncologists, nurses and patient, the

pharmacogenomics of the patient and the leukaemic cell’s biological features

(Pui, 2008). The facets that cannot be controlled is the response to

administered drugs due to the patient’s own genetic variation

(pharmacogenomics) and the leukaemic cell’s genomic profile.

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Currently, ten different chemotherapeutic drugs are used in a two to three year

treatment period comprising four phases (Inaba, et al., 2013). Many of the

drugs currently in use were developed before 1970. The first phase, an

induction stage, is a high-intensity therapy administered over 4-6 weeks at near

maximal tolerated doses. During induction, the leukaemic cell burden is

reduced by at least 2-5 logs and normal haematopoiesis is restored.

Chemotherapies used include a glucocorticoid (prednisone or dexamethasone),

vincristine and L-asparaginase, with or without anthracycline. The second

phase is a consolidation period; during this phase different drugs are used with

the aim of destroying residual leukaemic cells that did not respond to induction

phase. Chemotherapies include high-dose methotrexate, mercaptopurine and

asparaginase with frequent pulses of vincristine and glucocorticoids.

Consolidation can last 20-30 weeks and culminates in a reinduction therapy,

which repeats induction phase drugs. To prevent central nervous system

metastasis a third phase involves administration of drugs intrathecally. One

improvement to treatment protocols is the retirement of radiation in frontline

therapy, and the avoidance of its many adverse neurological effects. Currently

cranial irradiation may be used in salvage treatment for patients who relapse.

Finally, a maintenance phase, lasting 2 years or longer, comprises

uninterrupted daily mercaptopurine and weekly methotrexate, with or without

monthly pulses of vincristine and dexamethasone. Allogeneic haematopoietic

stem cell transplantation is used for very high-risk or relapsed patients. The

benefits of the procedure are more pronounced as the patients risk profile

increases (Balduzzi, et al., 2005).

The use of combination chemotherapy reduces the potential development of

drug resistance to individual agents and is more likely to elicit a response.

However, current conventional anticancer drugs have non-selective

mechanisms of action. They target important macromolecules or metabolic

pathways that are crucial to both malignant and normal cells. Therefore,

treatment of ALL is toxic and can damage or interfere with normal organ

function. Long-term effects of treatment remain a problem for social, cognitive

and physical development in children that continue into adulthood (Hudson,

2003; Schwartz, 1999). Specifically, chemotherapies result in early mortality,

cardiac complications, obesity, muscle weakness, neurosensory impairment,

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neurocognitive deficits or endocrine and metabolic disorders (Ness, et al.,

2011). The need for improving the long-term health of paediatric leukaemia

survivors means reducing dosage and administration schedules of existing

drugs, as is currently being adopted for low-risk patients (Kamps, et al., 2002;

Vora, et al., 2013). These adverse outcomes highlight the need for newer more-

effective therapies with fewer long-term effects.

Drug resistance

Fortunately, with modern therapy most children diagnosed with leukaemia are

cured. However there is a group of patients that remain impossible to cure with

current chemotherapy approaches. To effectively prevent relapse, therapy must

suppress leukaemic growth and provide leukaemic cell reduction while not

permitting the emergence of drug resistant clones. In the past two decades

there has been limited progress in chemotherapy regimens for relapsed

patients. Relapses that occur early in relation to the time of diagnosis, and are

located in the bone marrow, are the most aggressive and have the worst

survival outcomes (Bhojwani & Pui, 2013). In the continued effort to achieve a

cure for all patients, the significant scientific challenge of counteracting or

preventing drug resistance must be overcome. We know that drug resistance

results from the intrinsic drug sensitivity of leukaemic cells themselves by clonal

selection or after sequential genetic changes or by protection from their

immediate environment (Meads, et al., 2008). Unravelling the molecular

pathways underlying drug resistance in B-lineage ALL will lead to better

knowledge of the disease and the potential discovery of new genes or proteins

suitable for targeted therapy.

Targeted therapies in childhood leukaemia are appearing with the push for a

“genomic medicine” approach to treating disease. A prime example is the

success in targeting of the BCR-ABL1 fusion with an ABL tyrosine kinase

inhibitor (Dasatinib/ Imatinib) (Evans, et al., 2013). The discovery of genetic

alterations that link to prognostic outcomes or targeted treatment options will

expand in future. As more genotype-phenotype associations are made the

efficacy for cancer and germline sequencing of patients increases (Bhojwani &

Pui, 2013). Using genome variation, which includes DNA sequence, epigenetic

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changes, messenger RNA and micro RNA expression as a prognostic factor

and treatment indicator will lead to the greater individualisation of cancer

treatment. To increase the available number of targeted therapies, further

investigation of the biology of ALL is needed, and is the rationale for the work

presented in this thesis.

1.2 The bone marrow microenvironment The formation of cells into tissues, organs and systems is made possible

through the microenvironment. As every one of the trillions of cells within a

human has the same DNA sequence, there must be a dominant force that

drives differences in gene expression. Without the reciprocal communication of

cells with the microenvironment, they would remain largely plastic with no

determined phenotype. Early embryonic events such as vascular

morphogenesis, heart and endoderm-derived organ development and

innervation of tissues by neural cells and blood vessels, all rely on

microenvironment cues (Red-Horse, et al., 2007).

In tumourigenesis, the microenvironment plays a role in both tumour

suppression and promotion. Premalignant tumours may be more common than

currently recognised, but in the right context the microenvironment can

constrain tumours to a dormant state and likewise, aberrant signals from the

microenvironment can promote malignancy (Bissell & Hines, 2011; Potter,

2007). Although studies investigating the role of the bone marrow (BM)

microenvironment in haematological malignancies have been published for

decades, it is the solid-tumour microenvironment that has been most abundant

in the literature and therefore better defined. Across the gamut of solid-

tumours, stromal cells of the microenvironment (including fibroblasts, vascular

cells and immune cells) contribute to 7 of the 8 hallmarks of cancer, a

conceptual framework that unifies the genotypes and phenotypes of diverse

cancer types (Hanahan & Coussens, 2012). As stated by Douglas Hanahan

and Lisa Coussens, “Cancer cells do not manifest the disease alone, but rather

conscript resident and recruited normal cell types to serve as contributing

members to the outlaw society of cells.”

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Structure and composition of the BM microenvironment The most prominent common denominator for B-lineage ALL and normal B-cell

development is the BM origin of both. The normal BM microenvironment is a

complex organization of a heterogenous assembly of cells, including lineages

from haematopoietic stem cells, stromal cells and extracellular matrix (ECM)

(Travlos, 2006). Stromal cells are derived from mesenchymal stem cells (MSC)

(Seshi, 2000). However, the term MSC is currently under scrutiny as the

majority of cells identified as mesenchymal stem cells are more accurately

heterogenous cells that show a large degree of plasticity (Bianco, et al., 2008;

Lindner, et al., 2010; Wagner, et al., 2008). What is certain is that MSCs

differentiate into committed progenitors, which become osteoblasts,

chondrocytes, myoblasts, tenocytes, adipocytes, fibroblasts and reticular cells

(Figure 1.2). The umbrella term of stromal cells in relation to the BM,

incorporates mesenchymal progenitors, endothelial cells, fibroblasts, reticular

cells, adipocytes and osteoblasts (Kiel & Morrison, 2008). In addition to stromal

cells, regulatory factors including the ECM, cytokines, chemokines, growth

factors and neural peptides control important pathways and cell interactions

(Janowska-Wieczorek, 2001; Lichtman, 1981; Mayani, 1992).

Vascular endothelial cells contribute to tumour formation by delivering nutrients

through blood vessels and also producing pro-tumorigenic factors (Butler, et al.,

2010). Immune cells are also important contributors to tumour progression.

Immune cell effects are complex and initiated by cells previously present in the

tumour microenvironment or attracted by inflammatory chemotactic signals.

Adaptive immune cells are tumour-destructive and directly involved in tumour

cell cytotoxicity and complement-mediated lysis, whereas innate immune cells

are tumour-supportive promoting fibroblast activation, angiogenesis, tissue

remodelling, and suppression of adaptive immune responses (de Visser, et al.,

2006; Lin & Karin, 2007). The collective immune presence in tumours evolves

dependent on tumour stage and location, indicating an organised response (Lin

& Karin, 2007). Specific roles of tumour cells in B-precursor ALL have not been

elaborated.

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Haematopoietic and stromal cells exist within an abundant ECM, a three-

dimensional latticework of collagens, proteoglycans and glycoproteins. Stromal

cells within the BM synthesise ECM, which is not an inert scaffold. On the

contrary, it plays a role in cell adhesion and migration, cytokine presentation

and proliferation within the BM (Klein, 1995). Heparan sulfate proteoglycans are

known to avidly bind many growth factors and when bound attach to the ECM,

to act as a localised reservoir for the protein. In this way, the ECM assists in

establishing stable release of soluble growth factors. These same

proteoglycans can also bind growth factors to function as a solid-state ligand

which docks onto integrin adhesive receptors and initiates cell signalling. The

regulation of transforming growth factor-β (TGFβ) signalling by ECM proteins is

one of the better-understood examples. Large, inactive TGFβ complexes are

secreted from cells and upon binding with ECM components, such as fibrillins,

collagens and fibronectins, are held until activation. Activation of TGFβ can

occur by proteolysis or by mechanical strain (Hynes, 2009). This example

illustrates how ECM can regulate cell signalling through growth factor

presentation. The versatility of ECM molecules allows juxtaposition of growth

factors, integrins and growth factor receptors in a confined spatial context that

can encourage or inhibit cell signalling (Brizzi, et al., 2012). The precise

mechanisms of ECM interactions are not well defined. The hundreds of ECM

proteins in humans are predominately large, having several distinct domains,

highly-conserved and complex (Hynes, 2009). The conserved and complex

nature of ECM proteins suggests there would be many more biologically

important functions, with some components being common among all

echinoderms and chordates (which includes all vertebrates).

Haematopoietic stem cell niche (Leask & Abraham, 2006)

Three decades ago it was postulated that a localized niche in the BM was

necessary for haematopoietic stem cell (HSC) reconstitution (Schofield, 1978).

The niche in question was localised to the endosteal bone surface, the interface

of bone and BM (Gong, 1978). Even recent studies, that brought in more

complexity, followed the niche hypothesis by stipulating that differentiation of

dormant HSCs into progenitor cells is initiated by migration from the endosteal

niche to a perivascular niche (Wilson, 2006).

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Figure 1.3. Human long bone as a model for the bone marrow niche. a. The long bone is divided into 3 anatomical sections: the epiphysis at the end of the bones and the metaphysis below the endosteal line, which are filled with spongy/ trabecular bone and the diaphysis along the middle shaft filled with compact bone. The bones are covered in periosteum and the bone joints with articular cartilage. Red bone marrow, where haematopoiesis occurs, is found within the trabecular bone for the lifetime in addition to the medullary cavity in childhood. b. Within the bone marrow spaces of the spongy bone a wide variety of vascular, endothelial and perivascular cells known as stromal cells contribute to haematopoietic stem cell (HSC) maintenance and differentiation (image adapted from Kiel and Morrison, 2008) c. A scanning electron microscopy image illustrates the persavive extracellular matrix present in all aspects of BM function. Depicts co-culture of mesenchymal stem cells (MSC) and endothelial progenitor cells (EPC) in an artificial collagen, type 1 scaffold. (adapted from O’loughlin and O’brien, 2011).

Megakaryocyte

HSC

Endosteal cell

Sinusoidalendothelium

reticular cell

Osteoclast

b.a.

c.

MSC

EPC

Co

Sca

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However, the use of improved HSC markers in vivo and three-dimensional

imaging techniques have found that the anatomical location of approximately

two-thirds of HSCs is the BM space are found within trabecular, spongy bone

throughout the metaphysis, with the rest located throughout the diaphysis

(Figure 1.3). While HSCs are distributed throughout this space, a minority are

found near the endosteum (roughly 20%) and the vast majority are adjacent to

or near a sinusoid (Kiel, et al., 2005; Morrison & Scadden, 2014). Sinusoids are

the thin-walled blood vessels that allow easy passage of cells between the

circulation and haematopoietic tissue. Endosteal BM niches within the

trabeculae are associated with a rich network of blood vessels including

sinusoids very near the endosteal surfaces. While HSCs may not be in direct

contact with the endosteum, the two niches are capable of influencing each

other (Lassailly, et al., 2013). However, perivascular-associated mesenchymal

stromal cells and endothelial cells appear to be the main stromal cell types

involved in HSC maintenance and localisation, with a possibly more complex

and indirect role for mature osteo-lineage cells at the endosteal niche (Morrison

& Scadden, 2014).

Location of B-cell lymphopoiesis

Interactions within the BM play a critical role in the development of normal B-

cells (Kurosaka, et al., 1999; Nagasawa, 2006). Essential microenvironmental

components for B-cell development show some overlap with HSC requirements

and are in addition to essential transcriptional factors expressed by B-lineage

cells themselves. Essential components are released by endothelial and

mesenchymal stromal cells and include CXC-chemokine ligand 12 (CXCL12),

FLT3 ligand (FLT3), interleukin 7 (IL7), stem cell factor (SCF) and receptor

activator of nuclear factor-κB ligand (RANKL) (Nagasawa, 2006). Efforts to

identify cells responsible for expression of these essential microenvironment

components have been hindered by a lack of unique markers among stromal

cells and the redundancy in expression across different cell types. This has left

the source of some essential B-cell components well defined, while others are

not (Nagasawa, et al., 2011).

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Figure 1.2. Mesenchymal Stem Cells (MSC) have the potential to differentiate into divergent cell lineages. MSCs have a high capacity for self renewal before differentiating into a range of mesenchymal cell types. Mature cells form tissues such as bone, cartilage, muscle and tendons. MSCs are also the source of BM stromal cells including adipocytes, fibroblast and reticular cells (adapted from Caplan and Bruder, 2001).

MSC

Progenitor

Maturecell

Terminal differentiation

(Fibroblasts,reticular cells)

TendonTenocytes

Adipocytes

Stromal cells (fibroblasts, reticular cells)

MuscleMyoblasts

CartilageChondrocytes

BoneOsteocytes

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One well-defined stromal cell is the CXCL12-abundant reticular (CAR) cell that

is found throughout the BM and plays various roles. They have been found to

be essential for HSC maintenance, homing, B-cell and erythroid progenitor cell

maturation. CAR cells express not only CXCL12 but also SCF and vascular cell

adhesion molecule 1 (VCAM1) (Sugiyama, et al., 2006). It has been postulated

that the network created by CAR cells and their processes provides the

substructure for movement of HSCs and their progeny (Nagasawa, et al., 2011).

However, the redundancy of expression of CXCL12 in the BM, which is also

expressed by osteoblasts and endothelial cells, can serve to define niches

providing different functional roles in haematopoiesis.

Conditional deletion of CXCL12 from osteoprogenitors, mature osteoblasts,

osteoclasts and reticular cells (all expressing osterix), resulted in a loss of B

lymphoid progenitors, while HSC function was normal. Conditional deletion of

CXCL12 from limb bud-derived mesenchymal progenitors (expressing Prx1)

which differentiate into the majority of CXCL12-expressing cells in the BM with

the exception of vascular endothelial cells, was associated with a loss of HSCs,

HSC quiescence and common lymphoid progenitor cells (Greenbaum, et al.,

2013). This and other cumulative evidence suggest that early B-lymphoid

progenitors occupy endosteal niches in association with CXCL12-positive

osteo-lineage cells, which is an anatomically distinct site from the perivascular

niche where HSC cells and common lymphoid progenitors are associated with

CAR cells and CXCL12-positive endothelial cells (Ding & Morrison, 2013).

The movement of B-cell progenitors within the BM is driven by expression of

membrane receptors. Expression of the CXCL12 receptor (CXCR4) occurs at

all stages of development from HSC to immature B-cell and CXCR4 expression

drives the association with CAR cells. Lymphoid progenitor cells move from

their perivascular niche toward osteo-lineage CAR cells located at the

endosteum. From early-B to the pre-B cell stage there is also expression of the

IL7 receptor, and this drives pro- and pre-B cell association with IL7-expressing

stromal cells at perivascular sites and plays a crucial role in driving proliferation

at these stages. Pre-B cells then upregulate expression of CXCR4 in response

to complex rearrangements resulting in expression of interferon regulatory

factor 4 (IRF4) and migrate to CAR cells in a distinct niche away from HSCs.

The final move occurs after attenuation of IL7 signalling and exit from the cell

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cycle, which allows final immunoglobulin light chain rearrangements and

expression of an antigen-specific B-cell receptor (BCR). These last steps are

necessary for selection into the immature-B cell pool, where cells move toward

vascular endothelial cells before migrating into the blood stream to reach the

spleen for further processing. This outlines a three niche model for B-cell

differentiation involving a CXCL12-abundant endosteal niche, IL7-abundant

perivascular niche and CXCL12-abundant perivascular or reticular niche (Clark,

et al., 2014; Nagasawa, 2006).

B-lineage leukaemia niche

The microenvironment of B-lineage ALL has been found to hijack normal HSC

niches leading to the suppression of normal haematopoiesis (Colmone, et al.,

2008). In a xenograft model in immune-compromised mice, a B-precursor ALL

cell line (Nalm6) homed to CXCL12-positive vascular niches within the BM and

then disrupted chemokine CXCL12 expression. Consequently, CD34-positive

haematopoietic progenitor cells were found to be re-directed to malignant

leukaemic niches and to exhibit abnormal behaviour at these tumour-associated

sites. The vascular leukaemic niche of ALL is in contrast to that of myeloid

leukaemias, where the majority of leukaemic blasts home to the endosteal

niche (Schepers, et al., 2013). A role for the endosteal niche in ALL has been

recently suggested with a study by Boyerinas et al. (2013) finding that dormant

B-precursor ALL blast cells from a human patient preferentially engrafted to

osteopontin (OPN)-expressing cells in the endosteum of NOD scid gamma

(NSG) mice. The endosteal niche in B-precursor ALL engrafted mice showed

evidence of a positive feedback loop between stromal and leukaemic cells for

OPN expression, suggesting maintenance of quiescence at endosteal sites.

The BM microenvironment affects leukaemic cell survival

From early studies in ALL, the BM microenvironment was cited as providing

support to leukaemia cell survival. Manabe et al. (1992) were first to

demonstrate BM stromal cells supported leukaemic cell survival in vitro in

comparison to serum-free tissue culture medium. B-precursor ALL was the

leukaemic subtype that had the greatest benefit to survival when adhered to a

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BM stromal cell layer in vitro, further distinguishing the heterogeneity that exists

between the leukaemic lineages in regards to stromal dependency (Manabe, et

al., 1994). This beneficial in vitro interaction between B-precursor ALL cells and

BM stromal cells was most obviously demonstrated by direct cell-contact and to

a lesser extent by soluble factors alone (Ashley, et al., 1994). It was found that

within 30 minutes of contact with BM fibroblasts, B-precursor ALL cells

developed complex pseudopodia at sites of cell-cell contact and microvillus

projections, undergoing major shape changes that allowed penetration of the

fibroblast adherent layers (Hewson, 1996). Other leukaemic lineages, while

undergoing some shape changes, displayed no signs of migration within the

fibroblast layer. However, the direction of communication in the

microenvironment is not only BM stromal cells conferring supportive changes

onto ALL cells. ALL cells can impart a pro-angiogenic potential to BM

endothelial cells and produce an array of soluble factors that promote

neovascularisation (Veiga, et al., 2006). The exact role of the different growth

factors and cytokines in the leukaemic BM is not well defined, most likely they

form complex and dynamic networks where leukaemic blasts are in cross-talk

with stromal cells and facilitate complementary expression of soluble factors

(Ayala, et al., 2009; Wu, et al., 2005).

The BM microenvironment affects leukemic cell drug resistance

Environment–mediated drug resistance can be due to transcription of soluble

factors such as cytokines, chemokines and growth factors or the resistance can

be due to non-transcriptional mechanisms of cell adhesion (e.g. when tumour

cell integrins bind to fibroblasts or components of the ECM). Environment-

mediated drug resistance can precede minimal residual disease (the presence

of surviving tumour cells immediately after therapy) and the development of

acquired resistance. In leukaemia, the understanding that environment-

mediated drug resistance is largely caused by BM stromal cells is well

established.

Protection from the cytotoxic effects of chemotherapeutic drugs has been found

to occur after direct BM-leukaemia cell contact (Mudry, et al., 2000). Leukaemia

cell adhesion to the BM stromal cells has been shown to result in decreased

apoptosis through initiation of integrin signalling cascades, including

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phosphorylation of extracellular signal-regulating kinases (ERK1/2) and Akt,

that provide protection from cytotoxic cell death (Hazlehurst, 2003; Shain, 2000;

Tabe, et al., 2007). In T-cell ALL, it has been shown that gap junction coupling

between BM stroma and leukaemic lymphoblasts diminishes proliferation,

keeps cells in a quiescent state and protects them from drug-induced apoptosis

(Paraguassu-Braga & Paraguassu, 2003).

Resistance to (L-)asparaginase cytotoxicity in B-precursor ALL, was found in

co-culture experiments with BM-derived mesenchymal stromal cells

(immortalised hTERT and primary cells)(Iwamoto, et al., 2007). Stromal cells

were found to have 20-fold greater expression of asparagine synthetase

(ASNS) expression (which catalyses the reaction that forms asparagine),

compared to ALL cells (3 cell lines and primary blasts). It was postulated that

stromal cells provided excess asparagine for tumour cells, which are incapable

of producing their own supply and in this way stromal cells provided a protective

effect, resulting in viable leukaemic cells capable of proliferation. BM-derived

stromal cells (immortalised HS5) also protected B-precursor ALL cells from

cytotoxic effects of vincristine and cytarabine when in co-culture, with survival

40% and 60% higher, respectively, in two B-precursor ALL cell lines compared

to the absence of stroma (Tesfai, et al., 2012). However, no protective effect

was found for dexamethasone or L-asparaginase in this study. The opposing

findings on (L-)asparaginase sensitivity in B-precursor ALL cells co-cultured

with BM-derived stromal cells can be attributed to the heterogenous expression

of ASNS in BM stromal cell lines, even among sub-clones of the same cell line,

and the variable response of B-precursor ALL cells cultured with BM stromal

cells, as discussed by Iwamoto et al. (2007).

The response of B-lineage ALL, T-lineage ALL or myelogenous leukaemia cells

in the presence of BM stromal cells have can be very different and result in

unique adhesion-based protective mechanisms or survival capabilities (Ayala,

et al., 2009; Hall & Gibson, 2004). Although all leukaemias exist in the same

BM microenvironment, biological differences in the tumour cell itself appear to

exert distinctive control over the BM response, reaffirming that context is always

vital in microenvironment response.

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1.3 Connective tissue growth factor (CTGF) Relevance of CTGF in B-precursor ALL

Global gene-expression profiling using microarrays encompasses a subset of

over 20,000 genes of potential importance and is therefore well suited to

identifying new genes of interest. ALL, a relatively homogenous cancer that

allows easy isolation of malignant cells, is an ideal model system and many

investigators have used microarray to elucidate therapeutic targets and

diagnostic markers (Cheok, 2006). Using microarray technology, previous

studies conducted within our laboratory at the Telethon Institute for Child Health

Research have found that CTGF is a highly expressed gene in B-precursor ALL

(Boag, et al., 2007). We found CTGF to be upregulated 37-fold compared with

normal B-precursor cells from umbilical cord blood and 19-fold compared with

haematopoietic progenitor cells from healthy BM. The analysis revealed that

high expression levels of CTGF were restricted to B-lineage and not T-lineage

ALL. It was found overall that CTGF was highly expressed in 75% of B-

precursor ALL cases. This percentage was largely comprised of only four

different cytogenetic subgroups; hyperdiploidy, ETV6-RUNX1, MLL and BCR-

ABL. E2A-PBX1 translocations and other more infrequent aberrations did not

show significant CTGF expression across the independent cohorts. Protein

studies by western blot analysis confirmed the presence of CTGF in ALL cell-

conditioned media, confirming protein translation and secretion. Boag et al.

concluded that CTGF expression from B-precursor ALL cells was heterogenous

and could play a role in the pathophysiology of the disease. Moreover, other

microarray studies of adult and childhood B-precursor ALL samples found

CTGF was highly expressed compared to T-cell ALL, myeloid leukaemias and

control patient BM and peripheral blood samples (Sala-Torra, et al., 2005;

Vorwerk, et al., 2000).

Importantly CTGF expression is correlated with a poor prognosis in B-precursor

ALL. A gene identifier set correlated to a high-risk group of paediatric ALL

patients with the poorest clinical outcome, included CTGF expression (Kang, et

al., 2010). Similarly, in adult ALL high CTGF expression correlated with poor

overall survival of patients in a mortality hazard rate model (Sala-Torra, et al.,

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2005). Increased CTGF expression having an association with poor prognosis

suggests the protein may confer a cellular phenotype that benefits the

leukaemia cell. In an in vitro functional study, CTGF adsorption by human BM

stromal cells promoted adhesion to synthetic surfaces (Ono, et al., 2007). If

CTGF were proven to alter adhesion of BM microenvironment components to

leukaemia cells in vivo, this would support the possibility of it playing a role in

environment-mediated drug resistance. Normal function of CTGF

It has been over 20 years since the discovery of CTGF from human umbilical

vein endothelial cells (Bradham, 1991). The CTGF gene has been

independently identified and named several times since then, as IGFBP-

8/IGFBP-r2/HCS24/NOV2, in consequence of its multi-faceted nature. CTGF is

an ECM-associated protein of 36-38kDa and a member of the CCN family of

proteins. The family is named after the three founding proteins, CYR61/CCN1

(Cysteine rich 61), CTGF/CCN2 and NOV/CCN3 (Nephroblastoma

overexpressed), and now comprises six members, with the addition of Wnt-

induced secreted proteins Wisp-1/CCN4, Wisp-2/CCN5 and Wisp-3/CCN6.

Each member consists of a highly conserved four-module structure that allows it

to regulate a multitude of cellular responses (Figure 1.4). The four motifs bear

resemblance to other unrelated extracellular proteins and include an N-terminal

region with an insulin-like growth factor (IGF)-binding domain, followed by a von

Willebrand type C domain, a thrombospondin-1 domain, and a cysteine knot at

the C-terminal end (Bork, 1993). CTGF is strongly induced by TGF-β and other

growth factors and is tagged for secretion to the ECM, the protein has been

highly researched for its role in various fibrotic and desmoplastic diseases,

including atherosclerosis, organ fibrosis and fibrotic skin disorders (Jun & Lau,

2011; Leask, 2002; Shi-Wen, et al., 2008; Sonnylal, et al., 2010). CTGF is also

involved in many normal biological processes, such as wound repair, bone

formation, ECM remodelling and angiogenesis (Arnott, et al., 2011; Babic, et al.,

1999; De Winter, et al., 2008; Hall-Glenn, et al., 2012; Kondo, et al., 2002;

Leask & Abraham, 2006; Safadi, et al., 2003). These normal functions of CTGF

play an essential role in development of epithelial tissues, as seen in

endochondral bone formation where CTGF provides differentiation and survival

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signals to growth plate chondrocytes through ECM interactions (Hall-Glenn &

Lyons, 2011; Hall-Glenn, et al., 2013).

Known receptors for CTGF are cell type- and context-specific, allowing

remarkable functional versatility throughout the body. The known receptors

include heparan sulfate proteoglycans, the low-density lipoprotein receptor-

related proteins, TrkA and 6 integrins: α6β1, αvβ3, αvβ5, αIIbβ3, αMβ2,, α5β1 (Jun &

Lau, 2011).   A specific receptor has not been found, though there is evidence

CTGF may also function as an adaptor molecule facilitating binding of

extracellular proteins to their cell surface receptors (Shi-Wen, et al., 2008). The

known ligands of CTGF include: fibronectin, decorin, vitronectin, TGFβ, VEGF,

FGF2 and BMP (Jun & Lau, 2011). Canonical pathways activated by CTGF

include Notch, TGFβ, WNT and PI3K/AKT signalling pathways, though there is

no definitive signalling pathway for the protein. These known interacting

proteins, and potentially other undiscovered molecules, allow CTGF to act in an

autocrine and paracrine manner to effect functional changes in normal and

neoplastic cells. In only a limited number of studies has there been functional

insight into how CTGF contributes to disease pathology, these will be discussed

below.

Role of CTGF in human cancers CTGF has long been associated with human cancers. The role it plays in these

neoplasms is diverse and tumour-specific. Recurring patterns in clinical

outcome, histological desmoplasia and mechanisms of action have been found.

When CTGF is overexpressed compared with low–expressing normal tissue or

is underexpressed compared with high-expressing normal tissue, the functional

outcome favours tumour survival and disease progression. CTGF acts by

altering proliferation, drug resistance, angiogenesis, adhesion and migration,

contributing to metastasis. The pattern of CTGF expression and tumour

response helps to clarify the role of this matricellular protein across a multitude

of human cancers.

Across the gamut of human cancers with deregulated CTGF gene expression,

there are similarities to be drawn that can help us better understand the role

CTGF plays in cancer. The review of the literature aims to accomplish this by

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Figure 1.4. Conserved structure of CCN family members. CCN family members have a conserved four domain structure. A secretory signal peptide (SP) is followed by Module I, an Insulin-like growth factor binding domain (IGF-binding), then module II, a Von willebrand type C domain (VWC), this is linked with a protease susceptible hinge region to module III, a thrombospondin-1 domain (TSP-1) and lastly module IV, a cysteine knot domain (adapted from Leask and Abraham, 2006).

CCN1/ CYR61CCN2 / CTGFCCN3/ NOVCCN4/ WISP1CCN5/ WISP3

CCN5/ WISP2

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clarifying the common characteristics among distinct human cancers and CTGF

expression, exploring clinical outcome in relation to CTGF expression and

examining the location of CTGF expression in cancer and surrounding cells.

The molecular mechanisms are summarised according to CTGF functions in

human cancers, including autocrine control of proliferation and drug resistance

and paracrine control of angiogenesis, invasion and metastasis.

Deregulated CTGF expression in cancer CTGF was first associated with human breast and pancreatic cancers in the late

1990’s (Frazier & Grotendorst, 1997; Hishikawa, et al., 1999). To date, 27

human cancers have been linked to aberrant CTGF expression (Table 1.1).

They include cancers affecting patients from very young children to older adults

and arising from many tissue types and systems of the body. Identifying the role

CTGF plays in these cancers is complicated by the tissue-dependent and

seemingly complex functions of the protein. However, as a secreted protein,

many functions take place in the ECM and tumour microenvironment, and their

role in cancer progression and survival has been well established (Mbeunkui &

Johann, 2009; Mueller & Fusenig, 2004). Studies investigating CTGF in human

cancers report both up- and downregulated expression with varying survival

outcomes. The reports comprise varying numbers of patient samples (Table

1.1). Methods of CTGF analysis also differ. Despite this, consistent trends are

apparent between CTGF expression and clinical outcome.

When interpreting the role of CTGF in human cancer, it is important to establish

when that deregulation occurs. Expression of CTGF may be global for a cancer

type or specific to a sub-type, differentiation grade (poorly or well differentiated)

or tumour-stage (such as the TNM classification). Specificity of CTGF

expression is not only evident in tumour cells but also normal cells (Safadi, et

al., 2003). Of the cancers with known deregulated CTGF expression, 44%

(12/27) were found to have expression levels dependent on the degree of

tumour differentiation or TNM stage, as assessed by univariate or multivariate

analysis (Table 1.1).

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Location Corresponding normal tissue

Malignancy Patient samples (total)

References

Nervous system

GLIA Glioma (glioblastoma multiforme)

66^ Xie et al., 2004

Head and neck mucosa

ORAL MUCOSA, SINUS, TONGUE

Head and neck SCC 163^ Yang et al., 2011, Chang et al.,

2013 Skin MELANOCYTE Melanoma 10 Kubo et al., 1998,

Braig et al., 2011 Respiratory system

LUNG Lung Cancer (NSCLC and adenocarcinoma)

150^ McDoniels et al., 2002, Chang et

al., 2004,Chien et al., 2006

Digestive system

OESOPHAGUS Oesophageal cancer (SCC and adenocarcinoma)

113* Koliopanos et al., 2002, Zhou et al.,

2009 STOMACH Gastric cancer 195^ Liu et al., 2008,

Mao et al., 2011 COLON/ RECTUM

Colorectal cancer 255^ Lin et al., 2005, Lin et al., 2011

LIVER Intrahepatic cholangiocarcinoma

55* Gardini et al., 2005

Hepatocellular carcinoma

52^ Zeng et al., 2004, Mazzocca et al.,

2010 GALLBLADDER Gallbladder cancer 238* Alzarez et al.,

2008, Garcia et al., 2013

PANCREAS Pancreatic cancer 80^ Wenger et al., 1999, Dornhofer

et al., 2006, Bennewith et al.,

2009 Reproductive system

BREAST Breast cancera 55^ Xie et al., 2001

CERVIX Cervical cancer 57^ Wong et al., 2006, Xie et al.,

2012 OVARY Ovarian cancer 173^ Gery et al., 2005,

Kikuchi et al., 2007

PROSTATE Prostate cancer 704 Gorlov et al., 2010

Urinary system

KIDNEY Nephroblastoma (Wilm’s tumour)

67 Zirn et al., 2006

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Table 1.1. A topography of CTGF-associated neoplasms in humans. CTGF-associated neoplasms are found throughout the body. The comprehensive number of patient samples that have been studied in their association with CTGF is also featured. Significant correlations between CTGF expression and the degree of tumour cell differentiation is indicated by: ^, associated or *, not associated with tumour differentiation grade or TNM staging. SCC: squamous cell carcinoma, NSCLC: non-small cell lung carcinoma. a The mammary gland is part of the integumentary system more closely related to skin and subcutaneous tissue but grouped here to highlight gender differences. b Currently classified as Undifferentiated Pleiomorphic Sarcomas c Ileal carcinoids are derived from enterochromaffin cells and gastric carcinoids are derived from enterochromaffin-like cells, both enteroendocrine cells derived from the gut epithelial cell lineage with enteric nervous system properties.

Connective and soft tissue

CHONDROCYTE Chondrosarcoma 18^ Shakunaga et al., 2000

FIBROUS TISSUE

Fibrosarcomab and Fibrous histiocytomasc

42 Igarashi et al., 1998

Myofibroblastic tumour

12 Kasaragod et al., 2001

MESOTHELIUM Mesothelioma 24 Fujii et al., 2012

SKELETAL MUSCLE

Rhabdomyosarcoma 0d Astolfi et al., 2001, Croci et al.,

2004 Endocrine system

ENTEROCHROM-AFFIN CELL

Ileal carcinoidc , Gastric carcinoidc

179* Kidd et al., 2007, Cunningham et

al., 2010 Haematologi-cal system

LYMPH NODE Hodgkin lymphoma 44 Birgesdotter et al., 2010

Large B-cell lymphoma

240 Rosenwald et al., 2010

THYROID Thyroid Cancer 20^ Cui et al., 2011 LEUKOCYTE B-precursor

acute lymphoblastic leukaemia

666 Vorwerk et al., 2007, Boag et al., 2007, Sala-Torra et al., 2007, Kang

et al., 2010 PLASMA CELL Multiple myeloma 57 Munemasa et el.,

2007

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CTGF expression and clinical outcome Divergent CTGF expression in cancer cells compared to normal tissue can be

correlated with clinical outcome (Table 1.2). Normal tissue expression was

defined by specimens analysed in the relevant studies or data from GeneCards

microarray gene expression for normal tissues ("Genecards,"). No studies to

date have correlated CTGF expression with clinical outcome in connective

tissue neoplasms or neuroendocrine tumours, both of which have proven to be

affected by CTGF in experimental conditions, as discussed in section 5. (Croci, et al., 2004; Kang, et al., 2010; Kidd, et al., 2007; Rosenwald, et al., 2002; Wenger, et al., 1999) Higher CTGF expression in tumour compared to corresponding normal cells

Tumours overexpressing CTGF above the levels of their normal cell counterpart

correlate with poor clinical outcome. This is the case for B-cell acute

lymphoblastic leukaemia (Boag, et al., 2007; Sala-Torra, et al., 2007; Vorwerk,

et al., 2000), breast cancer (Wang, et al., 2009; Xie, et al., 2001), gastric cancer

(Liu, et al., 2008; Mao, et al., 2011), glioma (Xie, et al., 2004), hepatocellular

carcinoma (Mazzocca, et al., 2010; Xiang, et al., 2012), melanoma (Braig, et al.,

2011), oesophageal cancer (Deng, et al., 2007; Li, et al., 2010; Zhou, et al.,

2009), pancreatic cancer (Bennewith, et al., 2009; Dornhofer, et al., 2006),

prostate cancer (Gorlov, et al., 2010) and thyroid cancer (Cui, et al., 2011). In

these cancers CTGF expression in biopsy samples is associated with worse

survival outcomes and clinico-pathological findings, including advanced stage,

larger tumour size, increased metastasis, and poorer chemotherapy response.

In mesothelioma CTGF protein expression was only detectable in the

sarcomatoid subtype, which is the most aggressive and has the poorest

outcome (Fujii, et al., 2012). In multiple myeloma a cleaved CTGF fragment is

increased in plasma levels and associated with bone disease (Munemasa, et

al., 2007). In chondrosarcoma and pancreatic cancer CTGF is transiently

increased compared to normal skeletal muscle cells during early tumour stages,

suggesting a role in initial tumour development (Hartel, et al., 2004; Shakunaga,

et al., 2000).

In contrast, in gallbladder cancer higher expression of CTGF in tumour cells

leads to better patient outcomes, as CTGF is overexpressed compared to

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normal tissue and increases with advancing tumour stage (Garcia, et al.,

2013a)

and high CTGF expression correlates with a better survival outcome in patients

with advanced gallbladder cancer (Alvarez, et al., 2008). Functional studies

have revealed that CTGF increases proliferation of gallbladder cancer cells in

vitro, suggesting the microenvironment may be responsible for host-protective

functions (Garcia, et al., 2013b).

Lower CTGF expression in tumour compared to corresponding normal cells

Cancer cells with low expression of CTGF compared to normal high-expressing

cells correlate with poorer clinical outcomes. In colorectal cancer (Lin, et al.,

2005; Lin, et al., 2011), Wilm’s tumour (Li, et al., 2008; Zirn, et al., 2005; Zirn, et

al., 2006), intrahepatic cholangiocarcinoma (Gardini, et al., 2005) and non-small

cell lung cancer and lung adenocarcinoma (Chang, et al., 2004; Chien, et al.,

2006; McDoniels-Silvers, et al., 2002), reduced CTGF expression compared

with highly-expressing normal tissue was associated with worse survival

outcomes and increased tumour recurrence, advanced tumour stage and lymph

node metastases.

CTGF expression is tumour-stage dependent in both ovarian and cervical

cancer. In ovarian cancer CTGF expression is lost in early stages of the tumour

then regained (Gery, et al., 2005; Kikuchi, et al., 2007). In cervical cancer CTGF

is downregulated compared to matched-normal controls and upregulated in late

compared to early tumour stages (Wong, et al., 2006; Xie, et al., 2012). This

suggests that in ovarian and cervical cancer, CTGF plays a role in tumour

initiation. In head and neck squamous cell carcinoma, CTGF-expression is lost

in late stages of the tumour, suggesting a role in tumour progression (Yang, et

al., 2011).

Taken together, there is a consistent pattern between poor clinical outcome and

divergent CTGF expression compared with normal tissue. As seen in Table 1.2,

deregulated CTGF expression is most often associated with poor clinical

outcome, whether the gene is over expressed when CTGF expression is low in

normal tissue or under expressed when CTGF is found to be high in normal

tissue. The exceptions to this pattern, lymphoma and gallbladder cancer are the

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Table 1.2. Pattern of CTGF deregulation compared to normal tissue and its association with clinical outcome and cellular mechanisms of action. Deregulated CTGF is associated with a mainly poor prognosis. CTGF is associated with an increased (·) or decreased (‚) activity of several cellular mechanisms and its deregulation in cancer leads to increased tumour survival. DLBCL: diffuse large B-cell lymphoma, SCC: squamous cell carcinoma, AC: adenocarcinoma, NSCLC: non-small cell lung carcinoma. *Drug resistance was increased when CTGF was deregulated in the relevant tumour types.

Cancer type

Clin

ical

ou

tcom

e

Prol

ifera

tion

Drug

re

sist

ance

*

Angi

ogen

esis

Adhe

sion

M

igra

tion

Met

asta

sis

Higher CTGF Expression B-precursor acute lymphoblastic leukaemia

Poor Brain cancer Poor ? ? ? Breast cancer Poor ? ? ? ? Chondrosarcoma Poor Gastric cancer Poor ? ? Hepatocellular carcinoma

Poor ? ? ? Ileal carcinoid Poor Melanoma Poor ? Mesothelioma Poor ? Multiple myeloma Poor Oesophageal cancer Poor ? Pancreatic cancer Poor ? ? ? ? Prostate cancer Poor ? Thyroid cancer Poor ? ? Gallbladder cancer Good ? Lymphoma Good Lower CTGF Expression Cervical cancer Poor ? Colorectal cancer Poor ? ? Head and Neck SCC Poor ? ? ? Intrahepatic cholangiocarcinoma

Poor Lung cancer Poor ? ? ? ? Nephroblastoma Poor Ovarian cancer Poor ? ? ?

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only cancers where deregulated CTGF expression in tumour cells is associated

with better patient outcomes.

Location of CTGF expression and desmoplasia

Desmoplasia is a dense accumulation of fibrotic tissue surrounding a tumour.

As mentioned previously, CTGF has been shown to be actively involved in

fibrosis, whereby excess fibrous connective tissue is deposited. It is not

surprising that CTGF expression from both tumour and stromal cells has

associations with desmoplasia. Whether desmoplasia provides a protective

environment for the tumour or supports tumour elimination remains to be

determined for many cancer types. Therefore, there is no easily predictable

relationship between CTGF-associated desmoplasia and patient outcome.

CTGF expression in stromal cells

Elevated CTGF expression in stromal fibroblasts is implicated in the

desmoplastic response in breast cancer, colorectal cancer, desmoplastic

malignant melanoma and various connective tissue neoplasms including infant

myofibrosis, fibrosarcoma, malignant fibrous histiocytoma and malignant

hemangiopericytoma (Frazier & Grotendorst, 1997; Igarashi, et al., 1998;

Kasaragod, et al., 2001; Knowles, et al., 2011; Kubo, et al., 1998). Conversely,

high expression of stromal-CTGF in hepatocellular carcinoma was linked to a

lack of fibrous capsule around the tumour (Wang, et al., 2010; Xiang, et al.,

2012).

Aside from a role in desmoplasia, CTGF expression in stromal cells can

advance tumour growth or promote invasion in glioma, pancreatic and prostate

cancer. In prostate cancer, stromal cells expressing CTGF demonstrated

increased angiogenesis and tumour growth when co-injected with pancreatic

cancer cells (Yang, 2005). In glioma, stromal astrocytes at the tumour front

secrete high levels of CTGF and create a permissive microenvironment for

invasion (Edwards, et al., 2011). In pancreatic cancer, stromal-CTGF

expression contributed to increased angiogenesis and tumour-invasiveness

(Eguchi, et al., 2012; Ijichi, et al., 2011; Kwon, et al., 2007).

CTGF expression in tumour cells

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High tumour-CTGF expression was associated with an increased desmoplasia

or close proximity to fibrovascular stroma in hepatocellular carcinoma,

oesophageal cancer, Hodgkin’s lymphoma and ileal carcinoids (Mazzocca, et

al., 2010). Similarly, in diffuse large B-cell lymphoma, increased CTGF

expression was associated with a more stromal subtype (germinal centre-like)

and present in gene signatures associated with increased ECM deposition and

monocytic invasion (Blenk, et al., 2007).

As discussed previously, lymphoma and gallbladder cancer are the only human

cancers studied to date with CTGF-deregulation being linked to a good

prognosis. That there is an increased stromal component in lymphoma,

suggests CTGF-microenvironment interactions may be responsible for

improved patient outcomes. The composition of the microenvironment when

CTGF is deregulated has not been reported for gallbladder cancer. However, a

microenvironment-mediated role for CTGF in gallbladder cancer is supported by

evidence that TGFβ was found to produce anti-angiogenesis and anti-

proliferation factors, which maintained distant metastatic tumour cells in a state

of dormancy in vivo (Gohongi, et al., 1999). As CTGF is a known downstream

mediator of TGFβ, it is plausible that it could function through the same

signalling pathways in gallbladder cancer to mediate microenvironment

interactions. CTGF operating in this capacity could certainly be the means to

improved clinical outcome, as the presence of distant metastases is an

important independent factor predicting survival in gallbladder cancer (Alvarez,

et al., 2008).

Mechanisms of CTGF action in cancer

CTGF has been found to change tumour cell proliferation and drug resistance.

Further, CTGF changes the tumour microenvironment by altering angiogenesis

and invasion of new tissues, achieved through changes in adhesion and

migration and finally the formation of metastatic colonies. Following the pattern

seen in clinical outcomes, the effect of CTGF on these mechanisms is

dependent on whether CTGF is over- or underexpressed compared with normal

cell counterparts. In tumours where CTGF is overexpressed functional changes

serve to promote tumour cell survival or metastasis. In contrast, in tumours

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where CTGF is underexpressed compared with normal the presence of CTGF

reduces the aggressiveness of a tumour (Table 1.2).

Proliferation

CTGF has a proliferative role in gallbladder cancer, hepatocellular carcinoma,

malignant mesothelioma, oesophageal cancer, rhabdomyosarcoma, pancreatic

cancer and thyroid cancer (Fujii, et al., 2012; Garcia, et al., 2013b). In

hepatocellular carcinoma, increased proliferation was attributed to changes in

the cell cycle with increased numbers of cells in S-phase (Xiu, et al., 2012). In a

pancreatic mouse flank-tumour model, a CTGF monoclonal antibody (FG-3019,

Fibrogen Inc) reduced tumour growth (Aikawa, et al., 2006). In humans, a

phase 1 clinical trial of FG-3019 was used in locally advanced or metastatic

pancreatic cancer patients and was well tolerated (Heestand, et al., 2011).

Recently in pancreatic cancer, Neesse et al. found in vivo that gemcitabine

delivered alongside FG-3019 increased tumour cell death without altering

gemcitabine delivery, reported to be due to FG-3019 disrupting the survival

signal x-linked inhibitor of apoptosis protein (XIAP) (Neesse, et al., 2013).

CTGF has repeatedly been found to have no effect on in vitro proliferation of

breast cancer cells (Chen, et al., 2007; Pandey, et al., 2009; Shimo, et al.,

2006). However, the findings of Capparelli et al. (2012) have shown tumour

growth was inhibited when MDA-MB-231 breast tumour cells overexpressed

CTGF in vivo, as tumour-autophagy caused tumour lysis. This is an indirect

method of limiting proliferation of tumour cells. But tumour growth increased

when co-injected fibroblasts overexpressed CTGF, as fibroblast-autophagy

created nutrients for the developing tumour.

In cancers with reduced CTGF expression compared with normal cells an anti-

proliferative mechanism was found. CTGF overexpression inhibited tumour

proliferation in lung adenocarcinoma and non-small cell lung cancer, head and

neck cancer and ovarian cancer (Chang, et al., 2006; Chien, et al., 2006;

Kikuchi, et al., 2007; Moritani, et al., 2003). In ovarian cancer and lung cancer,

CTGF alters the cell cycle with more cells in G1-G0 and causing G1-S

checkpoint arrest. In these neoplasms the loss of CTGF would effectively

increase proliferation.

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Drug resistance

CTGF has been associated with drug resistance in glioblastoma multiforme,

breast cancer and thyroid cancer. CTGF was involved in modulating apoptosis

genes, which caused resistance to several apoptosis-inducing drugs. In

glioblastoma multiforme CTGF was associated with expression of the anti-

apoptotic genes, survivin and FLIP, and a decrease in pro-apoptotic PARP

expression (Yin, et al., 2010). In breast cancer, CTGF modulated expression of

anti-apoptotic genes Bcl-xL and cIAP1 through an integrin αvβ3/FAK/ERK1/2

pathway. Furthermore, breast cancer patients with high CTGF expression

correlated with a poor chemotherapeutic response (Wang, et al., 2009). In

thyroid cancer, CTGF overexpression was linked to drug resistance, with

knockdown studies indicating cleaved caspase-3 and -9, members of the cell-

apoptosis pathway, are modified (Cui, et al., 2011).

Angiogenesis

CTGF deregulation acts to increase tumour angiogenesis in tumours over- and

underexpressing CTGF compared with normal cell counterparts. CTGF

increased tumour angiogenesis in vivo in breast cancer, glioblastoma

multiforme and pancreatic cancer (Aikawa, et al., 2006; Kondo, et al., 2002; Yin,

et al., 2010). In all these cancer types CTGF is over expressed compared with

normal cells. In a bone metastasis model of breast cancer, treatment with an

anti-CTGF antibody reduced angiogenesis, revealing a role for CTGF at a

secondary site (Shimo, et al., 2006).

In lung adenocarcinoma, where CTGF is underexpressed compared with

normal cells, forced CTGF expression reduced angiogenesis in vivo. Further,

patient samples with high CTGF correlated with less angiogenesis (Chang, et

al., 2006). Again, the ultimate outcome of deregulated CTGF expression

increased angiogenesis, maintaining tumour progression.

Adhesion

Adhesion is linked to the invasive abilities of cancers, with the need to reduce

adhesion to extravasate from the primary tumour site and then increase

adhesion to colonise distant sites of metastasis. CTGF plays a role in

extravasation and colonisation. In ovarian cancer and colorectal cancer, CTGF

expression is reduced compared with normal tissue, correspondingly CTGF

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works to disadvantage the tumour. When recombinant CTGF is present, ovarian

cancer cells adhere more strongly to collagen 1, a major building block of the

ECM (Barbolina, et al., 2009). The low level of CTGF allows for reduced

adhesion and increased capacity for extravasation. Inducing CTGF expression

in colorectal cancer cells resulted in reduced peritoneal tumour dissemination.

CTGF inhibited the ex vivo adhesion abilities of colorectal cancer cells to

matrigel and excised peritoneum, acting at least partially through activation of

integrin α5 (Lin, et al., 2011). The reduced CTGF expression in colorectal

cancer may lead to an increase in adhesion and the ability of tumour cells to

seed the abdominal cavity, the precursor to peritoneal tumour dissemination.

Conversely, in gastric cancer CTGF is over expressed compared with normal

tissue. Increased CTGF promotes epithelial to mesenchymal transition in

peritoneal mesothelial cells. This provides a favourable environment for gastric

cancer cells to adhere to the peritoneum, an initial step in peritoneal tumour

dissemination (Jiang, et al., 2012).

Migration

Migration is used by cancer cells to spread within a tissue space and can occur

in many forms. It is required for the invasion of tissue barriers that occurs as

part of metastasis (Friedl & Wolf, 2003). In cancers that have higher expression

of CTGF compared with normal tissue, CTGF increases migration. This is the

case in glioma, gastric cancer, hepatocellular carcinoma, malignant melanoma

and pancreatic cancer (Mazzocca, et al., 2010). In glioma CTGF expression

was found to increase in intensity from the centre of the tumour to the infiltrative

front (Yin, et al., 2010). In glioma and gastric cancer activated nuclear factor

kappa-B (NFKB) suppressed E-cadherin and migration (Edwards, et al., 2011;

Mao, et al., 2011). In breast cancer activation of the integrin αvβ3/ERK1/2

pathway along with S100A4 was responsible for cell motility (Chen, et al.,

2007). CTGF was upregulated in invasive compared to non-invasive uveal

melanoma cell lines as determined by microarray and RT-PCR (Seftor, et al.,

2002).

In cancers where CTGF is under expressed compared with normal tissue,

CTGF inhibits migration and thereby promotes a favourable outcome for the

tumour when underexpressed. This is the case in cervical, colorectal, head and

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neck, lung and ovarian cancer (Barbolina, et al., 2009; Chang, et al., 2004;

Chang, et al., 2013; Chuang, et al., 2011; Lin, et al., 2005; Xie, et al., 2012;

Yang, et al., 2011). In head and neck cancer, loss of CTGF promotes migration

through a switch to N-cadherin expression and epithelial mesenchymal

transition (Chang, et al., 2013). This is the opposing mechanism to glioma and

gastric cancer.

Metastasis

Studies using in vivo metastasis models show differences in metastasisng

colonies due to alterations in adhesion, migration, invasion and anoikis. In

tumours with higher CTGF expression than in normal tissue metastasis was

increased, shown in breast cancer, gastric cancer, hepatocellular carcinoma,

pancreatic and prostate cancer (Aikawa, et al., 2006; Dornhofer, et al., 2006;

Gorlov, et al., 2010; Kang, et al., 2003; Mao, et al., 2011; Mazzocca, et al.,

2010; Minn, et al., 2005). The models ranged from mouse cardiac injections,

chicken embryo metastases and meta-analyses of human tissue microarrays

from primary and metastatic tumours. In breast cancer, CTGF was associated

with bone-metastasis gene-sets; it was not sufficient alone to induce metastasis

to bone, though CTGF enhanced metastasis in vivo when overexpressed with

Osteopontin (OPN) and Interleukin 11 (IL11). CTGF was upregulated in clinical

breast cancer bone metastasis samples compared with normal breast tissue.

However, the expression of CTGF was not different between bone metastasis

samples from other solid tumours. This suggests the involvement of CTGF in

bone metastasis may not be specific to breast cancer. The expression of CTGF

in clinical bone metastasis samples significantly correlated with interleukin 11

(IL11), a disintegrin and metalloproteinase with thrombospondin motifs 1

(ADAMTS1) and C-X-C chemokine receptor type 4 (CXCR4). (Casimiro, et al.,

2012).

CTGF monoclonal antibodies have led to reduced metastases in breast and

pancreatic cancer. A breast cancer metastasis model treated with murine CTGF

monoclonal antibody (JMab 31, JT Central Pharmaceutical, Japan) resulted in

significantly less osteolytic lesions (Shimo, et al., 2006). In pancreatic cancer,

the combined treatment of gemcitabine and a CTGF monoclonal antibody (FG-

3019) reduced liver metastases (Neesse, et al., 2013).

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In cancers with reduced CTGF expression compared with normal tissue, CTGF

acts to inhibit metastasis and therefore its underexpression leads to increased

metastasis. This is seen in mouse models for colorectal cancer, head and neck

cancer and lung cancer (Chang, et al., 2004; Chang, et al., 2006; Lin, et al.,

2005; Yang, et al., 2011). In colorectal cancer patients, low CTGF expression

was associated with an increase in peritoneal dissemination recurrence (Lin, et

al., 2011). In lung adenocarcinoma, cells with increased CTGF expression had

increased apoptosis after cell detachment, known as anoikis (Chang, et al.,

2012). Lung adenocarcinoma cells, with reduced expression, can escape

anoikis and undergo metastasis.

Conclusions CTGF activity has been investigated and reported in 27 human cancers, with

many more possibly still unrecognised. A common feature among these cancer

types is a pattern of deregulated CTGF expression and worse clinical outcome.

Stromal-expression of CTGF was also found to affect tumour survival through a

desmoplastic response. CTGF was found to regulate proliferation, drug

resistance and interactions with the stromal microenvironment.

Microenvironment changes due to CTGF gave an advantage to tumours by

modifying angiogenesis, adhesion, migration and metastasis. CTGF was found

to increase these mechanisms of action when it was over expressed in tumours

compared with normal tissue. In contrast, CTGF was found to decrease these

mechanisms of action in tumours where it was under expressed compared with

normal tissue. The ultimate outcome is that deregulated CTGF leads to an

increase in cellular mechanisms of action that support tumour cell survival.

Exceptions to this pattern include Hodgkin’s lymphoma, diffuse large B-cell

lymphoma and gallbladder cancer, where increased CTGF expression from

these tumours is associated with better prognosis. This is likely due to the

tumour-stroma interactions eliciting a protective fibrotic response, hindering

tumour progression or metastasis. Deregulated CTGF being associated with a

host-protective microenvironment has only been reported in these three cancer

types, reasons for this should be explored in future studies.

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The role of CTGF in human cancer is not straightforward. Each cancer has

proven to have modifications attributable to CTGF that are unique due to the

matricellular nature of the signalling protein. However, it is clear that when

CTGF is deregulated in cancer compared with its normal counterpart, it effects

changes that advantage the tumour. Early evidence of CTGF antibody use in

pancreatic and breast cancer mouse models is a promising model that targeting

specific proteins in the microenvironment can lead to improved patient

outcomes.

1.4 Aims and outline of the thesis

This thesis is guided by an overarching question: Is there a specific functional

role for CTGF in B-precursor ALL?

The question is of importance as in childhood B-precursor ALL, CTGF is the

most deregulated gene and has been associated with poor outcome and high-

risk stratification. Yet the functional role CTGF plays in B-precursor ALL,

contributing to the phenotype of the leukaemia cell, remains to be identified.

The hypothesis for this thesis is that secretion of the CTGF matricellular protein

initiates a cascade of events, mediated through the microenvironment, that

contribute to leukaemogenesis and/or tumour cell survival. This thesis

contributes new knowledge of childhood leukaemias, verifying the existence of

a functional role for CTGF and the nature of microenvironment interactions

between B-precursor ALL and BM stromal cells.

The specific Aims of this thesis were to:

1. Engineer stable CTGF expression in established human B-precursor ALL cell

lines

(PER-278 and PER-371) and characterise their ability to contribute to the

leukaemia cell phenotype through intracellular or autocrine mechanisms.

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2. Determine the effect of ectopic CTGF on an immortalised human BM stromal

cell line HS5, thereby verifying the potential of CTGF to be an intermediary in

B-precursor ALL cross-talk with components of the BM microenvironment.

3. Delineate the functional outcomes of CTGF-overexpression in B-precursor

ALL within the context of a murine BM microenvironment. This was

accomplished by establishing a xenograft model using immune-compromised

mice and engineered cell lines from Aim 1.

Chapter 2 provides a technical description of all materials and methods used to

establish experimental results for this thesis.

Chapter 3 covers the production of CTGF-overexpressing B-precursor ALL cell

lines and their characterisation (Aim 1).

Chapter 4 explores the changes to human BM stromal cell gene expression

due to treatment with ectopic CTGF (Aim 2).

Chapters 5 and 6 describe the PER-278 and PER-371 mouse xenograft

studies, respectively, due to differences between these cell lines in the

functional outcomes of xenografted mice (Aim 3).

Chapter 6 provides a summary and general discussion of the results that were

obtained as part of this PhD research and explores future research directions.

 

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Materials and Methods

I keep six honest serving-men,They taught me all I knew;

There names are What and Why and When,And How and Where and Who.

Rudyard Kipling

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Chapter 2 Materials and Methods

2.1 Cell lines and tissue culture

All cultured cell lines were verified to be free of mycoplasma contamination by

polymerase chain reaction (Tang, et al., 2000). Authentication of cell lines was

performed by short tandem repeat (STR) profiling on DNA using the GenePrint

10 System (Promega, Madison, WI, USA, #B9510) at the Johns Hopkins

genetic resources core facility (Baltimore, MD, USA).

2.1.1 Suspension cell lines ALL leukaemia cell lines used in this study, PER-255, PER-278, PER-371 and

PER-377, were generated at the Telethon Institute for Child Health Research in

the laboratory of Prof Ursula Kees according to previously published methods

(Kees, et al., 1987). Culture medium used for all suspension cell lines was

RPMI-1640 (MP Biomedicals, LLC) supplemented with 1mM sodium pyruvate

(MP Biomedicals, LLC), non-essential amino acids (MP Biomedicals, LLC), 2nM

2-mercapto-ethanol, and 2mM L-glutamine. Culture medium for suspension cell

lines was supplemented with 10% (v/v) fetal calf serum (FCS) (Invitrogen, Life

Technologies, Carlsbad, CA, USA). Cells were passaged twice weekly (split

1:2) and maintained in 24-well plates (Nunc, ThermoFisher Scientific, Waltham,

MA, USA) at 5% CO2 and 37°C. Suspension cell lines were quantitated using

the Vicell XR cell viability analyzer (Beckman Coulter).

2.1.2 Adherent cell lines The immortalised human bone marrow stromal cell line HS5 (CRL-11882)

(Roecklein & Torok-Storb, 1995b) and human embryonic kidney cell line 293T

(CRL-3216) were obtained from the American Type Culture Collection (ATCC,

Manassas, VA, USA). HS5 cells were maintained in RPMI-1640 supplemented

with 1mM sodium pyruvate, non-essential amino acids, 2nM 2-mercapto-

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ethanol, 2mM L-glutamine and 10% (v/v) FCS. Cells were passaged twice

weekly on reaching 80-90% confluence (split 1:10) and maintained in 75cm2

filter-top culture flasks (Nunc, ThermoFisher Scientific, Waltham, MA, USA).

293T cells were maintained in Dulbecco’s Modified Eagle’s Medium (DMEM,

Gibco, Life Technologies, Carlsbad, CA, USA) with 10% (v/v) FCS, 2mM L-

glutamine and 1% Penicillin/Streptomycin (Life Technologies, Carlsbad, CA,

USA). Cells were passaged thrice weekly on reaching 80-90% confluence (1:5)

and maintained in 100x20mm tissue culture dishes (BD Falcon, Becton

Dickinson, Franklin Lakes, NJ, USA). All adherent lines were cultured at 5%

CO2 and 37°C.

For passaging, cells were washed with phosphate buffered saline [PBS;

1.84mM KH2PO4, 2.68mM KCl, 136.87mM NaCl, 7.87mM Na2HPO4.2H2O] and

Trypsin-EDTA (Invitrogen, Life Technologies, Carlsbad, CA, USA) was used to

detach adherent cell lines from the culture dish or flask. Adherent cells were

quantitated using the trypan blue exclusion technique. Briefly, cells were mixed

1:1 with 0.1% Trypan Blue (Sigma Aldrich, St. Louis, MO, USA) in PBS and

pipetted into a coverslipped haemocytometer. The concentration of cells per ml

was found by the multiplication of the average viable cell count per square, the

cell dilution factor and 10,000.

2.2 Cell Transfections 2.2.1 Plasmids used in cell transfection To overexpress CTGF from leukaemia cell lines PER-278 and PER-371 two

techniques were attempted. The mammalian expression plasmid used for

electroporation, pcDNA3.1-CTGF, and its empty vector, pcDNA3.1-eGFP,

contained a cytomegalovirus (CMV) promoter and green fluorescent protein

(GFP) marker. Both were kindly donated by Prof David. R. Brigstock (Children’s

Research Institute, Columbus, OH, USA). Both vectors contained a neomycin

resistance gene. The mammalian expression plasmid used for lentiviral

infection, pCDH-MSCV-MCS-EF1-GFP-PURO (empty vector) was purchased

from SBI (System Biosciences, Mountain View, CA, USA, #CD713B-1) and

featured a murine stem cell virus (MSCV) promoter to drive expression of

CTGF, production of the CTGF plasmid is detailed in section 2.2.1.1, and an

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elongation factor 1α (EF1) promoter to drive expression of GFP. Both pCDH-

MSCV-MCS-EF1-GFP-PURO and pCDH-MSCV-CTGF-EF1-GFP-PURO

contained a puromycin resistance gene (PURO).

Lentiviral packaging plasmids were kindly donated by St. Jude Children’s

Hospital (Memphis, TN, USA). They include the major proteins of human

immunodeficiency virus (HIV-1): gag and pol (in plasmid pCDH-KGP1-1R), rev

and tat (in plasmid pCDH-RTR2) and envelope (in plasmid pCAG-VSVG).

2.2.1.1 Ligation of human CTGF insert into pCDH vector Double restriction digests using restriction enzymes BamHI (Promega, Madison,

WI, USA, #R6021) and NotI (Promega, Madison, WI, USA, #R6431) and

10xBuffer D (Promega, Madison, WI, USA) were performed individually for both

pcDNA3.1-CTGF, to obtain the full-length human CTGF insert, and pCDH-

MSCV-MCS-EF1-GFP-PURO, to produce sticky ends for insertion of CTGF.

Briefly, 4µg of plasmid DNA was added to 5 units (U) each of NotI and BamHI

and made up to 40µl with 1xBuffer D and 0.1% bovine serum albumin (BSA,

Sigma Aldrich, St. Louis, MO, USA). The solution was incubated at 37°C for 90

min. Following incubation, the restriction digest was deactivated by incubating

at 65°C for 10 min.

Digested plasmids were resolved using agarose gel electrophoresis. Molecular

biology grade agarose (Amresco, Solon, OH, USA) was melted in 1x TAE buffer

[40mM Tris, 5.7% glacial acetic acid, 1mM ethylenediaminetetraacetic acid

(EDTA)] and supplemented with SYBR Safe DNA stain (Invitrogen, Life

Technologies, Carlsbad, CA, USA). Samples were combined with 10xloading

buffer (4.4mM Orange G, 40% glycerol) and run across 3 lanes alongside a 1Kb

DNA ladder (Invitrogen, Life Technologies, Carlsbad, CA, USA). Samples were

run for 80 min at 80V. The linear pCDH-MSCV-MCS-EF1-GFP-PURO band and

CTGF insert from pcDNA3.1-CTGF were isolated under ultra-violet (UV) light

with a clean scalpel. Plasmid DNA was purified with a QIAquick gel extraction

kit for cleanup of DNA (Qiagen, Venlo, Limburg, Netherlands, #28704). Purified

DNA was quantitated using the Nano drop ND-1000 spectrophotometer

(ThermoFisher Scientific, Waltham, MA, USA). The linear pCDH vector and

sticky-ended CTGF insert were ligated together with LigaFast rapid DNA

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ligation system (Promega, Madison, WI, USA, #M8221), according to modified

manufacturer’s instructions, using only 20ng of both vector and insert, and

incubating for 24 hours at room temperature. Ligated pCDH-MSCV-CTGF-EF1-

GFP-PURO plasmid DNA was cloned through bacterial transformation,

explained in 2.2.1.2 and confirmed through DNA sequencing, explained in

2.2.1.3.

2.2.1.3 Transformation of chemically competent cells for DNA cloning Competent Top10 E.coli cells [in 75mM Cacl2/25% glycerol] were thawed on ice

for 15 min. After thawing, a 50µl aliquot was added to 10ng of plasmid DNA

(pCDH-MSCV-CTGF-E2A-GFP-PURO) in nuclease-free water, followed by a

further 30 min incubation on ice. Cells were then subjected to heat shock

transformation by incubation in a 42°C heat block for 30 sec, then returned to

ice and incubated for 2 min. Cells were added to 450µl of SOC medium [10mM

NaCl, 2.5mM KCl, 10mM MgCl2, 10mM MgSO4, 20mM glucose] over flame and

tubes were incubated for 60 min at 37°C with moderate shaking. At the

completion of the 60 min incubation, transformed cells were centrifuged for 5

min at 800x g and then resuspended in 100µl SOC. 50µl of transformed cells

were spread on prepared Luria broth [LB: 0.1% Bacto-tryptone (BD

Biosciences, San Jose, CA, USA), 0.05% Yeast extract (BD Biosciences, San

Jose, CA, USA), 170mM NaCl in distilled water (dH20)] agar plates containing

100µg/ml ampicillin (Sigma Aldrich, St.Louis, MO, USA). Agar plates were

incubated overnight at 37°C. The following day, single colonies were used to

inoculate 3ml of LB supplemented with 100µg/ml ampicillin. These cultures

were grown overnight at 37°C with vigorous shaking (250RPM) or for 6 hours

then diluted 1:500 into a conical flask with 50ml or 250ml LB supplemented with

100µg/ml ampicillin. The following day, glycerol stocks were prepared from

each culture by combining 100µl of culture with 100µl of 80% glycerol. These

stocks were frozen immediately at -80°C. The remainder of the overnight

culture was centrifuged in preparation for plasmid DNA extraction using the

QIAprep Spin Miniprep kit (Qiagen, Venlo, Limburg, Netherlands, #27104) or

Midi/Maxiprep HiSpeed plasmid kit (Qiagen, Venlo, Limburg, Netherlands,

#12643/12663) depending on volume and according to the manufacturer’s

instructions. Purified plasmid DNA was eluted in 30µl or 300µl of Tris-EDTA

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(TE) buffer and stored at -20°C. Miniprep DNA was not used for lentivirus

production.

2.2.1.3 DNA sequencing to verify CTGF insertion into pCDH plasmid Sequencing was carried out using BigDye version 3.1 (Applied Biosystems, Life

Technologies, Carlsbad, CA, USA). Firstly, pCDH-MSCV-CTGF-E2A-GFP-

PURO plasmid DNA was amplified by polymerase chain reaction (PCR)

performed on a C1000 Thermal Cycler (Bio-Rad Laboratories, Hercules, CA,

USA). All PCR reactions were assembled on ice in sterile 0.2 ml thin-walled

tubes (Bio-Rad Laboratories, Hercules, CA, USA). Briefly, 75ng of plasmid

DNA was combined with 3.5µl of 5x BigDye reaction buffer, 9.3µl of ultrapure

water (Baxter, Deerfield, IL, USA), 3.2µl of 1 µM sequencing primer and 1µl of

BigDye v3.1. Four primers spanning the CTGF insert were used to sequence

the plasmid as indicated:

CD_1F (5'-3', AGTGCGACTCCACCCTCCA)

CD_1R (5'-3', GCTGGCAGCAGCTGGAG)

CD_3F (5'-3', GCTCCCTGCATCTTCGGT)

CD_3R (5'-3', CTCTTCCAGGTCAGCTTC)

Samples were denatured at 96°C for 1 min, followed by 25 cycles of 96°C for 10

s, 50°C for 5 s and 60°C for 4 min. Samples were precipitated in 1.5mL

Eppendorf tubes (Eppendorf, Hamburg, Germany) by adding 2µl sodium

acetate (3M) and 50µl 100% ethanol (EtOH). The solution was incubated at

room temperature for 30 min in the dark. After incubation, DNA was centrifuged

at 13kRPM for 20 min at 4°C. Supernatant was aspirated and 200µl of 70%

EtOH was pipetted on top of DNA pellet, pellet was centrifuged a further 10 min

at 13kRPM at 4°C. Supernatant was aspirated and the plasmid DNA pellet was

left to air dry before being resuspended in 10µl of Hi-Di injection buffer. The

solution was vortexed and spun briefly before being transferred to a 96-well

plate suitable for the 3130x Genetic Analyzer sequencing platform (Applied

Biosystems, Life Technologies, Carlsbad, CA, USA). The plate was then loaded

onto a 3130x Genetic Analyzer (Applied Biosystems, Life Technologies,

Carlsbad, CA, USA) for capillary sequencing. Sequencing data generated from

BigDye sequencing was analysed using MacVector software (MacVector, Cary,

NC, USA).

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2.2.1 Linearisation of the pcDNA3.1 vector for electroporation The pcDNA3.1/eGFP vector was linearised with a BglII restriction enzyme

(Promega, Madison, WI, USA, #R6081) that cut distal to the CMV promoter

region. Digests were performed overnight at 37°C with Buffer D (Promega,

Madison, WI, USA). Digested DNA was cleaned up using the QIAquick PCR

purification kit (Qiagen, Venlo, Limburg, Netherlands, #28104) according to

manufacturer’s instructions. Plasmid DNA was then precipitated with EtOH.

Briefly, 2.5x 100% EtOH and 1.5x Sodium acetate (3M) were added to the

linearised pcDNA3.1/eGFP sample and incubated for 2 hours at -20°C.

Samples were then centrifuged at 13kRPM for 30 min at 4°C. Supernatant was

removed and 3 washes were performed in 500µl of 70% EtOH followed by

centrifugation at 13kRPM for 10 min at 4°C. The pellet was then left to air-dry,

resuspended in 30µl endotoxin-free TE buffer and quantitated before being

stored at -80°C.

2.2.2 Standard electroporation of B-precursor ALL cells Standard electroporation was performed with linear and supercoiled plasmid

DNA using the Bio-Rad gene pulser II (Bio-Rad Laboratories, Hercules, CA,

USA). Briefly, a cuvette was filled with 2x106 PER-278 cells and 5µg of linear or

supercoiled pcDNA3.1-eGFP plasmid DNA in 400µl of RPMI and left to stand

for 10 min at room temperature. The cells were then electroporated at high

resistance, 0.975mF capacitance and 0.3kV voltage and left to stand for 10 min

at room temperature. Then, foam residue was removed from the top of the

cuvette and cells were transferred to 5ml of normal media, seeded into 5-wells

of a 24-well plate and incubated at 37°C and 5%CO2.

2.2.3 Neon electroporation of B-precursor ALL cells Linearised or supercoiled pcDNA3.1-eGFP plasmid DNA was used in Neon

electroporation transfections (Neon transfection system, Life Technologies,

Carlsbad, CA, USA). Electroporation of 2x105 PER-278 cells with 1µg of

plasmid DNA was performed following manufacturer’s instructions. The

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suspension of electroporated PER-278 cells was added to 500µl of pre-warmed

culture media in a 24-well plate and incubated at 37°C and 5%CO2.

2.2.4. Selection of stable cells transfected with pcDNA3.1 vector PER-278 cells were selected after electroporation, with 1.1µg/ml G418 (Sigma

Aldrich, St. Louis, MO, USA, #A1720). Optimal G418 concentration for PER-278

cell selection was determined by using serial dilutions of G418 and measuring

cell viability in an MTT assay, outlined in 2.6.1. For selection of cells that had

incorporated the neomycin resistance gene, G418 was added 48 hours after

electroporation, 250µl of culture media was replaced with 2.2µg/ml G418 in

normal media for a final concentration of 1.1µg/ml G418. Media was replaced

again at day 5 and 9 post-electroporation with 1.1µg/ml G418 in normal media

and selection was performed for a total of 21 days.

2.2.5 Lentiviral production Lentiviral particles were produced by transiently transfecting 293T cells to

express the HIV-1 plasmids. Briefly, 3x106 293T cells were plated in a 100mm

culture dish in 10mL normal media. Two ratios of lentiviral plasmids were used

to transfect 293Ts: Ratio1 [12µg plasmid DNA, 6µg gag-pol, 2µg rev-tat and

2µg VSV-G envelope] or Ratio2 [20µg plasmid DNA, 10µg gag-pol, 6µg rev-tat

and 5µg envelope]. These two ratios of plasmids were used to transfect 293Ts

by two methods, either using CaCl2 or Fugene (Fugene6, Roche, Basel,

Switzerland). The CaCl2 method involved adding 50µl of 2.5M CaCl2 to the

vector and packaging plasmid DNA solution with enough 0.1xTE buffer to make

the solution up to 500µl. To this solution, 500µl of 2xHBS was added [50mM

HEPES, 1.5mMNa2HPO4 and 140mM NaCl, pH7.5] and the solution was

vortexed and incubated at room temperature for 1 min. The DNA and CaCl2

solution was then added dropwise to 293T cells that had been covered with 9ml

of fresh normal media. For the Fugene method, vector and packaging plasmid

DNA was made up to 400µl with normal media and added to 32µl Fugene made

up to 200µl in normal media. The combined solutions were incubated at room

temperature for 15 min. The DNA and Fugene solution was then added

dropwise to 293T cells that had been covered with 8ml of fresh normal media.

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For both methods of transfection, 293T cells were incubated at 37oC and

5%CO2 overnight and the next day media replaced with 5ml of fresh media that

was specific for target cell line intended for transduction. Media was collected

48 hours later and filtered through a 0.45µm filter (Sarstedt, Nümbrecht,

Germany) then frozen in aliquots at -80oC.

Lentiviral particles were titred on 293T cells. In 100mm culture dishes, 3x105

293T cells were plated with 5 ml of normal media in triplicate for each virus to

be titred. One spare plate was included, to determine cell count at transduction.

The next day, transduction was performed by addition of 3, 10 or 30µl of

lentiviral particles in 3ml normal media and 8µg/ml polybrene (Sigma Aldrich,

St. Louis, MO, USA) to 293T cells. After 3 hours at 37oC and 5%CO2, an extra

6ml of normal media was added per plate. The next day, media was replaced

with 9ml of fresh normal media. Transduction efficiency was measured 72 hours

after infection on trypsinised 293T cells by detection of the GFP marker present

on the pCDH plasmid (%GFP+ cells) using a LSRII flow cytometer (Becton

Dickinson, Franklin Lakes, NJ, USA). Lentiviral titre was calculated as an

average from all three volumes of viral particles using the following formula:

(cell count at transduction x %GFP+ cells) = Infective Units (IFU)/ml

(volume of lentiviral particles added (ml))

2.2.6 Lentiviral infection As lentiviral titres were below 1x107 IFU/ml, lentiviral particles were not diluted

for leukaemia cell line infection. To transduce PER-278 and PER-371 cells,

5x106 cells were resuspended in 1ml of undiluted lentiviral particles with 8µg/ml

polybrene. Cells were plated in one well of a 24-well plate and spun for 90 min

at 800x g at room temperature then incubated at 37oC and 5%CO2 for 90 min.

After incubation, cells were pelleted and resuspended in 5ml normal media to

be plated across 5 wells of a 24-well plate. Infected cells were then incubated at

37oC and 5%CO2 until selection with antibiotics, detailed in 2.2.7.

2.2.7. Selection of stable cells infected with pCDH vector Puromycin (Sigma Aldrich, St. Louis, MO, USA, #P8833) was used to select

infected PER-278 and PER-371 cells. Optimal puromycin concentrations were

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determined by using serial dilutions of puromycin and measuring cell viability in

an MTT assay, outlined in 2.6.1. Following 48 hours after lentiviral infection,

250µl of culture media was replaced with fresh media containing 1.6µg/ml

puromycin for PER-278 (in normal media for a final concentration of 0.8µg/ml)

and 0.6µg/ml puromycin for PER-371 (in normal media for a final concentration

of 0.3µg/ml). Cells were then split (1:2) twice weekly with puromycin in normal

media. Successful production of stable cell lines was determined by detection of

GFP using a LSRII flow cytometer, when cells reached >95% GFP+ cells, they

were frozen down with 10%DMSO (v/v) in normal media, to be stored in liquid

nitrogen.

2.3 RNA analyses 2.3.1 RNA extraction RNA extraction was performed using a phenol-chloroform based protocol and

involved the addition of 1mL of TRIzol (Invitrogen, Life Technologies, Carlsbad,

CA, USA) to 1x107 pelleted cells. Samples were vortexed and incubated at

room temperature for 5 min. After the addition of 0.2ml of chloroform (AnalaR,

Merck) samples were mixed and separated by centrifugation at 11,000x g for 15

min at 4°C. The upper aqueous phase was collected and adjusted to 35% EtOH

by the addition of 100% EtOH. The resulting solution was purified using an

RNeasy Mini Kit (Qiagen) following the manufacturer’s instructions. Samples

were eluted in 30µl of nuclease-free water. After isolation all samples were

quantitated using the Nano Drop ND-1000 spectrophotometer (ThermoFisher

Scientific, Waltham, MA, USA) and stored immediately at -80°C.

2.3.2 cDNA synthesis First strand cDNA synthesis was performed using the Moloney murine

leukaemia virus (M-MLV) reverse transcriptase (Promega, Madison, WI, USA,

#M3682) according to the manufacturer’s instructions. RNA was first denatured

at 65°C for 5 min to reduce secondary structure and then snap chilled on ice for

a further 5 min. Reactions were assembled on ice and consisted of 1µg of total

RNA, 4µl of 5 x reaction buffer (Promega, Madison, WI, USA), 500µM dNTPs

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(ThermoFisher Scientific, Waltham, MA, USA), 1µM OligodT primer, 10U of

RNase inhibitor, and 200U of MMLV RT enzyme (Promega, Madison, WI, USA,

#M3682). Reactions were adjusted to 20µl total volume with nuclease free H2O

mixed thoroughly and incubated at 37°C for 1 hour. After extension, specimens

were diluted 1 in 5 with nuclease free H2O and stored at -80°C until required.

2.3.3 Quantitation of CTGF gene expression Quantitative real-time PCR (qRT-PCR) was performed to measure expression

of CTGF mRNA in cell lines. CTGF expression was measured using the on-

demand assay Hs00170014_m1 (Applied Biosystems, Life Technologies,

Carlsbad, CA, USA). Reactions were performed in 384-well plates on an ABI

7900HT Fast Real-Time PCR System (Applied Biosystems, Life Technologies,

Carlsbad, CA, USA) with the following thermal profile, 50°C for 2 min then 95°C

for 10 min, followed by 40 cycles of 95°C for 15 s and 60°C for 1 min. CTGF

reactions were prepared by combining the following components per well, 1µl of

CTGF assay, 10µl of universal PCR master mix, 8µl of dH2O and 1µl of first

strand cDNA. CTGF gene expression was normalised using an endogenous

control GAPDH assay (Applied Biosystems, Life Technologies, Carlsbad, CA,

USA) comprising 10µl of universal PCR master mix, 1µl GAPDH assay, 8µl of

dH2O and 1µl of cDNA. For the relative standard curve method of expression,

standards were prepared from cDNA generated from the PER-377 cell line. This

cDNA was not diluted after cDNA synthesis and thus was approximately 5 times

more concentrated than test specimens, which were diluted 1 in 5 immediately

after cDNA synthesis. Standards were prepared by serial dilution and assayed

in duplicate to control for pipette error, while test specimens were assayed in

triplicate. The relative expression for each assay was calculated using the

standard curves. For relative quantitation using the comparative Ct (∆∆Ct)

method, no standard curve was prepared. Briefly, the Ct values obtained from

High CTGF and Low CTGF cells were directly normalized to GAPDH and then

compared to each other. The fold change expression difference between the

two samples is calculated by 2^(-ΔΔCt).

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2.3.4 Global gene expression to determine effect of CTGF on stable CTGF-overexpressing leukaemia cell lines RNA was analysed for suitable purity for downstream microarray analysis using

the Agilent 2100 Bioanalyzer (Agilent Technologies). RNA samples from

lentiviral-infected cell lines were analysed using the RNA 6000 Nano kit (Agilent

Technologies, #5067-1511), following the manufacturer’s instructions.

Electropherogram and RNA integrity number were used for quality control.

Samples were then sent for processing on GeneChip Human Gene 1.0 ST

Arrays (Affymetrix, Santa Clara, CA, USA) by the Ramaciotti Centre for Gene

Function Analysis (The University of New South Wales, Sydney, Australia).

Analysis of microarray data was performed by Denise Anderson (Biostatistician,

Telethon Institute for Child Health Research, Perth, WA, Australia), including

robust multi-array average (RMA) normalization and linear models for

microarray data (LIMMA) analysis using the R platform (www.r-project.org).

2.3.5 Global gene expression to determine effect of recombinant human CTGF on stromal cells

Recombinant human (rh)CTGF was kindly donated by Prof David. R. Brigstock

(Children’s Research Institute, Colombus, OH, USA). All technical steps

required for stromal cell gene expression microarrays were performed by Jette

Ford in the laboratory of Prof Ursula Kees, Telethon Institute for Child Health

Research, Perth, Western Australia. HS5 cells were incubated with 100ng/ml

rhCTGF or vehicle control (control buffer) for 8,16 or 48 hours. There were 3-4

experimental and control replicates at 8 and 16 hours, and 2 at 48 hours. For

hybridization to the HG-U133A microarrays (Affymetrix, Santa Clara, CA, USA)

cRNA was prepared following an adapted Affymetrix protocol as described

previously (Boag, et al., 2006). Briefly, RNA was reverse transcribed into double

stranded DNA and was then used to synthesize biotinylated cRNA, with the use

of a Bioarray High Yield RNA Transcript Labelling Kit (Enzo Life Sciences,

Farmingdale, NY, USA). Biotinylated cRNA was fragmented and hybridized to

the microarray and then washed and stained before scanning (GeneArray

Scanner, Agilent Technologies, Santa Clara, CA, USA) in accordance with

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Affymetrix protocols. Scanned images met stringent quality controls, having

scaling factors of <20, noise values below three and the signal ratios of the

housekeeping genes ACTB and GAPDH were <3 for all arrays. Principle

component analysis (PCA) was used to determine similarity of gene expression

patterns between the CTGF-treated and control HS5 samples.

Microarray analysis was performed by Julia Wells. Data were normalized by

RMA using GeneSpring (Agilent Technologies, Santa Clara, CA, USA).

Statistical analysis was performed using LIMMA and p-values were adjusted for

multiple testing using the Benjamini and Hochberg method for false discovery

rate (Benjamini & Hochberg, 1995; Smyth, 2004, 2005) on the R platform

(www.r-project.com). Data were analysed using Ingenuity Pathway Analysis

(IPA, Ingenuity, Redwood City, CA, USA). IPA was employed to gain

information about networks, canonical signalling pathways and biological

functions in CTGF-treated HS5 cells. The input dataset comprised genes from

the 8 hour time point showing a ≥2-fold difference compared to control cells,

and statistical difference in expression as determined by LIMMA p-value. A list

of secreted genes from the IPA input dataset were found by comparing the

dataset to that of the Secreted Protein Discovery Initiative (Clark, et al., 2003)).

The extracellular function of these secreted genes was determined manually

using GeneCards (Rebhan, et al., 1998)).

Validation of four genes from the microarray analysis was performed using qRT-

PCR, as described in section 2.3.3. Briefly, RNA was extracted from HS5 cells

after incubation in 100ng/ml rhCTGF for 8 hours as per the protocol described

in section 2.3.1, cDNA was then synthesized as per the protocol described in

section 2.3.2. Lastly, qRT-PCR was performed using the relevant Taqman

assays (Applied Biosystems, Life Technologies, Carlsbad, CA, USA) for

Collagen, Type 3, alpha 1 (COL3A1, #Hs00943809_m1), Lumican (Dornhofer,

et al., Hs00929860_m1), Lysyl Oxidise (LOX, #Hs00942480_m1) and Integrin,

alpha V (ITGAV, #Hs00233808_m1) all normalized to GAPDH. Gene

expression levels were quantified using the comparative Ct method as

described in section 2.3.3.

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2.4 Protein analyses Protein expression of CTGF was detected with two antibodies. The L-20 anti-

CTGF antibody is an affinity purified goat polyclonal antibody raised against a

peptide mapping within an internal region of CTGF of human origin (Santa Cruz

Biotechnology, Santa Cruz, CA, USA, #sc-14939). The H-55 anti-CTGF

antibody is a rabbit polyclonal antibody raised against amino acids 295-349 of

CTGF of human origin (Santa Cruz Biotechnology, #sc-25440). A summary of

primary, secondary and tertiary antibodies used in protein analyses are listed in

Table 2.1.

2.4.1 Cellular protein extraction Total protein was isolated from cell lines for analysis by western blotting. Cells

were pelleted by centrifugation and washed twice with ice-cold PBS. Cell pellets

were resuspended in one pellet volume of ice-cold PBS and then lysed using

100µl/1x107 cells of Evan’s protein lyses buffer [1mM EDTA, 1mM ethylene

glycol tetraacetic acid (EGTA), 1%NP-40, 50mM Tris-HCl, 120nM NaCl and

peptide inhibitors], and incubated on ice for 30 min. Samples were centrifuged

for 10 min at 13kRPM at 4°C and supernatants were transferred to fresh 1.5 ml

tubes. Protein samples were stored at -20°C or used immediately in

downstream assays.

Protein concentration in cell line extracts was determined using a bicinchoninic

acid (BCA) protein assay (Pierce, ThermoFisher Scientific, Waltham, MA, USA)

according to manufacturer’s instructions. Samples were diluted 1 in 10 and

together with standards [10µg/ml to 5mg/ml serial dilution of BSA], were added

to a 96-well flat-bottomed plate at 10µl per well. Standards were assayed in

duplicate, while protein samples were assayed in triplicate. After addition of

samples and standards, the plate was incubated at 37oC for 30 min, and the

absorbance was measured at 562nm on a Synergy plate reader (BioTek,

Winooski, VT, USA). Protein concentration in cell line extracts was calculated

using the standard curve.

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2.4.2 Secreted protein purification

Heparin-affinity enrichment of conditioned culture medium was necessary to

detect secreted CTGF. Cells were seeded in fresh culture medium at a density

of 1x106 cells per ml in 24-well plates (Nunc, Thermo Fisher Scientific, Waltham,

MA, USA), and grown for 24 hours prior to isolation of conditioned medium

(CM). Cells and CM were collected and centrifuged at 800x g for

5 min and 5ml of supernatants comprising the CM were then transferred to

fresh tubes containing 5ml of ice-cold PBS together with 50µl of heparin

agarose beads (Sigma Aldrich, St. Louis, MO, USA, #H6508). The solution was

then incubated for 24 h at 4°C on a fly-wheel. After 24 hours, beads were

collected by centrifugation at 800x g for 5 min at 4°C, then supernatant was

carefully removed by vacuum aspiration. Beads were washed twice with ice-

cold PBS and centrifugation at 800x g for 5 min at 4°C. After the second wash,

beads were resuspended in 1ml ice-cold PBS and transferred to 1.5 ml tubes.

Beads were collected by centrifugation at 800x g for 3 min at 4°C and the

supernatant was carefully aspirated, leaving a 50µl bead slurry. Bound protein

was prepared for western blot analysis by adding 19.25µl of 4x LDS sample

loading buffer (Invitrogen, Life Technologies, Carlsbad, CA, USA) and stored at

-80oC. After thawing, 7.7µl of 10x Denaturing agent (Invitrogen, Life

Technologies, Carlsbad, CA, USA) was added to the sample, which was

denatured at 70oC for 10 min. Samples were then quenched on ice for 2 min

and used for western blot.

2.4.3 Western blot Electrophoresis of NuPAGE Novex BisTris mini gels using the XCell surelock

Mini-Cell was carried out under manufacturer’s instructions (Invitrogen, Life

Technologies, Carlsbad, CA, USA). Electrophoresis using the mini-cell was

conducted using 4-12% BisTris pre-cast gels and MES running buffer with

antioxidant. Prior to electrophoresis, quantitated cellular protein samples were

combined with 4x LDS sample buffer and 10x Reducing agent and heated at

70oC for 10 min. Samples were then quenched on ice for 2 min then loaded

onto the pre-cast 4-12% Bis-Tris gel with a Precision Plus Protein Kaleidoscope

standards ladder (Bio-Rad Laboratories, Hercules, CA, USA). Gels were run at

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anti-Annexin V-PE

Primary Antibody Dilution Supplier

monoclonal mouse anti-Actin pan Ab-5

anti-BrdU-APC

mouse anti-CD19-APC

polyclonal rabbit anti-CTGF (H-55)

monoclonal mouse anti-Ki67

monoclonal rabbit anti-Pax5

1:50 FC BD (#556421)

1:5000 WB

1:50 FC

1:20 FC

Santa Cruz (#sc-25440)

1:800 WB1:100 E

1:100 IH Cell Signaling (#12709)

1:100 IH BD (#550609)

Table 2.1 List of primary, secondary and tertiary antibodies . Summary of the antibody name, dilution and supplier (with catalogue number). A dash indicates conjugation of the antibody to a fluorescent dye for flow cytometry or enzyme label for peroxidase staining. FC, flow cytometry, WB, western blot, E, elisa, IH, immunohistochemistry.

polyclonal rabbit anti-VwF 1:400 IH DAKO (#A0082)

Santa Cruz (#sc-14939) polyclonal goat anti-CTGF (L-20)

BD (#552598)

BD (#555415)ThermoFisher Scientific (#MS-1295)

goat anti-rabbit-Biotin

1:5000 E

1:10000 IH Vector Labs (#PK-6101)

polyclonal rabbit anti-goat-Biotin 1:5000 WB DAKO (#E0466)

Secondary/Teriary Antibody Dilution Supplier

GE Healthcare (#NA934)

polyclonal donkey anti-rabbit-HRP

HRP-streptavidin 1:3000 WB DAKO (#P0397)

1:800 WB1:100 E

1:10000 WB GE Healthcare (#NA9310)

polyclonal donkey anti-mouse-HRP

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145V for 60 min. Gels were transferred to mini nitrocellulose membranes (Bio-

Rad Laboratories, Hercules, CA, USA, #170-4158) using a semi-dry transblot

turbo (Bio-Rad Laboratories, Hercules, CA, USA).

Membranes were then washed in TBST [1xTris buffered saline, TBS [50mM

Tris-Cl and 150mM NaCl; pH7.5 with 0.1% Tween 20] for 3x 5 min, before being

blocked at room temperature for 1 hour with 5% skim milk powder in TBST, with

gentle agitation. After blocking, membranes were washed in TBST for 3x 5 min

and then incubated in 10mL primary antibody (anti-CTGF L-20, 1:800 dilution)

in diluent [TBST with 1% skim milk powder] overnight at 4oC with gentle

agitation. The next day, membranes were washed in TBST for 3x5 min and then

incubated in secondary antibody (rabbit anti-goat, 1:5000) in diluent for 1 hour

at room temperature with gentle agitation. Membranes were washed in TBST

for 3x 5 min and then incubated in HRP-Straptavidin (1:3000) in diluent for 1

hour at room temperature with gentle rocking. Membranes were washed in

TBST for 3x 5 min and then bound proteins were detected using an Immuno-

Star WesternC chemiluminescence HRP detection kit (Bio-Rad Laboratories,

Hercules, CA, USA), according to manufacturers instructions. Nitrocellulose

membranes were imaged on a Chemidoc MP imaging system (Bio-Rad

Laboratories, Hercules, CA, USA) at intervals until detected bands were

saturated.

Where it was necessary, membranes were stripped in stripping buffer [50 mM

Tris (pH 6.8), 2% SDS, 100 mM 2-mercaptoethanol] at 50°C for 30 min with

gently agitation, then washed three times in TBST for 5 min at room

temperature. Membranes were blocked and re-probed for anti-pan-Actin as a

loading control (1:5000, ThermoFisher Scientific, Waltham, MA, USA).

Secondary antibody was goat anti-mouse (1:10,000) and proteins detected as

previously described.

2.4.4 Enzyme-linked immunosorbent assay PER-278 Low, PER-278 High, PER-371 Low and PER-371 High were seeded

at 1.5x106 cells per well in fresh normal medium and incubated for 72 hours at

37oC and 5%CO2. Conditioned media was collected and cleared of cell debris

by centrifugation at 800x g for 5 min. After centrifugation, 5 ml of conditioned

medium was added to 5ml of 1xPBS with 50µl of Heparin-agarose beads, and

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the solution was incubated overnight on a fly-wheel at 4oC. The next day, the

solution was centrifuged at 800x g for 10 min at 4oC. Pellets were then washed

twice with 10ml Tris-HCl (10mM). Pellets were transferred to 1.5ml tubes and

washed with 1ml Tris-HCl (10mM). Protein was eluted from beads with 100µl

buffer [10mM Tris-HCl; 1.5M NaCl] and centrifuged at 1000x g for 3 min.

Supernatants were transferred to fresh 1.5ml tubes to be stored at -20oC for the

enzyme-linked immunosorbent assay (ELISA).

For ELISA, 96-well flat-bottom plates (Nunc, ThermoFisher Scientific, Waltham,

MA, USA) were coated with 2g/ml L-20 CTGF antibody. Plates were then

incubated for 24 hours at 4oC, flick-rinsed and patted dry on absorbent towel.

After coating plates with the CTGF capture antibody, wells were filled with 200µl

of blocking solution [1xPBS with 1% BSA and 5% sucrose]. Incubation with

blocking solution was performed for 2 hours at room temperature with gentle

agitation. Wells were then washed twice with PBST. In triplicate wells, 50µl

sample diluent [1xPBS with 1% BSA] and 50µl conditioned media sample was

added and in duplicate wells standards were added (0 to 0.5µg/ml rhCTGF

serially diluted across 12 standards). Plates were then incubated overnight at

4oC with gentle agitation. The next day, plates were washed four times with

PBST and 100µl of primary H-55 CTGF antibody was added to wells in diluent

solution to a concentration of 2µg/ml. Plates were then incubated at room

temperature for 2 hours with gentle agitation. After incubation, plates were

washed four times with PBST and then 100µl of secondary detection antibody

was added to wells (donkey anti-rabbit-HRP, 1:5000 in diluent solution). Plates

were then incubated at room temperature for 1 hour with gentle agitation. Plates

were then washed four times with PBST and 100µl of 3,3’,5,5’-

tetramethylbenzidine (TMB) reagent (Sigma Aldrich, St. Louis, MO, USA) was

added to each well. Plates were incubated at 37oC for 15 min then colour

development was stopped by addition of 100µl HCl (1M). Plate absorbency was

read at 450nm on a Synergy plate reader. Protein concentration in each

conditioned media extract was calculated using the standard curve.

Experiments were performed in triplicate.

2.4.5 Protein Array For detection of differential protein secretion from PER-371 High and PER-371

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Low cells, a label-based L-series human antibody array with membranes L-507

and L-493 was used (Ray Biotech, Norcross, GA, USA, #AAH-BLM-1000-4),

according to manufacturer’s instructions. HS5 cells were plated at 0.25x106

cells/ml in 7ml of normal media and left for 48 hours at 37oC and 5%CO2. After

incubation, either 1x106 cells/ml of PER-371 Low or PER-371 High cells, was

added to HS5 cells in 7ml of low-serum media (0.2%FCS). A control flask of

HS5 cells alone was incubated with low-serum media. HS5 and leukaemia cells

were co-incubated for 48 hours, then conditioned media was filtered through a

0.2µm nylon filter and 2x 3ml samples were added to dialysis vials. Dialysis

vials were placed in a foam holder inside a beaker containing 500ml of cold

PBS and left overnight at 4oC with gentle stirring. The next morning PBS was

replaced and dialysis vials were incubated a further 3 hours. Dialysed samples

were transferred to tubes and centrifuged at 1000x g for 15 min, and then

supernatants were combined from the two dialysed samples. The primary

amines of the proteins in the samples were then labelled with biotin. The

membrane arrays were incubated with 7.2µl/mg of 1x Labelling Reagent for 30

min at room temperature then filtered according to instructions. Biotinylated

samples were incubated with the membrane array to allow for interaction

between the sample proteins and the pre-printed capture antibodies for 1 hour

at room temperature with gentle agitation. Membranes were then incubated with

HRP-conjugated streptavidin and visualized by chemiluminescence, similar to

western blots (2.4.3).

Densitometry readings for duplicate protein dots per membrane were taken

using Bio-Rad Image Lab software (Bio-Rad Laboratories, Hercules, CA, USA).

Readings were discarded if signal intensity for dots was below background

levels. Normalistaion of intensity values above background were made in ratio

to positive controls within the array. Normalised signal intensities were then

compared across the three experimental conditions for each detectable protein,

PER-371 High+HS5, PER-371 Low+HS5 and HS5 alone.

2.5 Proliferation assays Proliferation of cells was determined in the presence of increasing

concentrations of IL7 (0-1ng/ml) in standard or low serum culture media (0.2%

FCS). The four lentiviral-infected B-precursor ALL cell lines (PER-278 High/Low

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and PER-371 High/Low) were plated at 1x105 cells per well for each IL7

experimental condition and 0.5x105 cells per well in low serum, in triplicate, in a

96-well round bottom plate (Nunc, ThermoFisher Scientific, Waltham, MA,

USA). Cells were incubated in the presence of low serum or IL7 for 48 hours,

0.5µCi of Thymidine, [methyl-3H] (PerkinElmer, Waltham, MA, USA, #NET027A)

was then added and cells were incubated at 37oC and 5%CO2 for 3 hours in low

serum or 24 hours with IL7. Cells were then lysed by freezing at -80oC. For

processing, cells were thawed and DNA was harvested onto a glass fibre

filtermat (PerkinElmer, Waltham, MA, USA, #1450-421) using a FilterMate

vacuum harvester (PerkinElmer, Waltham, MA, USA). The filtermat was dried at

60oC for 60 min, then sealed in a sample bag (PerkinElmer, Waltham, MA,

USA) with liquid scintillation cocktail fluid (PerkinElmer, Waltham, MA, USA,

#0013320). Radioactivity was assessed by counts per minute using a 1450

MicroBeta TriLux (PerkinElmer, Waltham, MA, USA). Experiments were

performed in triplicate.

Additional PER-371 proliferation assays were performed as above, but with the

exception of cells being suspended in conditioned media from HS5-leukaemia

cell co-cultures. Briefly, 2x106 HS5 cells in 2ml of normal media were plated on

a 6-well flat-bottomed plate (Nunc, Life Technologies, Carlsbad, CA, USA).

Cells were then left to adhere overnight. The next day, media was replaced with

either 2ml fresh normal media, fresh normal media with 100ng/ml rhCTGF,

2x106 PER-371 Low cells in normal media or 2x106 PER-371 High cells in

normal media. Plates were incubated for 72 hours and then conditioned media

was extracted, filter-sterilised and stored at -20oC until needed.

2.6 Drug sensitivity assays 2.6.1 Optimisation of antibiotics for stable cell line selection Optimisation of antibiotic concentration of G418 for the pcDNA3.1 vector and

puromycin for the pCDH vector were performed using MTT assays on a 96-well

flat bottom plate (Nunc, ThermoFisher Scientific, Waltham, MA, USA). Briefly,

the G418 titration curve contained 12 dilutions, each in triplicate, ranging from

0.5 to 1.6µg/ml in 50µl of normal media. The puromycin titration curve contained

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15 dilutions, each in triplicate, ranging from 0.05 to 1.5µg/ml in 50µl of normal

media. To each drug dilution, 1.5x105 PER-371 or PER-278 cells were added in

50µl of normal media. In addition, each plate contained 3 wells of 100µl normal

media as a negative control and leukaemia cells with no antibiotic as a positive

control. Plates were incubated for 3 days at 37oC and 5%CO2. On the third

day, 10µl of filtered 5mg/ml (3-(4 5-dimethylthiazol-2-yl)-2 5-diphenyltetrazolium

bromide (MTT, Sigma Aldrich, St. Louis, MO, USA) in 1xPBS was transferred to

each well. MTT was incubated for 6 hours at 37oC and 5%CO2, after which

100µl of 4% isopropanol was added to each well and resuspended to ensure all

formazon crystals were solubilised. The plate was then read at 495nm

absorbance on a Synergy plate reader (BioTek, Winooski, VT, USA). Drug

concentrations for selection of stable cell lines were determined as the

concentration required to kill 95% of cells in 3 days.

2.6.2 Sensitivity to chemotherapy drugs in CTGF-High and CTGF-Low cell lines Sensitivity to the cytotoxic drugs vincristine (VCR, Pfizer, New York City, NY,

USA) and cytarabine (1-β-d-arabinofuranosylcytosine,  ARAC, Pfizer, New York

City, NY, USA) was determined in vitro using the Alamar Blue assay (Life

Technologies, Carlsbad, CA, USA), according to manufacturer’s instructions.

Production of HS5-leukaemia cell conditioned media was performed as before,

see 2.5. Alamar Blue assays were set up using 96-well flat-bottomed plates

(Nunc, ThermoFisher Scientific, Waltham, MA, USA). First, serial dilutions of

ARAC (2µg/ml to 0.5ng/ml) or VCR (0.2µg/ml to 0.05ng/ml) were plated in

normal media, in triplicate wells. Cells were added at 1.5x105 cells in 50µl of

normal media or conditioned media from HS5-leukaemia cell co-cultures. Plates

were then incubated for 72 hours before addition of 10µl Alamar Blue. After a 3-

hour incubation, absorbance was read at 570nm and 600nm on a Synergy plate

reader (BioTek, Winooski, VT, USA). The EC50 (drug concentration that inhibits

cell growth by 50%) was determined by calculating the percentage difference

between treated and untreated cells for each drug concentration.

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2.6.3 Nucleoside transporter activity in PER-278 High or Low cells ARAC acts as a nucleoside analogue and inhibits DNA polymerase, primarily

killing cells undergoing DNA synthesis (S phase). Nucleosides must be taken

up by cells through one of two distinct families of human nucleoside

transporters: cumulative nucleoside transporters (CNTs) which are sodium-

dependent or equilibrative nucleoside transporters (ENTs) which are sodium-

independent. Uridine, a nucleoside, is taken up by cells through both

transporters. ARAC uses predominantly ENT1 in human leukaemic blast cells

(Hubeek, et al.). By measuring uptake of tritiated uridine (5,6-3H-uridine) into

cells, we obtained an approximate measure of nucleoside transporter activity.

The uridine uptake assay was based on methods previously published by

Macanas-Pirard et al. , with the exception of using nitrobenzylmercaptopurine

ribonucleoside (NMBPR, ENT1 inhibitor) PER-278 Low cells were plated at

4x105 cells per well in 50µl of normal media, in a 96-well conical-bottom plate

(Nunc, ThermoFisher Scientific, Waltham, MA, USA). 8µCi of 5,6-3H-uridine

(PerkinElmer, Waltham, MA, USA, #NET367001MC) was added to wells with

50µl of normal media, normal media with rhCTGF (100ng/ml in normal media)

or conditioned media from co-culture of HS5 cells with lentiviral-infected PER-

278 cell lines. After 15 min, cells were washed with 100µL of wash buffer

containing 1xPBS with 1mM uridine (Sigma Aldrich, St. Louis, MO, USA,

#U3003-5G). The plate was centrifuged at 1200RPM for 5 min at room

temperature to pellet cells, and washed 4 times with wash buffer. Cells were

resuspended in 50µl of wash buffer and then frozen at -80°C. 3H-uridine

incorporation was measured using a TRI-CARB 1500 liquid scintillation counter

(Packard Instrument Company, Canberra Industries, Meriden, CT, USA),

whereby cells were added to a scintillation vial with 2ml of Ultima Gold liquid

scintillation counter cocktail (PerkinElmer, Waltham, MA, USA, #0013320). 3H-

uridine incorporation was measured in counts per minute.

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2.7 NOD/SCID mouse xenografts

2.7.1 Mice Non-obese diabetic/ severe-combined immunodeficient (NOD/SCID) mice were

obtained from the Animal Resources Centre (Perth, WA, Australia) and

randomly assigned to experimental groups. The age of the mice at injection of

leukaemia cells ranged from 6 to 8 weeks of age. Animals were housed in

individually ventilated cages (IVC), on a 12-hour light/dark cycle and with

unlimited access to water and food including regular mushy chow. All animal

experimentation was approved by the Animal Ethics Committee of the Telethon

Institute for Child Health Research and conformed to NHMRC guidelines, n=

approx. 7 animals per group were analysed, as detailed in each figure legend.

2.7.2 Generation of NOD/SCID xenografts The ALL xenograft model has previously been established for use as a

preclinical model for therapy evaluation. NOD/SCID mice proved to have a

higher efficiency of engraftment and provide an accurate mirroring of human

paediatric ALL with the immunophenotype corresponding to the primary patient

sample (Liem, et al., 2004; Lock, et al., 2002). RNA and protein samples were

taken from PER-278 and PER-371 cell lines on the day of injection for

quantification of CTGF expression in RNA, protein and conditioned media by

qRT-PCR or western blot.

Xenograft studies were carried out using female NOD/SCID mice, however due

to availability in some instances male mice were used. Only groups of the same

sex were compared to each other. Female mice were sub-lethally irradiated

(250cGy) on the same day as injection, while male mice were injected without

irradiation. Mice were kept on 375mg Enrofloxacin (Bayer, Leverkusen,

Germany) and 165mg Amoxicillin (Sandoz, Princeton, NJ, USA) per 500ml

drinking water, for 4 weeks post-irradiation.

For PER-278 xenografts, female mice were used for homing, early stage, end

stage and chemotherapy experiments. For the snapshot of disease 24 hours

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post-ARAC injection male mice were used. All mice were tail-vein injected with

2x105 PER-278 Low or PER-278 High cells. End-stage data were analysed

from three experimental groups of mice (n=7). Homing, early stage,

chemotherapy response and post-ARAC time point data were analysed from

one experimental group of mice (n=7).

For PER-371 xenografts, female mice were used for end stage and

chemotherapy experiments. Male mice were used for homing, early and late

stage disease time points. Mice were injected with 1x106 PER-371 Low or PER-

371 High cells. End-stage data were analysed from two experimental groups of

mice (n=7). Homing, early stage and late stage time point data were analysed

from one experimental group of mice (n=7).

2.7.3 Chemotherapy regimen An induction phase drug regimen was administered to determine if CTGF

affects drug efficacy. Blood samples were used to determine levels of

leukaemic cells in the blood. When a mouse in the group had 1% leukaemic

engraftment in the blood, treatment was initiated for the whole group.

Chemotherapy was delivered as a single-agent using either vincristine (VCR,

Pfizer, New York, NY, USA) or cytarabine (ARAC, Pfizer, New York, NY, USA).

Drug concentration and regimen for maximally tolerated doses were determined

by Prof. Richard Lock (via correspondence, Childrens Cancer Institute Australia,

Sydney, NSW, Australia). Administration of VCR consisted of intraperitoneal

injections (0.5mg/kg) weekly for 4 weeks. Administration of ARAC consisted of

intraperitoneal injections (either 0.5mg/kg or 100mg/kg) daily for 5 days, 2

weeks off, then repeat of cycle. The higher dose for cytarabine represented the

clinically-relevant maximum tolerated dose. The lower dose facilitated detection

of drug resistance in the cells. Control mice were intraperitoneally injected using

the same regimen but with sodium chloride solution (0.9% sterile, Pfizer, New

York, NY, USA). For the PER-278 mouse cohort culled 24 hours post-ARAC

injection, this was done 24 hours after the first ARAC injection in the second

round of treatment.

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2.7.4 Mouse dissection and tissue preparation Mice were culled at specified time points or when they presented with two or

more identifiable leukaemic symptoms, including hind leg paralysis, weight loss,

ruffled fur, decline in activity, rapid breathing and hunched posture. At these

times, mice were anaesthetized with methoxyflurane (dosage to effect, Medical

Developments International, Springvale, VIC, Australia) and underwent a

cardiac puncture before being euthanised by cervical dislocation. Harvested

organs were halved and allocated to 4% Paraformaldehyde for immunostaining

or to 5%FCS in PBS (FACS buffer) for analysis by flow cytometry. Organs

extracted were hind-leg femurs and tibias, spleen, liver and lymph nodes. Blood

was collected in microtainer tubes with K2EDTA (BD Biosciences, San Jose,

California, USA).

2.7.5 Tissue analysis by flow cytometry A summary of primary and secondary antibodies used in flow cytometry are

listed in Table 2.1.

Bone marrows were flushed with a 19-gauge needle and ends of bones were

crushed. Flushed-bone marrow, spleens, livers and lymph nodes were filtered

through 100µm nylon cell strainers (Falcon, Corning Inc, Corning, NY, USA)

with ample FACS buffer to obtain single cell suspensions. Single cell

suspensions were then centrifuged at 800x g for 5 min at 4oC. Supernatant was

aspirated and pellets were resuspended in 5ml of RBC lysis buffer

(eBioscience, Affymetrix, San Diego, CA, USA). Mouse blood was also lysed,

by adding 80µl of blood to 1ml of red blood cell (RBC) lysis buffer (eBioscience,

San Diego, CA, USA). Cell suspensions were incubated at room temperature

for 5 min with occasional shaking. The reaction was stopped with 20ml (tissue)

or 10ml (blood) of 1x ice-cold PBS. Cells were then centrifuged at 800x g and

4°C. Cell pellets were resuspended in FACS buffer and analysed by flow

cytometry or quantitated using the Vicell for use in proliferation or apoptosis

assays.

Engraftment of GFP+ leukaemic cells was then determined using a LSRII flow

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cytometer (Becton Dickinson, Franklin Lakes, NJ, USA) running FACSDiva

software (Becton Dickinson, Franklin Lakes, NJ, USA) and using the blue laser

(488nm excitation, 530/30 band pass filter). Analysis was performed using

FlowJo (Tree Star Inc, Ashland, OR, USA). Cells were gated in hierarchy, first

gating live cells with a forward and side scatter plot (FSC vs SSC), then gating

out doublets using a side scatter area and width plot (SSC-A vs SSC-W), then

lastly gating GFP+ cells (GFP vs APC), as shown in Figure 2.1. As a control

representative bone marrow cells were stained for anti-human CD19 (BD

Biosciences, San Jose, CA, USA) by incubating 1x106 cells (after RBC lysis) in

5µL anti-CD19 and 100µL FACS buffer for 30 minutes in the dark on ice. Cells

were then washed in 1ml of 1x PBS and centrifuged at 800x g for 5min at 4°C.

Pellets were resuspended in 500µl FACS buffer for analysis by flow cytometry

using the red laser (633nm excitation, 660/20 band pass filter). GFP+ cells were

shown to overlap with CD19+ stained cells, verifying that the GFP fluorescence

was exclusive to injected leukaemia cells (data not shown).

Proliferation and apoptosis levels at time points of late stage disease were

determined using the BrdU:APC Flow Kit (BD Biosciences, San Jose, CA, USA,

#557892) or the Annexin V: PE apoptosis detection kit I (BD Biosciences, San

Jose, CA, USA, #559763), both used according to manufacturer’s instructions

and detected with the red laser (633nm excitation, 660/20 band pass filter).

For BrdU staining, mice were injected with 100µl of 10mg/ml BrdU (1mg)

intraperitoneally, 24 hours prior to sacrifice. For intra-cellular staining, 2x106

bone marrow cells were resuspended in 100µl BD Cytofix/Cytoperm buffer and

incubated at room temperature for 15 min. Cells were then washed with 1ml

Perm/Wash buffer and centrifuged 300x g for 5 min. Pellets were resuspended

in 100µl BD Cytoperm Plus buffer and incubated on ice for 10 min. Cells were

then washed in Perm/Wash buffer and resuspended in 100µl of BD

Cytofix/Cytoperm buffer for 5 min at room temperature. Cells were again

washed in Perm/Wash buffer, then resuspended in 50µl DNase (300µg/ml) and

incubated for 1 hour at 37oC. Cells were washed in Perm/Wash buffer and then

split into two aliquots, one resuspended in 50µl of anti-BrdU-APC (1:50 in

Perm/Wash buffer) or 50µl of Perm/Wash buffer only. Cells were then incubated

for 20 min in the dark at room temperature. After antibody incubation cells were

washed in Perm/Wash buffer and resuspended in 300µl FACS buffer to be

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analysed by flow cytometry. For Annexin V staining, bone marrow cells were washed twice with cold PBS

and then resuspended in 1ml of 1xBinding buffer at a concentration of 1x106

cells/ml. An aliquot of 100µl of the solution was added to 5µl of PE Annexin V,

cells were gently vortexed and incubated at room temperature for 15 min in the

dark. Cells were washed with 400µl of 1x Binding buffer, resuspended in 300µl

FACS buffer and analyzed by flow cytometry within the hour.

2.7.6 Histochemical and immunohistochemical (IHC) staining A summary of primary and secondary antibodies used in immunostaining are

listed in Table 2.1.

2.7.6.1 Tissue Processing Hind leg femurs and tibias were fixed in freshly thawed aliquots of 4%

paraformaldehyde (Sigma Aldrich, St. Louis, MO, USA, #P6148) in 1x PBS.

Tibias and femurs were immersed immediately in 5ml of 4% Paraformaldehyde

and then stored at 4oC for 24 to 48 hours, before being washed twice in 1x PBS

and stored at 4oC until decalcification. Bones were decalcified in 10%

ethylenediaminetetraacetic acid (EDTA, Sigma Aldrich, St. Louis, MO, USA,

#E9884) at 4oC for 8 days with gentle agitation. After decalcification bones were

dehydrated through a series of graded alcohols to xylene and infiltrated with

paraffin using a Leica ASP200 S tissue processor (Leica microsystems,

Wetzlar, Germany).

Paraffin-infiltrated bones were embedded into wax blocks. Tissue blocks were

stored at room temperature until sectioned with a Leica RM2135 microtome

(Leica microsystems, Wetzlar, Germany). Tissue was cut into 4µm sections and

adhered to SuperFrost Plus slides (ThermoFisher Scientific, Waltham, MA,

USA). Individual slides contained two sections from one mouse block, that

encompassed a longitudinal section through mid-bone to obtain the highest

amount of bone marrow. Slides were left to dry overnight at room temperature

and stored at room temperature until ready to use. For use in

immunohistochemistry and histology stains, slides were first melted at 60oC for

15-30 min.

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+Figure 2.1. Leukaemia engraftment was determined by GFP cell detection using flow cytometry. Gating (depicted by red line) was performed in hierarchy for the following populations: a. Live cells on a forward scatter and side scatter plot. b. Single cells on a side scatter-area and side scatter-width

+plot. c. GFP cell on a FITC by APC plot.

b.

a.

c.

F

ITC

-A

APC-A

SSC-A

FSC-A

SS

C-A

SS

C-W

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2.7.6.2 Immunohistochemistry

Immunohistochemistry was used to detect leukaemia cells (anti-Pax5)

proliferating cells (anti-Ki67) or megakaryocytes (anti-VwF) with antibodies and

concentrations given in Table 2.1.

Melted slides were deparaffinised using a Leica Autostainer XL (Leica

microsystems, Wetzlar, Germany). The protocol involved incubating 3x 3 min in

xylene (Hurst Scientific, Perth, WA, Australia), 2x 2 min in 100% EtOH, 1 min

95% EtOH, 1 min 70% EtOH, 1 min 40% EtOH and 5 min running tap water.

After rehydration slides were kept from drying out. Rehydrated slides were

rinsed 3x 5 min at room temperature in PBS with gentle agitation in between

each of the steps. All other incubations were performed in a humidified chamber

moistened with TBS.

Bone sections required low temperature antigen retrieval. Therefore, slides

were immersed in citrate buffer [10mM citric acid, 0.05% Tween 20; pH6.0] and

incubated overnight (approx. 16 hours) at 70oC. Slides were then cooled and

washed in TBS for 10 min. Slides were quenched for endogenous peroxidase

activity by incubating in 3%H2O2 in TBST for 10 min at room temperature with

gentle agitation. Slides were then washed 3x 5 min in TBST 0.01% [1x TBS with

0.01% Tween 20]. A border was drawn around tissue on the slides using a wax

pen (Dako, Glostrup, Denmark) then slides were blocked with 10% normal goat

serum (Vector Labs, Burlingame, CA, USA, #PK6101) in TBST 0.01% (diluent

solution) for 1 hour at room temperature in a humidified chamber. Blocking

solution was then tipped off slides to be replaced with 300-500µl of primary

antibody in diluent solution (anti-Pax5, anti-Ki67 or anti-VwF, dilutions in Table

2.1). Slides were incubated overnight at 4oC. The next day, slides were washed

3x 5 min in TBST 0.01%, before 300-500µl of secondary antibodies in diluent

solution were applied (anti-rabbit-biotin, anti-mouse-biotin and anti-rabbit-biotin,

respectively). Slides were incubated for 1 hour at room temperature. Slides

were then washed 3x 5 min and Elite ABC solution in TBST 0.01% was added.

Slides were then incubated at room temperature for 30 min. Slides were then

washed 3x 5 min.

Staining was visualized with NovaRed (Vector Labs, Burlingame, CA, USA,

#SK-4800) applied for 2-3 minutes depending on antibody. Slides were then

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Figure 2.2. Immunohistochemical staining was scored by the Nuance FX multispectral imaging system and inForm software (Perkin Elmer). multispectral cube was processed with a spectral library unmixing Nova Red and Haemtaoxylin. b. Sections were first segmented into bone marrow (red) or bone (green) tissue sections. c. Individual nuclei were then detected (green). d. Lastly unmixed Nova Red staining (desaturated of haematoxylin) was scored 0-3+, with 0-1 (blue), 1-2 (yellow), 2-3 (orange) and 3+ (maroon). Positive staining was the sum of 1-3+.

a. The

b.a.

c. d.

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rinsed in dH20 and washed twice in dH20. Slides were then counterstained with

Gill’s Formula Haematoxylin (Vector Labs, Burlingame, CA, USA, #H-3401) for

30 sec followed by 10 dips in 2% acetic acid in dH20 and 60 sec in Bluing

Reagent (Richard Allen Scientific, ThermoFisher Scientific, St. Louis, MO, USA,

#7301). Slides were dehydrated using a Leica Autostainer XL (Leica

microsystems, Wetzlar, Germany). The protocol involved incubating for 1 min in

40% EtOH, 1 min 70% EtOH, 1 min 95% EtOH, 2x 2 min in 100% EtOH and 3x

3 min in xylene. Slides were then coverslipped (Corning, New York, NY, USA)

using Permount mounting medium (ThermoFisher Scientific, St. Louis, MO,

USA).

2.7.6.3 Quantitative morphometry Quantitative morphometry was carried out using the Nuance FX multispectral

imaging system and inForm software (PerkinElmer, Waltham, MA, USA),

according to manufacturer’s instructions for acquisition of brightfield cubes and

4-bin scoring.

Multispectral cubes were obtained for 3 sections of both diaphysis and

epiphysis/metaphysis for each slide. A spectral library was created to unmix

Nova Red and Haematoxylin staining. For Pax5 and Ki67 stained slides, inForm

was trained to segment bone marrow tissue from bone. Using only bone

marrow segments, nuclei were detected for Haematoxylin or Nova Red stained

cells above 0.2% threshold and with 0.25µm roundness. Scoring was then done

for Nova Red stained nuclei using the 4-bin method, whereby, each nucleus

was given a score of 0-1 (no staining), 1-2 (slight staining), 2-3 (moderate

staining) or 3-4 (heavy staining), see Figure 2.2. Statistical analysis was

performed using the percentage of stained cells (% of nuclei with a score of 1-

4). For VwF stained slides, bone marrow segments were detected for

megakaryocytes stained with Nova Red above a threshold of 0.2% and 600

pixels, object count was determined for each image.

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Figure 2.3. Reticulin stain scoring. Scoring was performed on diaphysis and epiphysis/ metaphysis by two blinded observers based on pre-established levels of reticulin intensity: a. Score 0 with focal, fine reticulin (normal). b. Score 1 with diffuse fine reticulin (abnormal). c. Score 2 with diffuse fine reticulin and focal coarse reticulin (abnormal). d. Score 3 with diffuse coarse reticulin (fibrosis). Bone stains brown, nuclei stain red and reticulin fibres stain black. Scale bar represents 200mm.

b.a.

c. d.

0

2

4

6

8

10

5 10 15 20 25 30Difference in Population Means

Figure 2.4. Sample size required per treatment group (x axis) to detect a difference in population means (y axis). Calculated using a standard deviation of 6 based on a pilot study where the response within each mouse group was approximately normally distributed. If the true difference in the CTGF High and CTGF Low engraftment is 10% (as detected in the pilot study), we will need to study 7 mice per group to be able to reject the null hypothesis that the population means of CTGF High and CTGF Low are equal.

Expe

rimen

tal S

ampl

e Si

ze

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2.7.5.3 Silver stain Gordon and Sweets’ modified reticulin silver stain was performed on bone

sections (Gordon & Sweets Jr, 1936). Slides were deparaffinised in xylene and

rehydrated through graded alcohol to dH20. Slides were then exposed to

acidified permanganate solution for 8 min (1% potassium permanganate and

3% sulfuric acid) then rinsed in tap water followed by dH20. Slides were then

bleached in 5% oxalic acid for 2 min then rinsed twice in dH20. Slides were then

set with a 2% iron alum mordant for 8 min to produce sensitized sites for silver

deposition, then rinsed well in dH20. Slides were then treated with silver solution

for 3.5 min (5% silver nitrate, 3% sodium hydroxide and 3 drops concentrated

ammonia in 70% EtOH in 40 ml). Slides were then immediately placed in

formalin developer and agitated for 2 min (5% concentrated formalin in 70%

EtOH). Slides were then washed in dH20 and treated with 5% sodium

thiosulphate to remove unprecipitated silver and washed in dH20. Slides were

then counterstained with Kernechtrot for 5 min and rinsed in dH20. Slides were

then dehydrated through graded alcohol, cleared with xylene and coverslipped

with Ultramount mounting medium (Dako, Glostrup, Denmark). Reticulin

staining was scored manually on a scale of 0-3 from the average score given by

two blinded-observers (Figure 2.3).

2.8. Statistical analyses

Graphing of all data was performed using Prism 6.0 (GraphPad Software, De La

Playa, CA, USA). Survival curves were created by Kaplan Meier method.

Statistical comparison of means was performed by student t-test or log-rank

test. Results were considered statistically significant at p<0.05. Unless

otherwise indicated, average values were expressed as mean±SEM. For mouse

studies, group sizes of 7 were chosen to detect a 10% difference in population

means with a standard deviation of 6 (data from unpublished pilot experiment)

(Figure 2.4).

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333333333

Stable overexpression of CTGF in B-precursor ALL cell lines does not

alter cell function

If you want a wise answer,ask a reasonable question.

Johann Wolfgang Von Goethe

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Chapter 3 Stable overexpression of CTGF in

B-cell precursor ALL cell lines does not alter cell function  

3.1 Abstract The CTGF gene encodes for a matricellular protein found throughout the body

and associated with diverse biological functions. Deregulated CTGF has been

associated with 27 human cancers acting on various functional mechanisms

within the cancer cell and in association with surrounding stromal cells. In

childhood B-cell precursor (BCP) ALL, CTGF has been found upregulated in

75% of patient specimens compared to normal CD34+ haematopoietic

progenitor cells and to be associated with worse clinical outcomes. A functional

role for CTGF in BCP ALL has yet to be discerned.

In this study BCP ALL cell lines (PER-278 and PER-371) were successfully

transduced using lentiviral technology for stable overexpression of CTGF. RNA

overexpression was 3-fold higher on average in CTGF High transduced cells

compared to CTGF Low using qRT-PCR. CTGF overexpression was similar for

cellular and secreted protein levels. Quantification of CTGF in conditioned

culture media had a high correlation with CTGF mRNA expression levels

(Pearson correlation coefficient= 0.97).

PER-278 and PER-371 CTGF High cells were found to have no observable

differences in vitro in proliferation or sensitivity to two chemotherapy drugs

(vincristine and cytarabine) compared to CTGF Low cells. Following microarray

analysis, significant differences in global gene expression were seen between

PER-278 and PER-371 cell lines and between lentiviral-infected and uninfected

cell lines. These large differences in expression most likely overwhelm smaller

differences in expression due to higher CTGF expression that are common to

both cell lines. The lack of any perceptible response due to increased CTGF

expression in BCP ALL cells in vitro indicates any functional role for the protein

in this disease is likely to be mediated through microenvironment

intermediaries.

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3.2 Introduction Most cancers reach a stage of autonomous control independent of normal cell

signalling. At this stage intracellular production of essential proteins by the

tumour cell replaces extracellular mitogenic cues for proliferation and survival

(Martin, 2003; Ravandi, et al., 2003). This is in contrast to normal cells that are

able to identify upregulated mitogen stimulation and initiate cell-cycle arrest or

apoptosis. CTGF is a gene that is overexpressed in 75% of paediatric BCP ALL

patient specimens, occurring across the majority of chromosomal

rearrangements (Boag, et al., 2007). It has also been associated with worse

outcome in childhood BCP ALL patients with high-risk stratification (Kang, et al.,

2010). Importantly, in other human cancers it acts to alter proliferation through

various cell specific signalling pathways.

It is unknown if CTGF has an impact on intracrine or autocrine mechanisms in

BCP ALL. Therefore in this study two BCP ALL cell lines, derived from primary

patient specimens, were engineered to create stable populations with

upregulated CTGF expression. BCP ALL cell lines with high CTGF expression

were then assessed for changes in cell function. The potential for CTGF to

stimulate cell proliferation by itself or as a co-factor with the known B-cell

mitogen interleukin 7 (IL7) was measured by tritiated [3H]thymidine

incorporation. Altered sensitivity to essential chemotherapy drugs, vincristine

and cytarabine, was assessed by Alamar Blue viability assays. Lastly, potential

intracellular effects were determined by characterising global gene expression

of the BCP ALL cell lines using Affymetrix Human Gene 1.0 ST Arrays.

3.3 Results PER-278 and PER-371 cell lines were chosen for their low but detectable levels

of CTGF mRNA expression compared to a panel of ALL cell lines and primary

BCP ALL specimens, as measured by qRT-PCR (Welch, et al., 2013). Both cell

lines are derived from primary specimens obtained from patients whose details

are outlined in Table 3.1. Cell lines were authenticated by STR

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Table 3.2. Patient-derived B-precursor ALL cell lines maintain patient DNA profile. Single Tandem Repeat (STR) analysis of PER-278 and PER-371 cell lines were found to have 100% allelic concordance with their original patient specimens.

AMOLOGENIN

Locus Cell line PER-278 Cell line PER-371

CSF1PO

D13S317

D16S539

D5S818

D7S820

Th01

TPOX

vWA

X,Y X,Y

11,12 12,13

8,9 10,12

13,13 11,13

12,13 11,12

11,12 8,10

6,8 6,6

14,19 15,16

8,11 10,11

Feature Cell line PER-278 Cell line PER-371

1987Isolated 1988

malemaleGender

Specimen diagnosisdiagnosis

Phenotype B-precursor ALLB-precursor ALL

Genetic Feature E2A-PBX expression E2A-PBX expression

46,XY,der(16)t(1;16)(q2?1;p13),der(19)t(1;19)(q?13;p13)/46,X,_

Y,_?der(1)t(Y;1)(q12;?q21), add(11)(q21),der(19)t(1;19)

46,XY,der(9)t(1;9)(q23;p13),

der(19)t(1;19)(q23;p13)Karyotype

Table 3.1. Patient details for derived cell lines PER-278 and PER-371. Characteristics of two cell lines derived from primary patient specimens at Princess Margaret Hospital, Perth, Western Australia (Kees et al., 1990, Kees et al., 2003).

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analysis and found to have 100% accordance with the DNA profile of their

associated primary patient DNA profile (Table 3.2). (Kees, et al., 1990; Kees, et

al., 2003)

3.3.1 Optimisation of transfection in BCP ALL cell lines As haematopoietic cells are particularly hard to transfect, optimisation was

required for the transfection of the BCP ALL cell lines. Two electroporation

techniques were used and one lentiviral infection method.

3.3.1.1 Transfection by electroporation The pcDNA3.1 plasmid containing the full human CTGF coding region or the

pcDNA3.1-eGFP control vector was used for all electroporation attempts

(Figure 3.1a). Plasmid DNA was used in a supercoiled state or was digested

with a BglII enzyme cutting distal to the important coding sequences to ensure

successful chromosomal insertion.

Standard electroporation was performed at 300 V or using the Neon

transfection system at 1400 V (optimised from a 900 to 1700 V voltage range).

The PER-278 cell line together with pcDNA3.1-eGFP plasmid DNA was used

for optimisation and transfection efficiency was measured from 24 hours post-

electroporation by intracellular GFP expression. Cells were selected for viable

stable tranfectants from 48 hours with G418 antibiotic. Electroporation was

slightly more efficient at transfecting BCP ALL cells when supercoiled plasmid

DNA was used compared to linearised DNA (Figure 3.1b). However, within two

weeks no surviving transfected cells were detected. Low transfection efficiency

from 24 hours post-electroporation suggested the PER-278 BCP ALL cell line

did not successfully integrate plasmid DNA using the electroporation technique.

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Figure 3.1.Transfection of B-precursor ALL cell lines by electroporation was not successful in producing stable clones. a. The pcDNA3.1 plasmid with a human CTGF sequence inserted after the CMV promoter sequence. The empty vector plasmid containing reporter enhanced (e)GFP was used for optimisation. b. Transfection efficiency of plasmid DNA incroporation into PER-278 after electroporation with respect to time (days). The plasmid was transfected in supercoiled (blue line) or linear form (orange line). Transfection was performed by standard electroporation (solid line) or the Neon

+transfection system (dashed line). Data are expressed as the % GFP cells per total population of live and dead cells (n=1). Grey vertical bars represent addition of G418 to tissue culture media for selection of stable clones.

b.

a.

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 80  

3.3.1.2 Transduction by lentiviral infection To overcome low transfection efficiency, the use of lentiviruses was adopted.

Lentiviral ability to transduce dividing and non-dividing cells efficiently made

them an appealing candidate to establish stable transgene expression in our

BCP ALL cell lines. Manufacture of a lentiviral plasmid was performed using the

full human CTGF coding sequence excised from the pcDNA3.1-CTGF plasmid.

The CTGF sequence was then inserted into the empty vector pCDH-MSCV-

MCS-EF1-GFP-T2A-PURO (pCDH-EV) backbone (Figure 3.2a). Optimisation of

lentiviral transduction utilised two methods of lentiviral particle production,

namely by transiently transfecting 293T cells using CaCl2 or Fugene.

Optimisation of the ratio of pCDH vector and three packaging plasmids was

performed and preparations with the highest three viral titres were used to

transduce both PER-278 and PER-371. All lentiviral particles were used

undiluted and included CaCl2 (Ratio 1) with a titre of 1.0x106 IFU/mL, CaCl2

(Ratio 2) with a titre of 5.0x106 IFU/mL and Fugene (Ratio 1) with a titre of

4.3x106 IFU/mL. Transduction efficiency was measured after 48 hours by GFP

expression; subsequently lentiviral transduction using particles produced with

Fugene (Ratio 1) and CaCl2 (Ratio 2) methods proved most efficient in our BCP

ALL cell lines (Figure 3.2b).

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Figure 3.2. Transduction efficency of B-precursor ALL cell lines by lentiviral infection. a. The pCDH1-MSCV-CTGF-EF1-GFP (pCDH-CTGF) plasmid used in the described lentiviral infections, the empty vector plasmid omitted CTGF (pCDH-EV). b. Lentiviral transduction efficiency was expressed

+as the % GFP cells 48 hours after infection and measured by flow cytometry. Infections were performed on PER-371 (orange) and PER-278 (blue) cell lines. Lentiviral particles were generated using 293Ts with CaCl or Fugene 2transfection methods and two virus concentrations (Ratio1 or Ratio2).

b.

a.

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3.3.2.1 Verification of CTGF overexpression in stably transduced cell lines After selection of stably transduced cells with puromycin, chromosomal insertion

of the pCDH vector was verified by detection of GFP expression. Flow

cytometry analysis of transduced PER-278 and PER-371 cell lines showed GFP

expression in over 95% of cells. Mean fluorescence intensity differed between

pCDH-EV and pCDH-CTGF expression with simultaneous expression of the

transgene and GFP reducing intensity levels by a factor of one logarithm

(Figure 3.3a).

After verifying successful chromosomal insertion of plasmid DNA by GFP

expression, CTGF mRNA levels were then measured by qRT-PCR.

Approximately 3-fold overexpression of CTGF was detected using both CaCl2

and Fugene-produced lentiviral particles in pCDH-CTGF compared to pCDH-EV

PER-278 and PER-371 transduced cell lines (Figure 3.3b).

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Figure 3.3. Verification of stable CTGF mRNA in + precursor ALL cell lines PER-278 and PER-371. a. GFP expression

intensity was measured by flow cytometry for pCDH-empty vector (pCDH-EV), blue line, pCDH-CTGF, red line and uninfected stable cell lines, black. b. CTGF mRNA expression levels detected by qRT-PCR. Fold changes for pCDH-CTGF compared to pCDH-EV are displayed for both CaCl and Fugene 2production methods. Data are expressed as ratio of CTGF expression to housekeeping gene GAPDH. FC=fold change.

overexpression of B-

pCDH-CTGF

UninfectedpCDH-EV

b.

a.

FC=3.08 FC=2.59 FC=2.46 FC=3.37

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In addition to mRNA levels, CTGF protein levels in cell extracts and secreted

into culture supernatants was determined by western blot. Cellular protein

levels of CTGF in pCDH-EV transduced cell lines were just detectable and

overexpression of CTGF in pCDH-CTGF transduced cell lines indicated greater

expression in cells from Fugene compared to CaCl2-produced lentiviral particles

(Figure 3.4.a). As the CTGF protein is known to be matricellular, secreted levels

of the protein were detected from purified conditioned media samples separated

with heparin-agarose beads. Again CTGF expression was barely detectable in

pCDH-EV cell lines and protein upregulation in pCDH-CTGF transduced cell

lines was observed by western blot (Figure 3.4b).

Stratification of the transduced cell lines according to CTGF expression level

was done using cellular protein expression, as mRNA expression levels were

indistinguishable between CaCl2 and Fugene-produced lentiviral particles and

secreted protein levels have no loading control due to their purification

methods. In this manner, Fugene-produced pCDH-EV transduced cells were

termed CTGF Low (or Low), CaCl2-produced pCDH-CTGF transduced cells

were termed CTGF Intermediate (or Intermediate) and Fugene-produced

pCDH-CTGF transduced cells were termed CTGF High (or High).

Quantification of secreted CTGF in PER-278 Low and High and PER-371 Low

and High cell lines was determined by ELISA (Figure 3.4c). PER-278 High

conditioned media contained an average level of CTGF protein 3 times greater

than PER-278 Low (49.3 ng/ml compared to 16.5 ng/ml). Similarly, PER-371

High conditioned media contained significantly higher levels of CTGF protein

3.4 fold greater than PER-371 Low (39.5 ng/ml compared to 11.5 ng/ml,

p=0.04). These levels correlate well with the previously mentioned CTGF

mRNA expression levels of these cell lines (Pearson correlation coefficient=

0.97).

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Figure 3.4. Oprecursor ALL cell lines PER-278 and PER-371. a. CTGF cellular protein expression at 38 kDa measured by western blot. pCDH-CTGF and pCDH-EV stable cell lines were detected for both CaCl and Fugene production 2methods. Positive control was high-CTGF expressing cell line PER-377 and loading control was a pan-Actin antibody. b. Secreted CTGF protein expression from Heparin-purified conditioned media standardised by collection after 24 hours in culture. Positive control was PER-377. c. Fugene EV is designated CTGF Low and Fugene CTGF is designated CTGF High for PER-278 and PER-371. Concentration of secreted CTGF was measured by ELISA. Data are expressed as the mean protein concentration in ng/ml (n=3). Vertical bars show standard error of the mean.

verexpression of CTGF cellular and secreted protein in B-

pan-Actin

CTGF

PER-

371

EVPE

R-37

1 CT

GF

Posit

ive co

ntro

l

37KDa

37KDa

PER-

371

EVPE

R-37

1 CT

GF

PER-

278

EVPE

R-27

8 CT

GFPE

R-27

8 EV

PER-

278

CTGF

PER-

371

uninf

ecte

dPE

R-37

1 EV

PER-

371

EV

PER-

371

CTGF

PER-

371

CTGF

Posit

ive co

ntro

l

Fugene CaCl 2

PER-

278

uninf

ecte

d

37KDa CTGF

PER-

278

EVPE

R-27

8 CT

GF

Fugene CaCl 2

PER-

278

EVPE

R-27

8 CT

GF

b.

a.Fugene CaCl 2 Fugene CaCl 2

c.

PER-278 Low PER-371 Low PER-278 High PER-371 High

Cell line

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3.3.3 Characterisation of stable CTGF overexpressing cell lines After validation of 3-fold overexpression of CTGF in PER-278 and PER-371 cell

lines at the mRNA and protein level, the effect of increased levels of CTGF on

cell function was determined.

3.3.3.1 Proliferation Potential differences in the proliferation rate of both PER-278 and PER-371 cell

lines due to CTGF overexpression were investigated by tritiated [3H]thymidine

incorporation into the cells. Cells plated in low serum (0.2% FCS) revealed no

significant difference in proliferation between CTGF Low and High (Figure 3.5a).

To determine if CTGF could act as a co-factor for stimulation in these cell lines,

proliferation was measured in the presence of various concentrations IL7 (0.01

to 1 ng/ml). CTGF also had no effect on the proliferation of CTGF High cells in

the presence of IL7 (Figure 3.5b). However, our BCP ALL cell lines appeared

non-responsive to increasing concentrations of IL7 indicating no mitogenic

activation was produced by the protein. In fact lower counts of [3H]thymidine

incorporation were detected in all cells used in the IL7 proliferation assay

including media positive controls, although detected levels were still greater

than negative controls. This could be due to differences in the

seeding density of cells between assays (50,000 in low serum assay compared

to 100,000 in IL7 assay) and cells nearing confluence at the time of

[3H]thymidine incorporation in the IL7 assay.

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Figure 3.5. did not affect proliferation in vitro. Proliferation was measured by tritiated thymidine incorporation (counts/min) for PER-278 and PER-371 Low, Intermediate or High levels. a. Proliferation in low serum after 48hours (0.2% FCS) b. Proliferation after 48 hours incubation with IL7 at varying concentrations 0-1ng/ml (black to pale grey bars). Data are expressed as the mean isotope count per minute (n=3). Vertical bars show standard error of the mean.

PER-278 and PER-371 CTGF overexpression3[ H]

b.

a.

3 [H]

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3.3.3.2 Drug sensitivity

The effective dose capable of killing 50% of cells (ED50) was determined for

two chemotherapy drugs vincristine (VCR) and cytarabine (ARAC). Both drugs

have been used before in vitro and in vivo as effective agents against BCP ALL

primary cells and cell lines (Liem, et al., 2004; Tesfai, et al., 2012).

The viability of PER-278 and PER-371 cells was determined after treatment

with a serial dilution of a single chemotherapy drug. Representative kill curves

(expressed as the % difference in reduction of Alamar Blue between treated

and untreated cells) depict a plateau at higher drug concentrations of

approximately 30% viability for both VCR and ARAC (Figure 3.6). Every cell line

was successfully reduced in viability to determine ED50.

There was no effect on drug sensitivity due to increased CTGF expression in

either PER-278 or PER-371 cells (Figure 3.7). Marked differences in ED50

between cell lines did exist, with PER-371 showing reduced sensitivity to VCR

and PER-278 showing reduced sensitivity to ARAC compared to the other.

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VCR

Figure 3.6. for vincristine (VCR) and cytarabine (ARAC). Representative cell viability curves are depicted for High and Low cells to determine the effective dose to kill 50% of the cell population, ED50, after 72 hours incubation with two chemotherapy drugs: VCR with a. PER-278 and b. PER-371. ARAC with c. PER-278 and d. PER-371. Data are expressed as % difference in Almar Blue Reduction in drug treated compared to untreated cells.

PER-278 and PER-371 representative drug sensitivity curves

ARACc.

a.

b.

d.

371

371

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Figure 3.7. sensitivity to chemotherapeutic drugs in vitro. The effective dose to kill 50% of the cell population, ED50, was determined for PER-278 and PER-371cell lines using Alamar Blue after 72 hours incubation with the chemotherapy drugs: a. vincristine (VCR) and b. cytarabine (ARAC). Data are expressed as the mean ED50 concentration in µg/ml (n=3). Vertical bars show standard error of the mean.

PER-278 and PER-371 CTGF overexpression did not affect

VCRa.

ARACb.

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3.3.3.3 Microarray profiling With no observable differences due to increased CTGF expression in either

proliferation or drug sensitivity, changes in cellular gene expression patterns

were investigated. Microarray profiling of PER-278 and PER-371 cell lines with

CTGF at Low, Intermediate or High levels was performed in order to explore

potential intracrine changes taking place inside the cell.

RNA integrity analysis was performed on PER-278 and PER-371 mRNA

samples and all were determined to be of suitable quality for microarray

applications, as evidenced by 28S/17S ratio and RNA integrity number (Figure

3.8 and Table 3.3). Expression levels of CTGF mRNA and cellular protein were

determined by qRT-PCR and western blot and identified continued

overexpression of CTGF in CTGF High cells compared to CTGF Low (Figure

3.9). Secreted protein levels could not be determined after an 8 hour incubation

period. Differences between mRNA and cellular protein expression were

evident for CTGF High compared to Low and CTGF Intermediate compared to

Low for both PER-278 and PER-371 cells (Table 3.4). These RNA samples

were then run on an Affymetrix Human 1.0 ST array platform (conducted by the

Ramaciotti Centre for Gene Function Analysis, Sydney, Australia).

Normalisation of microarrays and LIMMA analysis was performed by

biostatistician Denise Anderson (TICHR, Perth, Australia). Plotting the data by

the variances of the first two principle components indicated the largest

differences in expression were between PER-278 and PER-371 cell lines and

then between uninfected and lentiviral-infected cells (Figure 3.10a). PER-371

Intermediate cells had an expression profile more closely associated with PER-

371 uninfected cells than their lentiviral-infected counterparts and was therefore

not used in further downstream analysis. LIMMA analysis revealed a large

number of significantly different genes that were altered by greater than 2-fold

between PER-278 and PER-371 cell lines (Figure 3.10b). Comparison of

CTGF-Low lentiviral-infected cell lines with uninfected parental cell lines again

revealed a multitude of genes with significantly different expression of greater

than 2-fold. However, no differences were found due to CTGF expression that

were common across the two cell lines, after comparing CTGF High to Low

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Table 3.3. RNA integrity number for PER-278 and PER-371 cell line samples. RNA integrity numbers (RIN) for all 8 samples used in the Affymetrix microarray. A RIN>7 represents RNA that is not degraded and suitable for use in microarray processing.

RNA sample RINPER-278 uninfected

PER-278 Low 1010

PER-278 Intermediate 9.9PER-278 High

PER-371 uninfectedPER-371 Low

PER-371 IntermediatePER-371 High

9.310

9.89.9

9.8

Figure 3.8. RNA integrity analysis for PER-278 and PER-371 cell line samples. Representative electropherogram with a suitable 28S/17S ratio for samples used in the Affymetrix Human 1.0 ST arrays.

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Table 3.4. Fold change of CTGF Hfor RNA and cellular protein expression. PER-278 and PER-371 cell line samples were collected after 8 hours incubation in normal media. RNA expression levels for CTGF were measured by qRT-PCR and cell protein CTGF expression levels were measured by western blot. Data presented as fold change for PER-278 and PER-371 Intermediate to Low and High to Low.

igh or Intermediate compared to Low

PER-278 Int/Low

PER-371 Int/LowPER-278 High/Low

PER-371 High/Low4.83.5

5.62.1

RNA (qRT-PCR)

4.4

4.16.4

2.6

Cell protein Fold Change

PER-

278

Low

PER-

278

Int

CTGF (CP)pan-Actin

PER-

278

Low

PER-

278

High

PER-

371

Low

PER-

371

Int

PER-

371

Low

PER-

371

High

b.

Figure 3.9. CTGF was overexpressed in the PER-278 and PER-371 cell line samples collected for microarray analysis. Samples were collected after 8 hours incubation in normal media. a. CTGF RNA expression levels as measured by qRT-PCR. Data are expressed as ratio of CTGF expression to housekeeping gene GAPDH. b. Cellular protein (CP) CTGF expression levels as measured by western blot. A pan-Actin antibody was used as a loading control.

RNA and protein

a.

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 94  

cells. Only CTGF itself was found to be significantly upregulated in unadjusted,

but not adjusted, analysis (unadjusted p-value= 0.01).

3.4 Discussion

The present study lentiviral transfection proved to be the optimal method of

transfecting BCP ALL cell lines. Previously published studies have identified the

Neon transfection system as capable of achieving high efficiency in difficult to

transfect cells, including stable transfection of human embryonic stem cells,

transient transfection of diffuse large B-cell lymphoma cell lines and even

transient siRNA transfection of B-cell ALL cell lines (Hagiya, et al., 2011; Jiang,

et al., 2011; Pham, et al., 2010). However, Neon and standard electroporation

failed to efficiently transfect BCP ALL cell lines with a CTGF transgene. As less

than 1% of cells showed incorporation of plasmid DNA, the method was not

sufficient for stable transfection.

As stable transfection was a requirement for in vivo studies, use of lentiviral

technology was adopted. Third generation lentiviral plasmids including the tat

gene, were transfected with a VSV-G envelope plasmid into 293T cells together

with the transfer plasmid containing the CTGF sequence. Transient transfection

of 293Ts was equally successful using both CaCl2 and Fugene methods so long

as the ratio of plasmids had been individually optimised. The VSV-G envelope

proved to have sufficient tropism for BCP ALL cells and incorporation of the

transfer plasmid into the chromosomal DNA proved successful. BCP ALL

transduction efficiency at 48 hours was 30% and puromycin selection enabled

greater than 95% purity. Lentiviral transduction was the preferred mechanism

for genetically engineering expression of a transgene in BCP ALL cell lines.

The BCP ALL engineered cell lines were found to have biologically relevant

levels of CTGF overexpression. A 3-fold upregulation in CTGF mRNA

expression was achieved in both PER-278 and PER-371 High cells compared

to empty-vector infected Low cells when measured by qRT-PCR. Further,

CTGF protein levels were 3- to 6-fold greater in CTGF High cells when

measured by densitometry of western blot bands. This fold change appears

small compared to the original microarray deregulation of 19.45-fold between

BCP ALL patient specimens and CD34+ haematopoietic progenitor cells found

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Figure 3.10. PER-278 and PER-371 CTGF High cells did not affect global gene expression patterns compared to CTGF Low cells. a. Principal component analysis (PCA) plot of the microarray data. The plot displays the variances of the first 2 principle components. Each dot represents a sample and each colour the type of sample. For PER-278 uninfected (green) to CTGF High cells (yellow) and PER-371 uninfected (purple) to CTGF High cells (pink). b. Volcano plots displays LIMMA statistical significance against fold change for three analyses: the comparison of cell lines (PER-278 vs PER-371), lentiviral infection (Low vs Uninfected) and CTGF expression (High vs Low).

PER-278 uninfectedPER-278 LowPER-278 IntermediatePER-278 HighPER-371 uninfectedPER-371 LowPER-371 IntermediatePER-371 High

b.

a.

High vs Lowlog fold change2log fold change2

log fold change2

-log

P-v

alue

10

-log

adj

uste

d P-

valu

e10

-log

P-v

alue

10

Low vs Uninfected PER-278 vs PER-371

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 96  

by Boag and colleagues (2007). However, in the same study validation of

microarray results by qRT-PCR found only 2.4 fold difference between average

CTGF expression in 18 BCP ALL patient specimens and 4 CD34+ umbilical cord

specimens. In additional studies a wide range of CTGF expression levels

existed among 14 primary BCP ALL patient specimens with the highest CTGF

level having 10-fold greater expression than non-detectable specimens by qRT-

PCR (Welch, et al., 2013). Similarly, CTGF expression levels in adult B-cell ALL

specimens spanned more than 70-fold from highest to lowest (Sala-Torra, et al.,

2007). Thus the CTGF levels in PER-278 and PER-371 High and Low cell lines

places them within the range recorded in primary samples, with Low CTGF-

expressing cells clearly toward the lower end of the spectrum and High CTGF-

expressing cells in the middle of the spectrum and they’re therefore acceptable

candidates for further study.

As there is large heterogeneity in CTGF expression among primary patient

samples, identifying an expression level where CTGF initially affects cell

function is close to impossible. It is more likely each tumour cell has its own

innate propensity to respond to the cues created by CTGF overexpression and

therefore each tumour may possess a unique threshold where CTGF

expression contributes to disease outcome.

In the present study, no autocrine or intracrine function for CTGF was detected

in BCP ALL cell lines as biologically relevant upregulation of CTGF expression

in BCP ALL cell lines did not elicit any observable changes in vitro. Neither

proliferation nor drug sensitivity was affected due to increased CTGF

expression. However, there was a very distinct response pattern to VCR and

ARAC in the two cell lines with PER-371 cells showing a 3.7-fold reduced

sensitivity to VCR compared to PER-278. Even more disparate was the

response to ARAC with PER-278 cells 25-fold less sensitive to the drug

compared with PER-371 cells. Global gene expression analysis found no

commonly deregulated genes due to altered CTGF in the cell lines. Lack of

common deregulated genes due to CTGF is not surprising considering the

significant gene expression differences between PER-278 and PER-371 cell

lines at the RNA level. With 2 biological replicates with a high variance in

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  97  

expression, the ability to determine deregulated gene patterns due to CTGF

becomes challenging.

Determining a functional role for CTGF in BCP ALL cells was investigated by

successfully engineering the overexpression of CTGF in two BCP ALL cell lines,

PER-278 and PER-371. In culture, CTGF overexpression was found to have no

effect on proliferation of cells or sensitivity to the chemotherapy drugs VCR or

ARAC. Further, global gene expression arrays, while detecting significant

changes in gene expression profiles due to cell line or lentiviral infection, found

no common alteration in gene expression between PER-278 and PER-371 High

cells due to upregulated CTGF.

The absence of an observable response in functional assays due to increased

CTGF expression could be attributed to the tests being performed in vitro. It is

plausible that as a secreted matricellular protein, any functional role of CTGF

involves interaction with the microenvironment. With the necessary intermediary

cells being absent in laboratory culture conditions.

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444444444Recombinant human CTGF has the

capacity to alter the gene expression profile of human BM

stromal cells

All life is an experiment.The more experiments you make the better.

Ralph Waldo Emerson

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Chapter 4 Recombinant human CTGF has the capacity to

alter the gene expression profile of human BM stromal cells  

4.1 Abstract CTGF belongs to the CCN family of matricellular proteins. The CCN family are

well known to interact with ECM components throughout normal life and in

disease. A unique role for CTGF may exist in B-cell precursor (BCP) ALL, the

most common cancer diagnosed in children. CTGF is significantly upregulated

in childhood BCP ALL patient specimens and is associated with poor outcome.

CTGF, as a secreted protein with known ECM functions, may act in childhood

BCP ALL to alter cellular interactions and structure of the extracellular space in

the BM microenvironment, the haematopoietic niche where the disease

originates.

In this study the effect of recombinant human (rh)CTGF on the gene expression

profile of a human BM stromal cell line, HS5, is explored at three incubation

times: 8, 16 and 48 hours. Significant differences in HS5 gene expression due

to rhCTGF supports a role for the protein in insulin-like growth factor 1 (IGF1)

and phosphoinositide 3-kinase/protein kinase C (PI3K/AKT) signalling

pathways. The potential involvement of CTGF in ECM remodelling and

abnormal wound response through its effects on HS5 cells is also put forward.

This microarray study presents strong evidence for a functional role of CTGF in

human BCP ALL through BM microenvironment interactions.

4.2 Introduction The CCN family of matricellular proteins are defined as such due to their role as

ECM-related signalling proteins. Together, the family are involved in a large

number of normal functions from embryonic chondrogenesis and bone

formation through to roles in adult wound healing (Jun & Lau, 2011). Though

the CCN family members are involved in similar activities they respond to

stimuli in their own unique fashion. CTGF/CCN2 is known to respond to various

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 102  

growth factors and environmental cues, largely by enacting a response at the

transcriptional level, with some instances of post-transcriptional regulation

(Leask & Abraham, 2006). The response to CTGF is not only specific compared

to other family members but also to the type and location of interacting cells.

Like all CCN family members, CTGF is deregulated in many human diseases

including cancers. This study investigates the role of CTGF in childhood BCP

ALL. The CTGF gene is known to be upregulated in the majority of childhood

BCP ALL cases and is associated with high-risk stratification in children and

worse overall survival in adults (Boag, et al., 2007; Kang, et al., 2010; Sala-

Torra, et al., 2005). A specific functional role for CTGF in BCP ALL has yet to

be recognised but as CTGF has associations with the ECM and is tagged for

secretion from the cell, the secreted protein may act through the

microenvironment in BCP ALL.

This study explores the ability of rhCTGF to modify the BCP ALL

microenvironment, consisting of stromal cells and regulatory proteins in the BM

niche. Global gene expression was assessed in an immortalised human BM

stromal cell line (HS5) after treatment with rhCTGF or control buffer for 8, 16

and 48 hours.

4.3 Results HS5 is a faithful representative of bone marrow stroma that supports

proliferation of hematopoietic progenitor cells when cocultured in serum-

deprived media with no exogenous factors (Roecklein & Torok-Storb, 1995a).

HS5 cells were incubated with 100ng/ml rhCTGF and RNA extracted at 8, 16

and 48 hours, hybridisation of RNA to Affymetrix HG-U133A arrays was

performed by research officer Jette Ford (TICHR, Perth, Australia) as described

in the materials and methods. After normalisation, principle component analysis

(PCA) of the first three principal components showed clear separation of the 48-

hour incubation data compared to 8 and 16 hours (Fig 4.1). To define the

accuracy of the expression profiles, data from the three untreated control times

were analysed in comparison to the originally published features of the HS5 cell

line (Roecklein & Torok-Storb, 1995a). At all three time points, control HS5

samples showed high expression of genes identified as showing strong positive

immunostaining or strong protein expression in the original immortalised cell

Page 123: The Bone Marrow Microenvironment is Essential for the ... · iv! ! overexpressing cell lines 2.3.5 Global gene expression to determine effect of recombinant human CTGF on stromal

Extracellular matrix

Lipid metabolism

Adhesion Cytokine Signaling

GENE FC GENE FC GENE FC GENE FC

COL3A1 15.0 NPTX2 3.7 TGFB2 15.3 CCL2 3.6

LOX 5.4 MAN2A1 3.6 EFEMP1 5.4 CCL7 2.8 LUM 4.8 GALNT11 3.5 DPP4 4.4 CCL8 2.5

COL1A2 4.2 PTX3 3.1 FN1 4.0 IL1R1 2.1

FN1 4.0 ASAH1 2.7 LAMB1 3.6 CXCL1 -8.8 LAMB1 3.7 COLEC12 2.7 NID2 3.6 CXCL6 -5.8

TGFBR3 3.6 HMMR 2.4 TGFBR3 3.5 IL32 -2.8 ITGAV 3.4 SERPINE2 2.3 SEMA3C 3.2 CXCL5 -2.6 COL5A1 3.3 LGALS8 2.2 TNFAIP6 3.0 CCL20 -2.5

FBN2 3.3 GALNT7 2.2 WNT5A 2.5 CCL3 -2.2

NID1 3.1 FADS1 2.1 ITGBL1 2.3 TUFT1 2.7

MATN3 2.5

FBN1 2.3 TFPI2 2.0

ECM1 -2.1

Figure 4.1. Ccaused by treatment with rhCTGF compared to control buffer. HS5 cells were treated with rhCTGF (100ng/ml) or control buffer for 8, 16 and 48 hours before collection of RNA for gene expression analysis a. Principal component analysis (PCA) plot of the microarray data. The plot displays the variances of the first 3 principle components. Each dot represents a sample and each colour the type of sample. 8 hour incubations are green, 16 hour are pink and 48 hour are blue. CTGF treatments are a lighter shade to control buffer. b. Venn diagram displaying the number of significantly altered probe sets for all three time points between CTGF-treated and untreated HS5 cells. Seven probe sets were deregulated at all three time points. Significance was determined by LIMMA analysis (p<0.05; R platform).

hanges to global gene expression in BM stromal cells (HS5)

16hr CTGF16hr control

8hr CTGF8hr control

48hr CTGF48hr control

b.

a.

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 104  

line including: interleukin 6 (IL6) and interleukin 8 (IL8) in the top 1% of

microarray probe sets and major histocompatability complex class I

(MHCI),colony stimulating factor 3 (CSF3/GCSF) and membrane metallo-

endopeptidase (MMN/CD10) in the top 10% of genes.

4.3.1 LIMMA analysis LIMMA analysis was performed to enable identification of statistically significant

differences from the small sample size with p<0.05. Treatment with rhCTGF

resulted in differential genes at all 3 times (Figure 4.1b). The greatest number of

significantly altered probe sets occurred 8 hours post rhCTGF treatment,

followed by 16 and then 48 hours and overlapping probes were present across

all three times. Only seven probe sets identifying 6 genes were significantly

different at all 3 times, and none showed consistent up- or downregulation

across the 48-hour period. Three patterns of deregulation were present. The

first involved ABI gene family, member 3 binding protein (ABI3BP) and tripartite

motif containing 22 (TRIM22) which were upregulated following 8 and 16 hours

treatment followed by downregulation at 48 hours post treatment compared to

their time-matched controls. The second pattern involved thymosin beta 10

(TMSB10) and proteasome subunit beta, type 4 (PSMB4) which showed

downregulation at 8 and 48 hours and upregulation at 16 hours post treatment

compared to controls. Lastly, the genes chemokine (C-X-C motif) ligand 1

(CXCL1) and chemokine (C-X-C motif) ligand 6 (CXCL6) were downregulated

at 8 hours then upregulated at 16 and 48 hours post treatment compared to

controls. Due to the small number of genes with continuous deregulation and

none with a consistent pattern of expression, further analysis focused solely on

genes deregulated 8 hours after rhCTGF treatment.

4.3.2 Ingenuity Pathway Analysis As the broadest range of deregulated HS5 genes was observed 8 hours post

treatment with rhCTGF, this time was chosen to perform Ingenuity Pathway

Analysis (IPA). The list of significant probe sets was filtered to include only

those with fold changes greater than 2 in the treated compared to control group.

This probe set list was used for IPA analysis to highlight top associated

networks, canonical pathways and biological functions associated with

Page 125: The Bone Marrow Microenvironment is Essential for the ... · iv! ! overexpressing cell lines 2.3.5 Global gene expression to determine effect of recombinant human CTGF on stromal

Tab

le 4

.1. In

gen

uit

y p

ath

way a

naly

sis

(IP

A)

for

dif

fere

nti

ally r

eg

ula

ted

gen

es b

etw

een

str

om

al cells (

HS

5)

treate

d w

ith

rh

CT

GF

(1

00n

g/m

l) o

r co

ntr

ol b

uff

er

for

8 h

ou

rs . T

he IP

A g

ene li

st c

om

prise

s genes

identif

ied s

ignifi

cantly

diff

ere

nt by

LIM

MA

and w

ith a

n

exp

ress

ion d

iffere

nce

gre

ate

r th

an tw

o-f

old

com

pare

d to u

ntr

eate

d c

ontr

ol c

ells

(B

enja

min

i and H

och

berg

-adju

sted p

-valu

e <

0.0

5, fo

ld

change >

2 a

nd <

2).

Num

ber

of upre

gula

ted (á

) and d

ow

nre

gula

ted (â

) genes

indic

ate

d w

ere

use

d to g

enera

te IP

A s

ignifi

cant netw

ork

, ca

nonic

al p

ath

way

and k

now

n b

iolo

gic

al f

unct

ion a

sso

ciatio

ns.

Cell

Cyc

le

Cellu

lar

Deve

lopm

ent

IGF

-1 S

ignalin

g

Andro

gen S

ignalin

g

1.C

ell

Cyc

le, D

NA

Replic

atio

n, R

eco

mbin

atio

n,

and R

epa

ir, G

ene E

xpre

ssio

n

2. C

arb

ohyd

rate

Meta

bolis

m, S

mall

Mole

cule

B

ioch

em

istr

y, C

onnect

ive T

issu

e D

isord

ers

á787

â622

Cell

Death

Ary

l Hyd

roca

rbon R

ece

pto

r S

ignalin

g

3. C

onnect

ive T

issu

e D

eve

lopm

ent and F

unct

ion,

Tis

sue M

orp

holo

gy,

R

NA

Post

Tra

nsc

riptio

nal M

odifi

catio

n

Cellu

lar

Gro

wth

and P

rolif

era

tion

Neure

glin

Sig

nalin

g

Cellu

lar

Move

ment

RA

N S

ignalin

g

IPA

Netw

ork

# G

en

es

To

p B

iolo

gic

al F

un

cti

on

sIP

A C

an

on

ical

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 106  

deregulation of HS5 cells due to rhCTGF (Table 4.1). IPA analyses for

deregulated HS5 genes 16 and 48 hours post CTGF treatment is provided as

supplementary material (Table S1 and S2). At 8 hours, the top IPA network and

biological function associated with rhCTGF was cell cycle and the top canonical

pathway was insulin-like growth factor 1 (IGF1) signalling (Figure 4.2). In

addition, the activation of phosphoinositide 3-kinase/ protein kinase B

(PI3K/AKT) signalling was associated with deregulated HS5 genes (Figure 4.3).

Many of the genes associated with the TGFβ network were found to be both

significantly up- and downregulated in CTGF-treated HS5 cells (Figure 4.4). IPA

analysis highlighted intracellular signalling cascades associated with

significantly deregulated HS5 genes after rhCTGF treatment.

4.3.3 Functions associated with secreted proteins HS5 cells may affect leukaemia cell activity via the secretion of proteins, which

was investigated with the use of a publically available protein database. The

IPA gene list comprised significantly deregulated HS5 genes after 8 hours

rhCTGF treatment compared to untreated control cells, p<0.05 and fold change

≥2. This list was further filtered to identify significantly differentiated expression

of genes associated with the cellular membrane or extracellular secretion.

Overlap between the list of deregulated HS5 genes and genes listed in the

secreted protein database initiative (SPDI) found 78 secreted genes were

significantly upregulated and 66 genes were significantly downregulated in HS5

cells post-CTGF treatment (Supplementary Tables S3 and S4).

Page 127: The Bone Marrow Microenvironment is Essential for the ... · iv! ! overexpressing cell lines 2.3.5 Global gene expression to determine effect of recombinant human CTGF on stromal

Figure 4.2. CTGF dpathway. HS5 cells were treated with rhCTGF (100ng/ml) or control buffer for 8 hours and significantly altered probe sets due to CTGF treatment were determined by LIMMA (Benjamini and Hochberg-adjusted p-value <0.05, fold change >2 and <2). IPA analysis of the filtered gene list determined Insulin-like growth factor 1 (IGF1) signalling pathway to be the top canonical pathway associated with deregulated HS5 genes. Red indicates overexprerssion and green indicates underexpression of the gene.

eregulates HS5 genes involved in the IGF1 signalling

Page 128: The Bone Marrow Microenvironment is Essential for the ... · iv! ! overexpressing cell lines 2.3.5 Global gene expression to determine effect of recombinant human CTGF on stromal

Figure 4.3. CTGF deregulates genes involved in the PI3K/AKT signaling pathway. HS5 cells were treated with rhCTGF (100ng/ml) or control buffer for 8 hours and significantly altered probe sets due to CTGF treatment were detremined by LIMMA (Benjamini and Hochberg-adjusted p-value <0.05, fold change >2 and <2). IPA analysis of the filtered gene listdetermined the phosphoinositide 3-kinase/ protein kinase B (PI3K/AKT) canonical signalling pathway to be associated with deregulated HS5 genes. Red indicates overexpression and green indicates underexpressionof the gene.

Page 129: The Bone Marrow Microenvironment is Essential for the ... · iv! ! overexpressing cell lines 2.3.5 Global gene expression to determine effect of recombinant human CTGF on stromal

Figure 4.4. eregulates HS5 genes involved in TGFb networksHS5 cells4were treated with rhCTGF (100ng/ml) or control buffer for 8 hours and significantly altered probe sets due to CTGF treatment were determined by LIMMA (Benjamini and Hochberg-adjusted p-value <0.05, fold change >2 and <2). IPA analysis of the filtered gene list determined Transforming growth factor b (TGFb) networks to be the top associated IPA network with deregulated HS5 cells. TGFb network functions were associated with cell cycle, DNA replication, recombination and repair and gene expression.

CTGF d .

Red indicates overexprerssion and green indicates underexpression of the gene.

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 110  

The list of differentially expressed secreted HS5 genes was analysed for the

most frequently associated extracellular functions (Table 4.2). The greatest

number of significantly deregulated secreted genes was associated with ECM

interactions, followed by lipid metabolism, adhesion and cytokine signalling.

4.3.4 Verification of deregulated genes by RT-PCR RNA expression by RT-PCR was performed to validate the deregulation of 4

secreted HS5 genes. Three were the top upregulated genes associated with the

ECM; collagen, type 3, alpha 1 (COL3A1), lysyl oxidase (LOX) and lumican

(Dornhofer, et al.), and one was the upregulated cell membrane binding protein

integrin, alpha V (ITGAV). Expression of HS5 mRNA extracted from cells after

treatment with rhCTGF for 4, 8 and 16 hours were compared to untreated

control cells. These results were confirmed if genes showed greater than 1.5-

fold upregulation due to rhCTGF. Validating the deregulation of LOX at 4 and 8

hours and ITGAV at 8 hours post CTGF treatment (Figure 4.5). Failure to verify

upregulation of COL3A1 and LUM due to CTGF treatment could be attributed to

the biological activity of rhCTGF being reduced between microarray studies and

RT-PCR validation several years later. However, those CTGF-deregulated

genes associated with secretion that were confirmed by qRT-PCR support the

findings of the microarray analysis.

Page 131: The Bone Marrow Microenvironment is Essential for the ... · iv! ! overexpressing cell lines 2.3.5 Global gene expression to determine effect of recombinant human CTGF on stromal

SYM

BOL

CCL2

FC 3.6

GEN

Ech

emok

ine

(C-C

mot

if)

ligan

d 2

SYM

BOL

TGFB

2

FC 15.3

GEN

ETr

ansf

orm

ing

grow

th

fact

or, b

eta

2

SYM

BOL

NPTX

2

FC 3.7

GEN

E

neur

onal

pen

traxin

2

SYM

BOL

COL3

A1

FC 15.0

GEN

Eco

llage

n, ty

pe 3

, al

pha

1

CCL7

2.8

chem

okin

e (C

-C m

otif)

lig

and

7EF

EMP1

5.4

EGF

cont

aini

ng fi

bulin

-like

EC

M p

rote

in 1

MAN

2A1

3.6

man

nosid

ase,

alp

ha, c

lass

2A

, mem

ber 1

LOX

5.4

lysyl

oxid

ase

CCL8

2.5

chem

okin

e (C

-C m

otif)

lig

and

8DP

P44.

4di

pept

idyl-

pept

idas

e 4

GAL

NT11

3.5

polyp

eptid

e G

alNA

c Tr

ansf

eras

e 11

LUM

4.8

lum

ican

IL1R

12.

1in

terle

ukin

1 re

cept

or,

type

IFN

14.

0fib

rone

ctin

1PT

X33.

1pe

ntra

xin 3

, lon

gCO

L1A2

4.2

colla

gen,

type

1,

alph

a 2

CCL3

-2.2

chem

okin

e (C

-C m

otif)

lig

and

3LA

MB1

3.6

lam

inin

, bet

a 1

ASAH

12.

7N-

acyls

phin

gosin

e am

idoh

ydro

lase

1FN

14.

0fib

rone

ctin

1

CCL2

0-2

.5ch

emok

ine

(C-C

mot

if)

ligan

d 20

NID2

3.6

nido

gen

2CO

LEC1

22.

7co

llect

in s

ub-fa

mily

m

embe

r 12

LAM

B13.

7la

min

in, b

eta

1

CXCL

5-2

.6Ch

emok

ine

(C-X

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Mot

if) L

igan

d 5

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R33.

5Tr

ansf

orm

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grow

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fact

or, b

eta

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ptor

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edia

ted

mot

ility

rece

ptor

TGFB

R33.

6tra

nsfo

rmin

g gr

owth

fa

ctor

, bet

a re

cept

or 3

Il32

-2.8

inte

rleuk

in 3

2SE

MA3

C3.

2se

map

horin

3C

SERP

INE2

2.3

serp

in p

eptid

ase

inhi

bito

r, cla

de E

, mem

ber 2

ITG

AV3.

4in

tegr

in, a

lpha

v

Lipi

d M

etab

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mEx

trace

llula

r Mat

rixCy

toki

ne s

igna

lling

Adhe

sion

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6-5

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emok

ine

(C-X

-C

Mot

if) L

igan

d 6

TNFA

IP6

3.0

tum

or n

ecro

sis fa

ctor

, al

pha-

indu

ced

prot

ein

6LG

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2.2

lect

in, g

alac

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ndin

g,

solu

ble,

8CO

L5A1

3.3

colla

gen,

type

5,

alph

a 1

CXCL

1-8

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emok

ine

(C-X

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Mot

if) L

igan

d 1

WNT

5A2.

5wi

ngle

ss-ty

pe M

MTV

in

tegr

atio

n sit

e fa

mily

, m

embe

r 5A

GAL

NT7

2.2

polyp

eptid

e G

alNA

c Tr

ansf

eras

e 7

FBN2

3.3

fibril

lin 2

ITG

BL1

2.3

inte

grin

, bet

a-lik

e 1

FADS

12.

1fa

tty a

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nido

gen

1

TUFT

12.

7tu

ftelin

1

Page 132: The Bone Marrow Microenvironment is Essential for the ... · iv! ! overexpressing cell lines 2.3.5 Global gene expression to determine effect of recombinant human CTGF on stromal

Tabl

e 4.

2. T

op fu

nctio

ns o

f sec

rete

d HS

5 ge

nes

dbu

ffer f

or 8

hou

rs. T

he ta

ble

com

prise

s se

cret

ed g

enes

iden

tifie

d by

LIM

MA

as g

reat

er th

an 2

-fold

and

sig

nific

antly

diff

eren

t due

to

rhCT

GF

com

pare

d to

con

trols

(Ben

jam

ini a

nd H

ochb

erg-

adju

sted

p-v

alue

<0.

05, f

old

chan

ge >

2 an

d <2

). Th

e filt

ered

gen

e lis

t for

se

cret

ed p

rote

ins

were

gro

uped

into

the

mos

t com

mon

ly as

socia

ted

extra

cellu

lar b

iolo

gica

l fun

ctio

ns: e

xtra

cellu

lar m

atrix

func

tions

, lip

id

Met

abol

ism, a

dhes

ion

and

cyto

kine

signa

ling.

FC,

fold

cha

nge

betw

een

CTG

F-tre

ated

com

pare

d to

unt

reat

ed H

S5 B

M s

trom

al c

ells.

iffer

entia

lly re

gula

ted

afte

r tre

atm

ent w

ith rh

CTG

F (1

00ng

/ml)

or c

ontro

l

SYM

BOL

FCG

ENE

SYM

BOL

FCG

ENE

SYM

BOL

FCG

ENE

SYM

BOL

MAT

N3

FC 2.5

GEN

E

mat

rilin

3

FBN1

2.3

fibril

lin 1

TFPI

22.

0tis

sue

fact

or p

athw

ay

inhi

bito

r 2

PLAU

R-2

.1 p

lasm

inog

en a

ctiva

tor,

urok

inas

e re

cept

or

MM

P12

-2.1

mat

rix m

etal

lope

ptid

ase

12

ECM

1-2

.1ex

trace

llula

r mat

rix

prot

ein

1

TIM

P2-2

.3TI

MP

Met

allo

pept

idas

e In

hibi

tor 2

TIM

P1TI

MP

Met

allo

pept

idas

e In

hibi

tor 1

Lipi

d M

etab

olis

mEx

trace

llula

r Mat

rixCy

toki

ne s

igna

lling

Adhe

sion

PLAU

-5.7

plas

min

ogen

act

ivato

r, ur

okin

ase

-2.8

Page 133: The Bone Marrow Microenvironment is Essential for the ... · iv! ! overexpressing cell lines 2.3.5 Global gene expression to determine effect of recombinant human CTGF on stromal

Figure 4.5. Validation of two genes upregulated in HS5 cells after treatment with CTGF. RNA expression of stromal cells (HS5) treated with rhCTGF (100ng/ml) or control buffer for 8 hours was measured by RT-PCR for Collagen, type 3, alpha1 (COL3A1), lysyl oxidase (LOX), lumican (LUM) and integrin, alpha V (ITGAV). Data are expressed as a comparative ratio of HS5 cells normalised to GAPDH then comparing treatment with rhCTGF (HS5+rhCTGF) to untreated control buffer (HS5). A greater than 1.5 fold change was required to validate upregulation of the tested RNA, confirming LOX and ITGAV to be upregulated due to rhCTGF. (n=1).

ECM-associated

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 114  

4.4 Discussion The longitudinal effects of CTGF were assessed by gene expression profiling of

HS5 cells at 8, 16 and 48 hours post rhCTGF treatment. It was shown that

CTGF altered intracellular signalling to influence gene expression at every

assessed time. CTGF is a growth-factor inducible immediate-early gene in

normal cell function (Bradham, 1991). Given its transcription occurs minutes

after mitogenic stimulation, the decision was made to focus on HS5 genes

deregulated after the shortest incubation time, being 8 hours with rhCTGF.

Microarray analyses indicated that in response to CTGF treatment stromal HS5

cells deregulated genes associated with cell cycle, IGF1 and PI3K/AKT

signalling pathways. PI3K/AKT pathway activation can induce cell cycle

progression and macrophage survival. PI3K/AKT signalling is known to regulate

CTGF expression in a cell-dependent manner, with smooth muscle cells

increasing CTGF expression and vascular endothelial cells decreasing CTGF

expression via PI3K/AKT activation (Samarin, et al., 2009). In a non-small cell

lung carcinoma cell line IGF1-dependent AKT phosphorylation was suppressed

by CTGF overexpression (Chien, et al., 2006). In this study, activation of MEK

and AKT in HS5 cells was likely an IGF1-independent phenomenon, as in

stromal cells the IGF1 receptor (IGF1R) was downregulated in response to

CTGF. IPA analyses also suggested a direct link between CTGF and activation

of the PI3K/AKT signalling pathway via binding of an integrin-receptor and

subsequent activation of integrin-linked kinase (ILK), protein phosphatase 2

(PP2A) and AKT. Upregulation of ITGAV suggests it could function as an

integrin-linked transmembrane receptor for CTGF in HS5 cells. In osteoarthritic

chondrocytes, TGFβ, a mediator of CTGF action, was found to upregulate

ITGAV and in turn increase phosphorylation of PI3K and AKT (Kostopoulou, et

al., 2012). TGFβ2 was a gene significantly upregulated in HS5 cells due to

CTGF treatment. IPA analyses indicated CTGF modulated HS5 genes

associated with survival and proliferation networks and pathways.

Many of the secreted genes differentially expressed by HS5 cells due to CTGF

treatment are involved in ECM remodelling. LOX and ITGAV were validated as

upregulated by rhCTGF in HS5 cells by qRT-PCR. CTGF has been found to

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  115  

induce LOX synthesis in cultured cardiac fibroblasts, in association with atrial

fibrillation (Adam, et al., 2011; Lavall, et al., 2013). ITGAV, an integrin

heterodimer alpha chain, when co-located with a beta subunit forms an integrin

receptor that has been shown to promote migration and survival when

expressed in cancer cells (Desgrosellier & Cheresh, 2010; Jandova, et al.,

2012; Uhm, et al., 1999). Primary BM-derived mesenchymal stromal cells are

also known to express ITGAV (Shur, et al., 2002). These proteins are also

targetable and inhibitors of both ITGAV and LOX have been previously

proposed as anti-cancer agents (Barker, et al., 2012; Nemeth, et al., 2007; van

der Horst, et al., 2011).

In this study, a subset of deregulated HS5 genes involved in ECM remodelling

are associated with the wound healing response which suggests BCP ALL cells

may hijack a normal fibrotic response in the BM through CTGF secretion.

Stromal cell expression of CTGF is known to play an important role in organ

fibrosis with secretion of CTGF by fibroblasts causing the overstimulation of

genes associated with the wound healing response (Leask, 2002; Sonnylal, et

al., 2010). A fibrotic stroma in solid cancers has also been associated with

misappropriated wound healing cues (Dvorak, 1986). In primary mesenchymal

stromal cells, knockdown of CTGF expression was shown to reduced

proliferation and promote differentiation into adipocytes but not fibroblasts

(Battula, et al., 2013). In leukemia CTGF may act in a similar fashion to promote

fibrosis.

In this study, rhCTGF was able to significantly deregulate the gene expression

profile of the human BM stromal cell line HS5. IPA analyses identified cell cycle

regulation as the top network and biological function associated with CTGF

incubation for 8 hours. Significantly altered canonical pathways included the

IGF1 signalling pathway, which appeared to be activated independently of the

IGF1 gene. Deregulated genes were associated with PI3K/AKT pathway

activation, and ITGAV, may act as the transmembrane receptor activating the

pathway. Secreted genes deregulated in response to 8 hour CTGF treatment

revealed strong associations with ECM remodelling and similarities with the

normal wound healing response. Follow-up studies are needed to validate more

genes of interest and determine protein expression and phosphorylation levels

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in human stromal cells after exposure to CTGF protein. The presented

microarray analyses provide plentiful evidence that CTGF secreted from BCP

ALL cells activates intracellular signalling pathways in human BM stromal cells.

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555555555CTGF contributes to drug sensitivity in PER-278 B-precursor ALL cells in

the BM microenvironment

The body is a big sagacity,a plurality with one sense,

a war and a peace,a flock and a shepherd.

Friedrich Nietzsche

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Chapter 5 CTGF contributes to drug sensitivity in PER-278 B-cell precursor ALL

 

5.1 Abstract In childhood B-cell precursor (BCP) ALL patients who relapse are faced with

reduced treatment options and worse survival outcomes. Early relapses are

more likely to derive from sub-populations within the diagnostic leukaemic

mass. The CTGF gene is upregulated in 75% of primary cases of childhood

BCP ALL and has been associated with worse clinical outcome in high-risk

patients, suggesting a potential role in leukaemia cell drug resistance. A role for

CTGF in BCP ALL has not been functionally defined, however associations

between CTGF and many human cancers provide evidence of a tumour

promoting function for the protein.

To assess the effects of CTGF on leukaemia cell outgrowth and drug resistance

in BCP ALL, NOD/SCID xenografts were generated using the BCP ALL patient-

derived cell line PER-278 engineered to overexpress CTGF. Comparison

between these PER-278 CTGF High and Low xenografts found no difference in

overall survival or organ engraftment at 24 hours and 3 weeks post-injection to

represent survival and proliferation of leukaemia cells at homing and early stage

disease. Organ engraftment at end stage disease revealed an increased

percentage of leukaemic cells in PER-278 High engrafted lymph nodes

compared with PER-278 Low cells (67.2% versus 43%, p=0.04). In PER-278

Low xenografts treatment with low dose ARAC significantly increased survival

compared with saline-treated controls (p=0.003). This is in contrast to PER-278

High xenografts that did not show a significant difference between low dose

ARAC and saline treated mice groups. The PER-278 xenograft model found

differences due to CTGF overexpression in end stage lymph node engraftment

and reduced drug sensitivity to ARAC, establishing that CTGF can affect

disease outcomes in the context of a leukaemia-infiltrated BM

microenvironment.

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5.2 Introduction Improving relapse rates and treatment options in BCP ALL remains a major

hurdle to improving disease outcomes (Bailey, et al., 2008). A common cause

of relapse is sub-clones from within the diagnostic leukaemic cell population, in

these cases resistance is inherent in the primary disease and not an acquired

event after exposure to chemotherapy drugs (Choi, et al., 2007). In 94% of

diagnosis-relapse sample pairs, DNA modifications found in sub-clones to be

responsible for relapse were associated with an ancestral leukaemic cell from

one of the various levels of hierarchy since time of diagnosis (Mullighan, et al.,

2008). Increased expression of CTGF is found in 75% of diagnosis specimens

of childhood BCP ALL and has also been identified in a gene-set with

associations to high-risk paediatric patients that have the poorest clinical

outcomes (Boag, et al., 2007; Kang, et al., 2010).

In order to investigate BCP ALL biology, mouse models are used that provide

excellent platforms to introduce more complex microenvironment interactions

contributing to tumourigenesis and drug response. For leukaemia studies the

NOD/SCID xenograft mouse model has been proven to establish disease with

similar features to the human patient (Lock, et al., 2002). The NOD/SCID model

does however have limitations in mimicking the clinical conditions found in

patients, most importantly differences in mouse and human genomes potentially

omit important xenograft-host interactions (Meyer & Debatin, 2011). The

importance of replicating an immune response as in human tumours is in direct

opposition to the necessity of using immune-compromised mice that allow

propagation of foreign human cells. The use of the NOD/SCID strain is a

suitable compromise that maintains some residual immune functioning, with

reduced NK cell activity and small populations of functioning mature

macrophages (Shultz, et al., 1995b). This improves the biology of the leukaemia

model by providing partial immunological selective pressure that would be

present in greater abundance in human patients.

In this study, a functional role for CTGF was investigated using NOD/SCID

xenografts. The BCP ALL cell line PER-278 was found to be characteristically

similar to the primary patient specimen it was derived from (see section 3.3).

PER-278 cells were previously engineered to stably overexpress CTGF and

GFP producing PER-278 High cells or expressed GFP alone producing PER-

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278 Low cells (see section 2.2.5-7). PER-278 High and Low cells were then

used to create xenografts by injecting 2x105 cells into the tail-vein of NOD/SCID

mice, under both irradiated and non-irradiated conditions (see section 2.7.2).

The effect of CTGF overexpression on leukaemia cell growth in the BM was

assessed at times specific for homing, early and end stage disease and

included the response to single-agent chemotherapy drugs ARAC and VCR.

5.3 Results 5.3.1 CTGF expression level at time of injection CTGF expression levels were measured for PER-278 High and Low cells before

inoculating NOD/SCID mice. Three experimental times were examined: homing

at 24 hours post-injection, early stage disease at 3 weeks post-injection and

end stage at presentation of clinical signs of morbidity. Cellular and secreted

protein was measured by western blot (Figure 5.1). CTGF overexpression in

PER-278 High compared with PER-278 Low cells was verified at the cellular

protein and secreted protein level (Table 5.1).

5.3.2 Survival outcomes and organ engraftment throughout spread of leukaemia cells Flow cytometry was used to detect GFP-expressing leukaemia cells in organs

and peripheral blood and showed good correlation with CD19-expressing cells

(data not shown). However, detection of GFP+ cells in the peripheral blood was

not a good indicator of disease progression with sustained low levels of

detection throughout disease progression and maximal detection of 20% in

PER-278 High and 11% in PER-278 Low xenografts (Figure 5.3e). For this

reason, survival was determined by observable symptoms in the mice, which

were sacrificed when they presented with the first signs of a moribund

phenotype. Survival of PER-278 xenografts was not affected by CTGF

overexpression with both PER-278 High and PER-278 Low xenografts having a

median survival time of 49 days (p=0.34; Fig 5.2a). This shows CTGF had no

effect on survival outcomes of PER-278 xenografted mice.

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PER-278 High/LowHoming (24hrs)

PER-278 High/LowEarly disease (Wk3)

PER-278 High/LowEnd stage disease

2.93

9.686.40

2.93

Cell protein (western)

17.06

Fold Change Secreted protein (western)

17.06

Table 5.1. Fold change difference between PER-278 High and Low cells before tail-vein injection into NOD/SCID mice. Cellular and secreted protein CTGF expression was measured by densitometry from western blot bands. Overexpression of CTGF in PER-278 High compared to Low cells was analysed for 3 experimental times (homing, early and end stage disease).

PER-

278

Low

CTGF (CP)pan-actin

CTGF (CM)PE

R-27

8 Hi

gh

PER-

278

Low

PER-

278

High

Hom

ing

& ea

rly s

tage

End

sta

ge

Figure 5.1. CTGF protein expression levels for PER-278 High and Low NOD/SCID xenografts. Cellular (CP) and secreted protein (CM) levels of CTGF were detected by western blot for cells used in tail-vein injection of NOD/SCID mice. Data represents CTGF expression for 3 xenograft experiments (homing, early and end stage disease). Anti-pan-actin was used as a loading control for cellular protein.

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The ability of human leukaemia cells to home to the BM, the primary site of BCP

ALL, was not affected by CTGF overexpression with PER-278 High having

0.006% and PER-278 Low cells having 0.004% infiltration of GFP+ cells (Figure

5.2b). Within 24 hours, PER-278 High and Low cells were also capable of

homing to spleen with 0.063% versus 0.021% infiltration, liver with 0.04%

versus 0.11% infiltration and lymph node with 0.12% versus 0.04% infiltration.

No discernible difference was observed between BM engraftment of PER-278

cells with High and Low CTGF expression at early or end stage disease (Fig

5.2c and 5.2d). A gradual increase in BM engraftment was discernible between

homing and end stage disease with the mean percentage of leukaemia cells

increasing from 0.005% at 24 hours to 0.3% at 3 weeks and 75% at end stage

disease (mean of 7 weeks). This rapid expansion of leukaemia engraftment

toward end stage disease reflects the progress of disease in patients and was

also noted in xenografted mice for the spleen, liver, lymph nodes and peripheral

blood (Figure 5.3b-e). End stage leukaemia engraftment was lower in the

extramedullary sites of haematopoiesis, reaching approximately 50% mean

engraftment in the spleen and 70% in the liver. In the lymph nodes differences

in leukaemia engraftment at end stage disease were detected with PER-278

High having 67.2% engraftment compared with 43.0% in PER-278 Low

xenografts (p=0.04; Figure 5.3d). This finding was an exception with CTGF

expression resulting in uniform engraftment in all other detected organs.

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Figure 5.2. PER-278 NOD/SCID xenografts showed no difference in survival or BM engraftment between High and Low injected cell lines.

5Mice were injected via the tail-vein with 2x10 PER-278 High or Low cells. a. Kaplan-Meier survival curve for PER-278 Low (dashed line) and PER-278 High xenografted mice (solid line). Data are expressed as the percent survival of mice against time (n=15). BM engraftment was determined for 3 times: b. homing at 24 hours post injection, c. early stage disease at 3 weeks and d.

+end stage disease. Data are expressed as the mean % GFP cells detected by flow cytometry (n=6-7, homing and early stage times, n=15, end stage from two separate experiments. Each dot represents an individual mouse). Vertical bars show standard error of the mean.

b. Homing (bone marrow)

c. Early stage (bone marrow) d. End stage (bone marrow)

a.

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Figure 5.3. Rapid engraftment of leukameia at end stage disease for PER-278 NOD/SCID xenografts. Leukaemia engraftment was analysed at

5three times (homing, early and end stage disease) after injection of 2x10PER-278 High (triangle) or Low cells (circle). a. Engraftment was determined in the in BM and in the extramedullary organs; b. spleen, c. liver and d. lymph nodes. e. Leukaemia burden in peripheral blood was also determined. Data

+are expressed as the mean % GFP cells detected by flow cytometry (n=6-7, homing and early stage times, n=15, end stage, from two separate experiments; student t-test: *, p<0.05). Vertical bars show standard error of the mean.

Spleenb. Liverc.

Bloode.Lymph nodesd.p=0.04

Bone marrowa.

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 126  

5.3.3 Response to single agent chemotherapy Experiments were performed to determine if CTGF overexpression in BCP ALL

cells played a role in drug sensitivity to single dose chemotherapy agents VCR

or ARAC. Chemotherapy treatment or saline were administered to PER-278

xenografts from day 25 post-injection, determined by the first mouse to display

1% engraftment in peripheral blood (Figure 5.4a). Kaplan-Meier survival plots

were constructed for both VCR and low dose ARAC chemotherapy protocols

(Figure 5.4b and 5.4c). Survival outcomes due to VCR treatment were

significantly higher compared with saline controls for both PER-278 Low (79

days versus 49 days survival, p=0.0003) and PER-278 High (77.5 days versus

49 days survival, p=0.004). Survival outcomes due to low dose ARAC were

significant for PER-278 Low xenografts, with 63 days versus 49 days survival in

control groups (p=0.003; Figure 5.3d). However, PER-278 High xenografts

while displaying a trend for prolonged survival due to drug treatment compared

with saline controls, did not reach significance with 59.5 days versus 49 days

survival (p=0.23; Figure 5.3e). Both PER-278 High and Low xenografts were

more sensitive to VCR, with longer survival times after the last chemotherapy

dose, than to low dose ARAC.

Treatment of PER-278 xenografted mice with a maximally tolerated dose of

ARAC (100mg/kg) found PER-278 Low cells responded with high sensitivity

and with minimal numbers succumbing to drug toxicity (1/7 mice). PER-278

High xenografts responded to treatment with reduced leukaemia engraftment

seen in the BM, however due to drug toxicity all mice (6/6) were unable to finish

two rounds of treatment (Supplementary Figure S1.1). This prevented a proper

comparison of high dose ARAC response between PER-278 High and Low cell

lines, though low BM engraftment of leukaemia cells at time of sacrifice

indicated they were sensitive to higher ARAC doses.

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Figure 5.4. Kaplan-Meier survival curve of PER-278 High and Low engrafted NOD/SCID xenografts treated with single agent chemotherapy

5Mice were injected via the tail-vein with 2x10 PER-278 High or Low cells. a. Percentage leukaemic engraftment in the peripheral blood determined treatment initiation at day 25 post-injection. b. PER-278 Low or c. PER-278 High xenografted mice were treated with saline (dashed line) or with 0.5 mg/kg VCR once a week for 4 weeks. d. PER-278 Low or e. PER-278 High xenografted mice were treated with saline (dashed line) or with 0.5 mg/kg ARAC, five times a week then left for 2 weeks before another 5 days of treatment. Grey arrows indicate first and last drug injection. Data are expressed as the percent survival of mice against time. (Saline treated, n=15 from two separate experiments. Chemotherapy treated, n= 5-6). (Log-Rank test: **, p<0.01, ***, p<0.001).

b. c.

d. e.

a.

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5.3.5 Snapshot of disease 24 hours post ARAC dose To further characterise the reduced sensitivity to low dose ARAC seen in PER-

278 High xenografts, a snapshot of ARAC response was taken. Prior to

establishing xenografts, CTGF expression in secreted protein was confirmed to

be upregulated in PER-278 High cells with a 3.14-fold greater expression than

PER-278 Low cells (Figure 5.5a). Mice were sacrificed 24 hours after a single

ARAC dose, administered within the ARAC protocol on the first day of the

second round of treatment. In addition to ARAC, BrdU (1mg) was delivered

intraperitoneally for detection of proliferation.

BM engraftment levels for both PER-278 High and Low xenografts were

reduced in the ARAC snapshot compared with end stage disease, confirming

suitable timing for measuring the effect of ARAC on an earlier stage of disease

progression. A trend was evident for increased engraftment in PER-278 Low

BM compared with PER-278 High, with 57.6% and 32.0% engraftment

(p=0.052; Figure 5.5b). The reduced mean BM engraftment seen in PER-278

High cells was partly a result of increased variation in engraftment between

mice, with the data suggesting only a sub-population of PER-278 High cells

contained reduced numbers of leukaemia cells in the BM.

Gating cells by flow cytometry that were positive for both BrdU and GFP

antibodies allowed detection of proliferating leukaemia cells within the whole

BM sample. In the BM population, PER-278 Low cells showed a trend for more

proliferating leukaemia cells compared with PER-278 High (p=0.13; Figure

5.5c). To account for the slight increase in the numbers of leukaemia cells

present in PER-278 Low compared with PER-278 High BM, proliferation was

assessed as a percentage of the GFP+ leukaemia cell sub-population within the

BM, consequently PER-278 High and Low xenografts were found to have a

similar mean percentage of proliferating cells (Figure 5.5d). Proliferation of

stromal cells was also comparable between PER-278 High and Low

xenografted mice, as defined by the BrdU+ GFP- population in the BM (Figure

5.5d). In summary, ARAC treatment produced no observable differences in the

proliferation of PER-278 xenografts.

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PER-

278

Low

PER-

278

High

CTGF (CM)

a. Bone marrowb.

Proliferating leukaemic cells

+ +(BRDU GFP )24hrs post ARAC dose

c.

Proliferating non-leukaemic cells -+(BRDU GFP )

24hrs post ARAC dose

d.

Figure 5.5.24 hours post ARAC dose.

1 mg BromodeoxyUridine (BrdU) and a. CTGF secreted protein levels in PER-278 Low and High cells before xenograft injection. b. Leukemia engraftment in the BM 24 hours post-ARAC dose. c. Percent of proliferating

+ +leukaemic (BRDU GFP ) cells in the BM and d. percent of proliferating cells + +(BRDU ) in the leukaemic sub-population (GFP ). e. Proliferation of non-

-+leukaemic cells (BRDU GFP ) in the BM population. Data are expressed as + +the mean % GFP or BRDU cells detected by flow cytometry (n=6-7, each

dot represents an individual mouse). Vertical bars show standard error of the mean.

Snapshot of proliferation in PER-278 NOD/SCID xenografts 5Mice were injected via the tail-vein with 2x10

PER-278 High or Low cells. When peripheral blood reached 1% engraftment mice were treated with ARAC, at 0.5 mg/kg for 5 days. After 2 weeks recovery mice received one dose of ARAC in addition to

were sacrificed 24 hours later.

Proliferating cells ) +(BRDUin leukaemic sub-population

e.

% B

one

mar

row

cells

% B

one

mar

row

cells

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 130  

Apoptotic leukaemia cells in the BM were measured by Annexin V+ GFP+ flow

cytometry. PER-278 Low xenografts were found to have a significantly greater

mean percentage of apoptotic leukaemic cells compared with PER-278 High

(p=0.039, Figure 5.6a). Again to account for the slight increase in leukaemia

cells in the BM of PER-278 Low xenografted mice, apoptosis was counted as a

percentage of the GFP+ leukaemic sub-population. A reverse in the trend for

apoptotic leukaemia cells was observed, with 6.0% of PER-278 High leukaemia

cells undergoing apoptosis compared with 3.9% in PER-278 Low leukaemia

cells (p=0.16; Figure 5.6b). The data suggests the existence of two separate

cell populations within PER-278 High leukaemia cells, with only a subset of cells

in PER-278 undergoing increased apoptosis (3/ 7 mice).

As no significant differences where observed in apoptosis 24 hours after ARAC

treatment, control mice were used to compare apoptosis levels. BM cells from

untreated PER-278 xenografts at end stage disease were used as a baseline

measure of apoptosis in leukaemia-engrafted mice. No significant difference

was found due to CTGF overexpression in the percentage of apoptotic

leukaemic cells or apoptotic stromal cells in the BM of PER-278 xenografts

(Figure 5.6c and 5.6d). In comparison to control mice, the ARAC snapshot

contained a higher population of stromal cells undergoing apoptosis than

leukaemic cells (6.6% leukaemic versus 0.44% stromal apoptotic cells,

p=0.0001; Figure 5.6). This reflects the non-specific cell targeting of ARAC,

further evidenced by stromal cells in the ARAC snapshot having higher levels of

apoptosis compared with untreated controls (6.6% ARAC versus 3.3% controls;

p= 0.02).

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Apoptotic cells in leukaemic sub-population

+(Annexin V )

Figure 5.6. 5 Mice were injected via the tail-vein with 2x10

PER-278 High or Low cells. When peripheral blood reached 1% engraftment mice were treated with ARAC, at 0.5 mg/kg for 5 days. After 2 weeks recovery mice received one dose of ARAC in addition to

were sacrificed 24 hours later.poptotic cells in the

leukaemic sub-population ( within the BM. c. Percent of a d. To evaluate post-ARAC

apoptosis levels, untreated PER-278 High and Low xenografted mice received saline and were sacrificed at end stage disease. Percent of apoptotic leukaemic cells apoptotic non-leukaemic cells Data are

++ expressed as the mean % GFP or Annexin cells detected by flow cytometry (n=6-7, ARAC treated mice, n=3-6, saline treated mice. Each dot represents an individual mouse). Vertical bars show standard error of the mean. (student t-test: *, p<0.05)

Snapshot of apoptosis in PER-278 NOD/SCID xenografts 24 hours post ARAC injection.

1 mg BromodeoxyUridine (BrdU) and a. Percent of apoptotic leukaemic

+ +cells in the BM (Annexin V GFP ). b. Percent of a+GFP ) poptotic non-

+ -leukaemic cells in the BM (Annexin V GFP ).

+ +(Annexin V GFP ) was detected and e. percent of + -(Annexin V GFP ) in the BM.

poptotic leukaemia cells+ + untreated (Annexin V GFP )

Ad. e.

a. Apoptotic leukaemia cells+ +ARAC snapshot (Annexin V GFP )

b.

p=0.039

Apoptotic non-leukaemic cells+ -ARAC snapshot (Annexin V GFP )

c.

% le

ukae

mia

cel

ls

Apoptotic non-leukaemic cells + - untreated (Annexin V GFP )

% B

one

mar

row

cells

% B

one

mar

row

cells

% B

one

mar

row

cells

% B

one

mar

row

cells

% L

euka

emia

cel

ls

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 132  

5.3.6 PER-278 Low cells could not be sensitized to ARAC by secreted proteins from BM co-cultures Experiments were performed in culture to ascertain if secreted products from

co-cultures of PER-278 and HS5 BM stromal cells could alter PER-278 Low cell

viability to ARAC. PER-278 Low cells were exposed to serial concentrations of

ARAC in the presence of conditioned media from either HS5 co-incubations

with PER-278 Low cells or co-incubations with PER-278 High cells. Conditioned

media was not successful in modifying PER-278 Low response to ARAC

(Figure 5.7a).

For ARAC to be activated it must cross the cellular membrane. To discover if

transfer of ARAC across the cell membrane could be altered in PER-278 High

xenografts, uptake of tritiated [3H]uridine was measured. Uptake of [3H] uridine

is measured over a much smaller time period than cell viability, 15 minutes

compared with 72 hours, and is therefore capable of detecting differences

missed after long incubation times. Uridine uses the same equilibrative

nucleoside transporter (ENT1) as ARAC, in addition to two other concentrative

nucleoside transporters. Therefore, changes seen in the uptake of [3H]uridine

indicate potential differences in ARAC uptake. However, no difference was

found in [3H]uridine uptake by PER-278 Low cells in the presence of secreted

proteins from stromal (HS5) cells co-incubated with rhCTGF or PER-278 High

cells compared with HS5 cells alone (Figure 5.7b).

Reduced sensitivity to low dose ARAC in PER-278 High xenografts was not

reproduced in PER-278 Low cells via the activity of secreted proteins produced

by stromal cells exposed to high CTGF levels.

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Figure 5.7. Reduced drug sensitivity to ARAC by PER-278 High cells was not replicated in presence of secreted proteins from stromal-leukaemia cell interactions. Secreted products in conditioned media were collected from HS5 stromal cells cultured with either PER-278 High cells, PER-278 Low cells or rhCTGF (100ng/ml) for 48 hours. a. Cell viability of PER-278 Low cells treated with ARAC was measured in the presence of HS5+PER-278 Low (open circle) or HS5+PER-278 High (closed circle) conditioned media (CM). Data are expressed as the mean % difference (treated vs untreated) in reduction of Alamar Blue (n=3). b. Nucleoside transporter activity, to determine uptake of ARAC, was measured in PER-278 Low cells after 15

3mins in the presence of [ H]Uridine with either normal media, media+rhCTGF, CM from HS5, HS5+CTGF or HS5+PER-278 High co-cultures. Data are expressed as the mean isotope count per minute (n=3). Vertical bars show standard error of the mean. (student t-test: *, p<0.05)

a.

b.

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5.4 Discussion The use of a maximum tolerated dose of ARAC in xenografted mice was

successful in prolonging survival regardless of CTGF expression levels,

therefore a low dose concentration of ARAC was used to increase the likelihood

of acquired drug resistance. The insights gleaned from this low dose resistance

then served to highlight the capability of CTGF to influence response to

chemotherapy drugs. Treatment with a low dose ARAC found increased

survival in PER-278 High compared with PER-278 Low xenografts. Follow up

experiments failed to find the responsible mechanism. Proliferation and

apoptosis were measured in the BM of PER-278 xenografted mice 24 hours

post ARAC treatment, PER-278 High xenografts revealed a trend for reduced

levels of apoptosis compared with PER-278 Low xenografted mice. Peak ARAC

activity is possibly not captured 24 hours post drug administration, with studies

in humans indicating that the plasma levels of ARAC after bolus injection peak

after 15 minutes and were undetectable by 6 hours after injection (Spriggs, et

al., 1985). Additionally, the use of male and female mice for time points and

initial survival experiments might present differences in proliferation and

apoptosis that are unrelated to leukaemia engraftment, although no differences

in survival were found between untreated PER-278 High and Low xenografts in

either mouse gender. Another factor that could mask CTGF effects is the timing

of ARAC delivery, with the possibility that CTGF has not established drug-

protective modifications to the microenvironment at the initiation of treatment.

Further experimental work is essential to clarify the significance of drug

resistance due to CTGF in a leukaemia xenograft model.

A significant finding that resulted form CTGF overexpression in PER-278

xenografted mice, involved the increased engraftment of leukaemia cells in the

lymph nodes of PER-278 High compared with PER-278 Low xenografts.

Increased lymph node metastases due to CTGF have been previously reported

in gastric, breast and pancreatic cancer (Dornhofer, et al., 2006; Liu, et al.,

2008; Xie, et al., 2001). The current NOD/SCID xenograft model fails to address

whether leukaemia cells in the lymph node are a population expanded from

time of tail-vein injection or a case of true metastasis from BM-originating

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  135  

leukaemia cells. The clinical impact of higher lymph node engraftment in BCP

ALL due to CTGF expression requires further validation.

The homing process is a response to long distance adhesion and migration

cues usually delivered by circulating cytokines. In the xenograft mouse model,

systemic delivery of leukaemic cells via the tail-vein of NOD/SCID mice allows

for leukaemia-driven positioning within the BM in response to interactions with

the relevant cytokines and chemotactic signals. PER-278 High and Low

NOD/SCID xenografts were found to have equivalent levels of homing to the

BM, spleen and liver after 24 hours, indicating that CTGF played no role in

influencing leukaemia cell systemic migration. In the present study, homing was

assessed by flow cytometry, as the technique allows a higher sample rate and

robust antibodies compared with immunohistochemical methods. However, the

geography of leukaemia cells is not assessed and the leukaemia cell niche

within the BM has been indicated as important for perturbing normal HSC

function (Schepers, et al., 2013a). Progression of leukaemia cells from homing

to early and end stage disease was comparable between PER-278 High and

Low xenografted mice. While this indicates CTGF does not play a role in

expansion of leukaemia cells in PER-278 cells, it also provides an unbiased

baseline to test for differences in response to chemotherapy drugs. Survival and

drug response findings highlight that PER-278 mouse xenografts responded in

a unique fashion to CTGF overexpression compared with PER-371 xenografted

mice, which are discussed in Chapter 6.

PER-278 xenografts showed no difference in homing, disease progression or

overall survival between CTGF High and Low expressing cell lines.

Overexpression of CTGF in PER-278 xenografts resulted in significantly greater

peripheral lymph node engraftment at end stage disease, though this did not

modify survival outcomes. Inreased CTGF reduced sensitivity to low dose

chemotherapy in PER-278 xenografts. The mechanism of drug resistance

remains to be determined with repeated in vivo modelling needed. These

results provide new evidence in BCP ALL that CTGF exists as functionally

active protein within the context of the BM microenvironment and could

influence drug resistance in the clinical setting.

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666666666CTGF confers a growth advantage

to PER-371 B-precursor ALL cells in the BM microenvironment

We shall not cease from explorationAnd the end of all our exploring

Will be to arrive where we startedAnd know the place for the first time.

T.S. Eliot

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Chapter 6 CTGF confers a growth advantage to

PER-371 B cell-precursor ALL cells in the BM microenvironment

 

6.1 Abstract B cell-precursor (BCP) ALL is a cancer of genetic mutations. Initial

chromosomal rearrangements in the disease have been well defined however

the additional mutations required to initiate malignancy are still not clearly

understood. Recent studies indicate that at diagnosis the primary leukaemia

contains a multitude of sub-clones with distinct DNA mutations. In BCP ALL, the

most deregulated gene was identified as CTGF through microarray studies of

primary patient specimens. Overexpression of CTGF in BCP ALL was

associated with poor outcome in patients identified as high-risk at diagnosis.

Functionally defining the role of CTGF in BCP ALL is vital in order to expand on

and discover mechanisms of action relevant to patient outcomes in the disease.

To define a functional role for CTGF in BCP ALL, NOD/SCID xenograft mouse

models were established using a primary patient-derived cell line, PER-371,

engineered to overexpress CTGF. Leukaemia cell expansion, survival and

response to ARAC chemotherapy were analysed with respect to High and Low

CTGF expression. CTGF was not found to alter drug response to ARAC or

affect early leukaemia engraftment in xenografts with this cell line. However,

increased BM engraftment at late stage disease was found in PER-371 CTGF

High xenografted mice with significant difference in the percentage of

leukaemia cells compared with CTGF Low controls (43.7% versus 6.3%,

p=0.01). This differential engraftment at late stage correlated with a more

aggressive disease, as a significant reduction in overall survival was seen in

PER-371 CTGF High compared with CTGF Low xenografted mice (89 versus

70 days post-injection, p=0.01). The mechanism by which CTGF

overexpression led to more aggressive disease in PER-371 xenografts were

due to the influence of CTGF on stromal-leukaemia cell interactions. High

CTGF caused increased stromal cell proliferation at early stage disease,

increased reticulin fibre deposition at late stage disease and altered secretion of

proteins that are associated with ECM remodelling. This study defines a new

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functional role for CTGF in BCP ALL, working indirectly through BM

microenvironment interactions to enable enhanced disease progression.

6.2 Introduction Childhood BCP ALL results from two or more cytogenetic ‘hits’ that occur in

normal B-cell progenitors, resulting in arrested development at the BCP cell

state. The initial genetic mutations have been well defined for the major sub-

types and appear to originate largely from a pre-natal period. However, the

additional essential genetic alterations required for the pre-leukaemic cell to

become malignant are not well defined. Genomic profiling of patients at

diagnosis has revealed a multitude of sub-clone populations within the ‘bulk’

leukaemia cell mass (Mullighan, 2013). This indicates that early leukaemic

progenitors frequently produce genetically divergent daughter cells.

In BCP ALL, the CTGF gene was 19-fold overexpressed compared with CD45+

haematopoietic progenitor cells (Boag, et al., 2007). Overexpression of CTGF

was found in 75% of BCP ALL paediatric cases and associated with a gene

subset indicative of poor outcome in patients identified as high-risk at diagnosis

(Kang, et al., 2010). Identification of a functional mechanism, whereby CTGF

could influence disease outcome in BCP ALL, has not yet occurred.

The current study investigates a functional role for CTGF in BCP ALL using the

cell line PER-371, which has previously been found to strongly resemble the

disease characteristics of the primary patient sample (see section 3.3). For the

purposes of detecting differences attributable to higher CTGF expression,

lentiviral technology was used to establish two PER-371 cell populations, CTGF

High and Low (see section 2.2.5-7). In chapter 5, a potential role for the PER-

278 cell line in reduced sensitivity to low-dose ARAC was explored. Despite

many common characteristics between PER-278 and PER-371, mouse

xenograft models revealed pronounced differences in phenotype. For this

reason the two cell lines have been presented separately to highlight their

distinct outcomes, however a consistent approach in methodology and

experimental outline were followed between the two chapters.

NOD/SCID mice were inoculated with 1x106 PER-371 High or Low cells via tail-

vein injection (see section 2.7.2). The effect of high CTGF expression in PER-

371 xenografts was assessed at four times; at homing, early and late

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tumourigenesis and end stage disease, which included the leukaemic cell

response to low-dose ARAC. Differences in survival outcomes of PER-371

xenografts due to increased CTGF expression were investigated further to

decipher essential mechanisms. Mechanistic studies included proliferation

assays and apoptosis assays in vivo. Complementary immunostaining of BM

sections to characterise megakaryocytes, reticulin fibre deposition, leukaemia

and proliferating cells was also carried out. Lastly, identification of modified

secreted proteins was performed using conditioned media from co-culture of

PER-371 CTGF High cells with HS5 stromal cells.

6.3 Results 6.3.1 CTGF overexpression in cells used for PER-371 xenografts Overexpression of CTGF in conditioned media of PER-371 High cells was

confirmed by western blot before tail-vein injection of NOD/SCID mice (Figure

6.1). Fold change differences in CTGF expression between PER-371 High and

PER-371 Low cells were interpreted for RNA and conditioned media (Table

6.1). Conditioned media overexpression was between more than 11.8 and 26.5-

fold higher in PER-371 High cells compared with Low, which is greater than the

originally detected levels after lentiviral transduction. Differences in secreted

media for CTGF expression are likely due to the scant and therefore variable

detection of PER-371 Low CTGF in western bands from conditioned medium.

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PER-371 High/LowHoming (24hrs)

PER-371 High/LowLate disease (Wk11)

PER-371 High/LowEarly disease (Wk3)

PER-371 High/LowEnd stage disease

1.06

1.59

1.06

1.66

RNA (qRT-PCR)

11.81

26.46

26.46

Fold Change Secreted protein (western)

13.47

Table 6.1. 6before injection of 1x10 cells into the tail vein of NOD/SCID mice. CTGF

RNA expression was detected by qRT-PCR and secreted protein levels by densitometry on western blot bands. Leukaemia engraftment was analysed at 4 times (homing, early, late and end stage disease).

Fold change difference between PER-371 High and Low cells

PER-

371

Low

CTGF (CM)

PER-

371

Low

PER-

371

High

PER-

371

High

PER-

371

Low

PER-

371

High

Hom

ing

at

e st

age

Early

&

l E

nd s

tage

Figure 6.1. and Low cells intended for NOD/SCID inoculation. Secreted protein from PER-371 High and Low conditioned media (CM) was detected by western blot

6prior to injection of 1x10 cells into the tail vein of NOD/SCID mice. Leukaemia engraftment was analysed at 4 times (homing, early , late and end stage disease).

CTGF secreted protein expression levels for PER-371 High

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6.3.2 Survival outcomes and response to single agent chemotherapy Survival studies of PER-371 xenografts found PER-371 High cells resulted in a

more aggressive disease with a significantly reduced median survival, 89 days

post-injection, compared with 70 days in PER-371 Low xenografts (p=0.01;

Figure 6.2a). This shows CTGF was capable of accelerating leukaemic growth

in PER-371 xenografted mice.

To characterise chemotherapy response, PER-371 xenografted mice were

started on a low dose ARAC treatment protocol from day 40, after the first

mouse reached 1% engraftment in peripheral blood. Low-dose ARAC treatment

significantly extended survival in PER-371 High xenografted mice, to 84.5 days

compared with 70 days survival in saline controls (p=0.004; Figure 6.2b).

Surprisingly, PER-371 Low xenografted mice treated with low-dose ARAC

showed no difference in survival compared with controls, with 82 days for ARAC

treatment versus 89 days survival for saline controls (p=0.11; Figure 6.2c). As

survival curves for both groups of ARAC treated xenograft mice found they

succumbed to disease in a similar time frame post ARAC treatment, significant

differences in survival between treated and untreated groups is a consequence

of differential survival in the untreated mice. As reduced median survival in

untreated PER-371 High xenografted mice showed a distinct separation in

timing with the last ARAC injection and the increased median survival in

untreated PER-371 Low xenografted mice overlapped with the end of ARAC

treatment. Additionally, both PER-371 High and Low xenografted mice

responded with high sensitivity to high-dose ARAC with little toxicity

(Supplementary Figure S1). Collectively, PER-371 cells were found to have no

difference in response to ARAC due to CTGF expression.

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Figure 6.3. PER-371 NOD/SCID xenografts showed increased BM engraftment in CTGF High compared to Low cells at late stage disease.

6Mice were injected via the tail-vein with 1x10 PER-371 High and Low cells. Bone marrow engraftment was determined at 4 times: a. homing at 16 hours post injection, b. early stage disease at 8 weeks, c. late stage disease at 10

+weeks and d. end stage disease. Data are expressed as the mean % GFP cells detected by flow cytometry (n=6-7, homing, early and late stage times, n=11-12, end stage. Each dot represents an individual mouse). Vertical bars show standard error of the mean. (student t-test: *, p<0.05).

b.a.

c. d.

Homing (bone marrow) Early stage (bone marrow)

Late stage (bone marrow) End stage (bone marrow)

p=0.01

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6.3.3 Organ engraftment throughout spread of leukaemia The percentage of engrafted leukaemia cells in the BM and extramedullary

organs was assessed at four times after injection. Homing of cells to the BM

was assessed at 16 hours, early stage disease at 3 weeks, late stage disease

at 11 weeks and end stage disease, when mice were sacrificed due to clinical

presentation of leukaemia.

In the BM, the primary site of leukaemogenesis, CTGF had no effect on

homing, with no difference in infiltration of leukaemia cells between CTGF High

and Low groups (Figure 6.3a). At early stage disease a trend for higher BM

engraftment was seen for PER-371 High compared with Low xenografted mice

and by late stage disease mean engraftment between the two groups was

significantly different, with 43.7% engraftment in High and 7.6% engraftment in

Low xenografted mice (p=0.01; Figure 6.3b and 6.3c). At late stage disease a

similar trend for increased engraftment of PER-371 High cells compared with

PER-371 Low is evident in the spleen, liver, lymph nodes and blood (Figure

6.4). Leukaemia engraftment in the BM at end stage disease, which is an

independent time for each group, returned to comparable levels of engraftment,

with 65.6% in PER-371 High and 76.7% in PER-371 Low xenografted mice

(Figure 6.3d). In the BM, increased leukaemia engraftment due to CTGF were

found from early stage disease with the separation between High and Low

CTGF-expressing cells most significant at late stage disease.

PER-371 cells were capable of early homing to the BM, with both PER-371

High and Low cells detectable at 16 hours post tail-vein injection, with a mean

of 0.005% and 0.002% GFP+ cells, respectively (Figure 6.3a). The only other

organ with detectable infiltration of GFP+ cells at 16 hours was the spleen, with

0.003% in both CTGF High and Low xenografted mice (Figure 6.4b). For all

examined organs, the overall percentage of leukaemia cells detected at early

stage disease was increased compared with 16 hours post injection regardless

of CTGF expression (Figure 6.4). The overall percentage of leukaemic cells

were found to increase again at late stage disease and reached a peak at end

stage disease engraftment. Across both xenograft groups slower early

leukaemic growth was followed by rapid expansion near end stage disease.

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Figure 6.2. engrafted NOD/SCID xenografts treated with chemotherapy drugs or saline. a. PER-371 Low (dashed line) and PER-371 High xenografted mice (solid line) were untreated and injected only with 0.9% saline on the same days as chemotherapy treated mice. Percentage leukaemic engraftment in the peripheral blood determined treatment initiation with ARAC at day 40 post-injection with low dose ARAC (0.5 mg/kg), five times a week then 2 weeks recovery before another 5 days of injections or treated with saline (dashed line) for b. PER-371 High and c. PER-371 Low xenografted mice. Grey arrows indicate first and last ARAC injection. Data are expressed as the percent survival of mice against time. (saline treated, n=11-12, chemotherapy treated treated, n= 5-6). (Log-Rank test: **, p<0.01, ***, p<0.001).

Kaplan-Meier survival curve of PER-371 High and Low

c.

a.

b.

a.

50

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Figure 6.4. PER-371 NOD/SCID xenografts. Leukaemia engraftment was analysed at 4

6 times (homing, early, late and end stage disease) after injection of 1x10PER-371 High (triangle) or Low cells (circle). a. Engraftment in BM. Engraftment in the extramedullary organs: b. spleen, c. liver and d. lymph nodes. e. Leukaemia burden in peripheral blood was also determined. Data

+are expressed as the mean % GFP cells detected by flow cytometry (n=6-7, homing, early and late stage times, n=11-12, end stage. Each dot represents an individual mouse). Vertical bars show standard error of the mean. (student t-test: *, p<0.05).

Rapid engraftment of leukaemia at end stage disease for

BloodLymph nodes

Bone marrow Spleen

Liver

b.a.

c.

d. e.

p=0.04

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 148

6.3.4 Snapshot of proliferation and apoptosis at late stage disease To understand differences seen in BM engraftment at late stage disease

proliferation (detected 24 hours after BrdU injection) and apoptosis (detected by

Annexin V labelling) were measured in xenograft BM cells by flow cytometry.

When assessed as a proportion of total BM, there was a trend for higher

proliferation of leukaemic cells (mean BrdU+ GFP+) in PER-371 High

xenografted mice (2.3%) compared with Low (0.22%), although this did not

reach statistical significance (p=0.10; Figure 6.5a). As there were more PER-

371 High cells overall in the BM, we assessed the number of proliferating cells

as a proportion of leukaemic cells. As a percentage of leukaemic cells, the trend

for higher levels of proliferation in PER-371 High xenografted mice is less

pronounced (Figure 6.5b). The number of proliferating non-leukaemic cells in

the BM was found to be comparable between CTGF High and Low xenografted

mice, with 2.9% and 2.2% mean BrdU+ GFP- cells respectively (Figure 6.5c).

Overall no discernible differences in proliferation were found due to CTGF

expression from PER-371 cells.

Apoptosis was then measured at late stage disease in the whole BM of

xenografted mice. When measured as a proportion of total BM cells, there were

significantly more apoptotic leukaemia cells in PER-371 High xenografted mice

with a mean of 0.67% compared with PER-371 Low xenografted mice, with a

mean of 0.3% of BM cells (p=0.04; Figure 6.5d). To account for the differences

in overall leukaemic cell numbers, apoptotic cells were measured as a

proportion of the leukaemic cell sub-population in the BM. When analysed in

this way, there was a trend for decreased apoptosis in the leukaemic

subpopulation of PER-371 High xenografted mice compared with Low, with a

mean of 16% and 37% apoptotic cells respectively (p=0.12; Figure 6.5e). The

percentage of Annexin+ GFP- non-leukaemic apoptotic cells in the BM, was

similar between groups (Figure 6.5f). Overall a small trend for decreased

apoptosis in the BM of PER-371 High compared with PER-371 Low xenografted

mice was found at late stage disease.

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a.b.

Prol

ifera

ting

leuk

aem

ic ce

lls+

+ in

the

BM (

BRDU

GFP

)

Apo

ptot

ic le

ukae

mic

cells

++

in th

e BM

(Ann

exin

GFP

)Ap

opto

tic n

on-le

ukae

mic

cells -

+

(Ann

exin

GFP

)in

the

BM

Pro

lifera

ting

non-

leuk

aem

ic ce

lls-

+

(BRD

U G

FP)

in th

e BM

c.

d.

Pr

olife

ratin

g ce

lls

in le

ukae

mic

sub-

popu

latio

n

+(B

rdU

)

Apop

totic

cel

ls in

leuk

aem

ic su

b-po

pula

tion

+ (A

nnex

in)

p=0.

044

e.f.

% Bone marrow cells % Bone marrow cells

% Bone marrow cells

% Bone marrow cells% Bone marrow cells

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Figure 6.5. Snapshot of proliferation and apoptosis in PER-371 cells at late stage disease.

6 disease, 11 weeks after injection of 1x10 PER-371 High (square) or Low cells (circle) onto NOD/SCID mice. a.

d.

f. Data are expressed as the mean %

+ + + GFP , Annexin or BRDU cells detected by flow cytometry (n=6-7, each dot represents an individual mouse). Vertical bars show standard error of the mean. (student t-test: *, p<0.05)

Leukaemia engraftment was analysed at late stage

Percentage of proliferating leukaemic + +cells (BRDU GFP ) in the BM and b. percentage of proliferating cells

+ +(BRDU ) in the leukaemic sub-population (GFP ) within the BM. c. + -Percentage of proliferating non-leukaemic cells (BRDU GFP ) in the BM.

+ +Percentage of apoptotic leukaemic cells (Annexin GFP ) in the BM and e. +percentage of apoptotic cells (Annexin ) in the leukaemic sub-population

+(GFP ) within the BM. Percentage of apoptotic non-leukaemic cells + -(BRDU GFP ) in the bone marrow.

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6.3.5 Immunohistochemistry on BM sections of PER-371 xenografted mice Bone marrow sections from PER-371 Low and High xenografted mice were

immunohistochemically stained for detection of leukaemia cells, with an anti-

Pax5 antibody, proliferating cells, with an anti-Ki67 antibody and

megakaryocytes, with an anti-VwF antibody. Additionally, an Ag+ stain was

performed to identify reticulin fibres within the BM. Multispectral imaging of both

the diaphysis and epiphysis/metaphysis of the mouse femur and tibia was

obtained before analyses of positive staining by calculating the percentage of

antibody-stained cells in the BM compared with haematoxylin-stained nuclei.

Pax5+ immunostaining detecting leukaemia cells

Leukaemia cell detection by IHC allowed analysis of the location and proximity

of tumour cells. In the diaphysis, leukaemia cells were more commonly found as

a mass of cells than dispersed freely (Figure 6.6b). Whereas, in the epiphysis

and metaphysis leukaemia cells were found as small populations of cells that

were more dispersed throughout the space (Figure 6.7b). At early stage

disease, the first detectable groups of Pax5+ cells were more commonly found

proximal to the epiphyseal plate in the metaphysis and sometimes epiphysis.

Differences in leukaemic engraftment due to CTGF were found at late stage

disease with a greater percentage of Pax5+ cells found in the diaphysis of PER-

371 High compared with PER-371 Low BM sections, with a mean of 56% and

10% Pax5+ cells, respectively (p=0.008; Figure 6.6a). Whereas, at early and

end stage disease in the diaphysis there was no significant difference between

the mean percentage of Pax5+ cells in PER-371 High compared with PER-371

Low xenografted mice. The epiphysis and metaphysis revealed similar findings

as the diaphysis in the BM with an increased mean percentage of Pax5+ cells

found in PER-371 High (with 60%) compared with PER-371 Low xenografted

mice (with 24%) at late stage disease (p=0.01; Figure 6.71a). A trend was found

at early stage disease in the epiphysis and metaphysis, with double the average

number of Pax5+ cells in PER-371 High compared with Low xenografted mice

which did not reach significance. At both early and end stage disease was there

no significant difference in the percentage of Pax5+ cells between the two

groups, therefore CTGF was found to significantly influence the engraftment

level of Pax5+ leukaemic cells specifically at late stage disease in the BM.

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 152

Ki67+ immunostaining detecting proliferating cells

To determine if leukaemia cells were the predominant cell type undergoing

proliferation, Ki67+ staining was performed. No pattern was evident for Ki67+

staining in the BM, instead large numbers of Ki67+ proliferating cells were found

throughout the diaphysis, epiphysis and metaphysis at all stages of disease

progression (Figure 6.8b and 6.9b). At early stage disease, a greater

percentage of Ki67+ cells were found in PER-371 High compared with PER-371

Low BM sections in the diaphysis (p=0.02) and epiphysis/metaphysis (p=0.03;

Figure 6.8a and 6.9a). Whereas at late and end stage disease there there was

a similar population of Ki67+ cells between the two groups. Increased Ki67+ cells

in PER-371 High compared with PER-371 Low xenografted mice at early stage

disease preceded the difference found in Pax5+ cells at late stage disease.

VwF+ immunostaining detecting megakaryocytes

To investigate the influence of the immune presence in NOD/SCID mice, VwF+

staining was performed detecting megakaryocytes. Megakaryocytes were

present throughout the BM with distinctive VwF+ staining, blood vessels were

also detected with the VwF antibody, but the specificity for endothelial cells was

not sufficient for use in quantification (Figure 6.10b). Megakaryocytes were

primarily associated with a vascular morphology. The average number of

megakaryocytes was assessed across the entire BM space and not segregated

into diaphysis and epiphysis/metaphysis. PER-371 High and PER-371 Low

xenografted mice contained comparable counts of megakaryocytes in the BM

(Figure 6.10a). The highest number of megakaryocytes was found at early

stage disease and decreasing populations were detected at late and end stage

disease. The lowest number of megakaryocytes at end stage resulted in a 13-

fold reduced cell count for PER-371 High and a 3-fold reduced cell count for

PER-371 Low xenografted mice when compared with early stage disease. At

late stage disease, differential populations of megakaryocytes were found, with

a higher count in PER-371 Low compared with PER-371 High BM sections (p=

0.004; Figure 6.10a). Overall, megakaryocytes were found to decrease in

number across the BM as the leukaemia stage progressed, with high CTGF

expression from PER-371 cells resulting in reduced megakaryocyte numbers at

late stage disease.

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b.

a.

Pax5PER-371 HighPER-371 Low

Early stage disease

PER-371 Low PER-371 HighLate stage disease

PER-371 Low PER-371 HighEnd stage disease

Diaphysis

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Figure 6.66marrow. Mice were injected via the tail-vein with 1x10 PER-371 High and

Low cells. At 10 weeks mice were sacrificed and bone marrows were fixed in paraformaldehyde for 48 hours and later decalcified in 10% EDTA for 7 days and embedded in paraffin wax for immunohistochemistry. a. Leukaemic cells in the diaphysis, detected by immunohistochemistry with a paired box 5 antibody (Pax5, 1:100 dilution). Data are expressed as % positively stained nuclei (n=6-7, early and late stage. n=5, end stage.) Vertical bars represent standard error of the mean. b. Representative diaphysis sections of PER-371 Low and High at early, late and end stage time points. Scale bar represents 500mm.

. Leukemic-burden in diaphysis of PER-371 engrafted bone

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b.

a.

Pax5PER-371 HighPER-371 Low

Early stage disease

PER-371 Low PER-371 HighLate stage disease

PER-371 Low PER-371 HighEnd stage disease

Epiphysis/ Metaphysis

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Figure 6.7. Leukemic-burden in epiphysis/metaphysis of PER-371 6engrafted bone marrow. Mice were injected via the tail-vein with 1x10 PER-

371 High and Low cells. At 10 weeks mice were sacrificed and bone marrows were fixed in paraformaldehyde for 48 hours and later decalcified in 10% EDTA for 7 days and embedded in paraffin wax for immunohistochemistry. a. Leukaemic cells in the epiphysis/metaphysis, detected by immunohistochemistry with a paired box 5 antibody (Pax5, 1:100 dilution). Data are expressed as % positively stained nuclei (n=6-7, early and late stage. n=5, end stage.) Vertical bars represent standard error of the mean. b. Representative epiphysis/metaphysis sections of PER-371 Low and High at early, late and end stage time points. Scale bar represents 500mm.

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b.

a.

Ki67

PER-371 HighPER-371 LowEarly stage disease

PER-371 Low PER-371 HighLate stage disease

PER-371 Low PER-371 HighEnd stage disease

Diaphysis

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Figure 6.86burdened bone marrow. Mice were injected via the tail-vein with 1x10 PER-

371 High and Low cells. At 10 weeks mice were sacrificed and bone marrows were fixed in paraformaldehyde for 48 hours and later decalcified in 10% EDTA for 7 days and embedded in paraffin wax for immunohistochemistry. a. Proliferating cells in the diaphysis, detected by immunohistochemistry with a Ki67 antibody (1:100 dilution). Data are expressed as % positively stained nuclei (n=6-7, early and late stage. n=5, end stage.) Vertical bars represent standard error of the mean. b. Representative diaphysis sections of PER-371 Low and High at early, late and end stage time points. Scale bar represents 500mm.

. Proliferating cells in diaphysis of PER-371 leukaemia-

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b.

a.

Ki67PER-371 High

PER-371 Low PER-371 High

PER-371 Low

Late stage disease

Early stage disease

PER-371 Low PER-371 HighEnd stage disease

Epiphysis/ Metaphysis

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Figure 6.9leukaemia-burdened bone marrow. Mice were injected via the tail-vein with

61x10 PER-371 High and Low cells. At 10 weeks mice were sacrificed and bone marrows were fixed in paraformaldehyde for 48 hours and later decalcified in 10% EDTA for 7 days and embedded in paraffin wax for immunohistochemistry. a. Proliferating cells in the epiphysis/metaphysis, detected by immunohistochemistry with a Ki67 antibody (1:100 dilution). Data are expressed as % positively stained nuclei (n=6-7, early and late stage. n=5, end stage.) Vertical bars represent standard error of the mean. b. Representative epiphysis/metaphysis sections of PER-371 Low and High at early, late and end stage time points. Scale bar represents 500mm.

. Proliferating cells in epiphysis/metaphysis of PER-371

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a.

VwFPER-371 HighPER-371 Low

Early stage diseaseb.

PER-371 Low PER-371 HighLate stage disease

PER-371 Low PER-371 HighEnd stage disease

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Figure 6.10. Megakaryocyte count in6burdened bone marrow. Mice were injected via the tail-vein with 1x10 PER-

371 High and Low cells. At 10 weeks mice were sacrificed and bone marrows were fixed in paraformaldehyde for 48 hours and later decalcified in 10% EDTA for 7 days and embedded in paraffin wax for immunohistochemistry. a. Megakaryocyte count, detected by immunohistochemistry with a von Willebrand factor antibody (VwF, 1:400 dilution) in the BM. Data are expressed as average number megakaryocytes per BM (sum for 6 images). (n=6-7, early and late stage. n=5, end stage.) Vertical bars represent standard error of the mean. b. Representative BM sections of PER-371 Low and High at early, late and end stage time points. Scale bar represents 500mm. VwF is a positive stain for endothelial cells (open arrow) and megakaryocytes (filled arrow).

diaphysis of PER-371 leukaemia-

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Ag+ stain for reticulin fibres

In response to the findings of chapter 4, where human HS5 cells were found to

secrete ECM remodelling genes due to CTGF treatment, the location and

density of reticulin connective tissue was analysed by Ag+ staining. Reticulin

fibre deposition was scored on early and late stage BM sections. Fine reticular

fibres in normal BM sections were associated with blood vessels and dense

reticulin fibre networks were most often associated with the endosteum (Figure

6.11b and 6.12b). At early stage disease, increased reticulin deposition was

found in PER-371 High BM compared with PER-371 Low for both diaphysis

(Figure 6.11a) and epiphysis/metaphysis (Figure 6.12a) although this did not

reach statistical significance. In late stage disease, the same trend remained

with the average reticulin score found to be significantly higher in PER-371 High

BM compared with PER-371 Low (p=0.04; Figure 6.11a). Reticulin connective

tissue was found to be more abundant and with thicker fibre density in PER-371

High compared with PER-371 Low xenografted mice at late stage disease.

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a.

Ag stain

PER-371 HighPER-371 LowEarly stage disease

b.

PER-371 Low PER-371 HighLate stage disease

Diaphysis

Figure 6.11. Reticulin connective tissue density in diaphysis of PER-371 leukaemia-burdened bone marrow. Mice were injected via the tail-vein with

61x10 PER-371 High and Low cells. At 10 weeks mice were sacrificed and bone marrows were fixed in paraformaldehyde for 48 hours and later decalcified in 10% EDTA for 7 days and embedded in paraffin wax for immunohistochemistry. a. Reticulin connective tissue density, scored by an Ag stain of the diaphysis. Data represents average reticulin score per mouse (n=6-7, early and late stage. n=4-5, end stage.) Vertical bars represent standard error of the mean. b. Representative diaphysis sections Ag stained for PER-371 Low and High at early and late stage time points. Ag detects reticulin fibres (open arrow). Scale bar represents 500mm.

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a.

Ag stain

PER-371 HighPER-371 LowEarly stage disease

b.

PER-371 Low PER-371 HighLate stage disease

Epiphysis/ Metaphysis

Figure 6.12. Reticulin connective tissue density in epiphysis/ metaphysis of PER-371 leukaemia-burdened bone marrow. Mice were

6injected via the tail-vein with 1x10 PER-371 High and Low cells. At 10 weeks mice were sacrificed and bone marrows were fixed in paraformaldehyde for 48 hours and later decalcified in 10% EDTA for 7 days and embedded in paraffin wax for immunohistochemistry. a. Reticulin connective tissue density, scored by an Ag stain of the epiphysis/ metaphysis. Data represents average reticulin score per mouse (n=6-7, early and late stage. n=4-5, end stage.) Vertical bars represent standard error of the mean. b. Representative epiphysis/ metaphysis sections Ag stained for PER-371 Low and High at early and late stage time points. Ag detects reticulin fibres (open arrow). Scale bar represents 500mm.

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 166

Correlation between the immunohistochemical and histochemical detection of

cells within the BM

An invading leukaemia front present in a PER-371 High BM diaphysis at early

stage disease illustrates the various BM cell components in relation to each

other (Figure 6.13a). Clear overlap was seen in Ki67+ and Pax5+ staining and

an inverse relationship existed between the location of Pax5+ staining and VwF+

megakaryocytes. Reticulin connective tissue was densely deposited with thick

processes at the site of increased Pax5+ leukaemic cells and abundant fibres

also present in the BM space adjacent to the leukaemia cell front. To determine

if the patterns between Pax5 expression and Ki67, VwF expression and Ag

staining were not due to chance the Pearson’s correlation coefficient was

calculated for the immunohistochemical outcomes presented in Figures 6.6 to

6.12.

The Pearson’s correlation coefficient was used to determine if a relationship

existed among the immunohistochemical stains for PER-371 High and Low

xenografted mice across early and late stage leukaemia engraftment (Figure

6.13b). Confidence in the correlation coefficient (r value) was determined from

the r value and sample size at two alpha levels, p<0.05 and p<0.01. Across all

investigated histochemical staining relationships, PER-371 Low cells were more

commonly linked to the expression of other cell types at early stage disease,

where the opposite was true for PER371 High cells, which showed greater

significant relationships at late stage disease. Pax5+ leukemia cells were found

to have a strong linear relationship with Ki67+ proliferating cells at late

compared with early stage disease for both PER-371 High and Low xenograft

mice, with the exception of PER-371 Low engrafted cells in the diaphysis. An

inverse relationship existed between Pax5+ leukemia cells and VwF+

megakaryocytes at both stages of disease progression. Surprisingly, the

inverse relationship between Pax5+ and VwF+ expression levels was significant

for PER-371 Low xenografted mice at early stage disease (r= -0.8 in the

diaphysis and -0.74 in the epiphysis/ metaphysis) and for PER-371 High

xenografted mice at late stage disease (r= -0.81 in the diaphysis and -0.85 in

the epiphysis/ metaphysis). CTGF was found to influence the relationship

between reticulin score and percentage of Pax5+ leukemic cells at late stage

disease in the diaphysis. In PER-371 High BM sections there was a strong

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Figure 6.13associations significant by Pearson's correlation coefficient.

6a. Representative images from a mouse injected via the tail-vein with 1x10 PER-371 High cells and sacrificed after 3 weeks (early stage disease). BM femur and tibia were fixed in paraformaldehyde for 48 hours and later decalcified in 10% EDTA for 7 days before embedding in paraffin wax for immunostaining. Sections 4 mm thick, from the diaphysis were stained for leukaemia cells (Pax5 antibody, 1:100 dilution), proliferating cells (Ki67 antibody, 1:100 dilution), megakaryocytes (VwF antibody, 1:400 dilution) and reticulin fibers (Ag stain). Sections are at equivalent locations within the BM, with no more than 40 mm between images in the z-stack orientation. Scale bar represents 500mm. b. Pearson's correlation coefficient between Pax5 and Ki67, VwF and Ag staining immunostaining for PER-371 High and Low xenografts in the diaphysis (DIA) and epyphysis/ metaphysis (EP/ME) for both early and late stage disease. Data is expressed as correlation coefficient values (r) with red text indicating p<0.01 and blue text indicating p<0.05.

. Invading leukaemia front depicts immunostaining

Pax5

Ag stain

Ki67

VwF

Early stage disease

Late stage disease

Pearson's correlation coefficient

+ +Pax 5 and Ag0.91

PER-371 cell line

CTGF High

+ +Pax 5 and Ki67

+ +Pax 5 and VwF

0.32

-0.45

CTGF High

CTGF High

DIA

0.75

0.39

-0.52

EP/ME

0.92

0.89

-0.81

DIA

0.53

0.93

-0.85

EP/ME

-0.76 CTGF Low-0.47 -0.13 0.97

-0.80 CTGF Low-0.74 -0.65 -0.25

0.82 CTGF Low0.95 + no Agscore 0.29

a.

b.

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 168

linear correlation between reticulin score and Pax5+ staining (r=0.92), in

contrast to PER-371 Low BM sections where no coefficient could be measured

as none scored above zero for reticulin deposition in the diaphysis, despite a

mouse from the group demonstrating 64% Pax5+ leukemic cells. Results from

the Pearson corellation coefficients supported many of the relationships

observed among the antibodies and histochemical stains tested in PER-371

engrafted BM sections.

sections found evidence for a causal relationship between CTGF and reticulin

deposition in the diaphysis at late stage disease.

6.3.6 BCP ALL proliferation in the presence of conditioned media from stromal-leukaemia cell cultures To determine if BM secreted proteins contained the necessary elements

responsible for the differences in leukaemia cell engraftment in PER-371 High

and Low xenografted mice, conditioned media from HS5 and PER-371 cell line

co-cultures were used to assess changes to leukaemia cell proliferation in vitro.

Proliferation of BCP ALL cell lines was measured by tritiated [3H]thymidine

incorporation after a 48 hour incubation in the presence of conditioned media

from HS5 BM stromal cells co-cultured with PER-371 Low or High cells.

Secreted proteins produced by HS5 and PER-371 High co-cultures did not alter

proliferation in PER-371 High or Low cells (Figure 6.14a). The conditioned

media from HS5 and PER-371 co-cultures also had no effect on proliferation in

PER-278 High or Low cells (Figure 6.14b). In vitro proliferation assays found

that secreted proteins from BM stromal-leukaemia cell interactions were unable

to replicate the difference in leukaemia cell growth due to CTGF in PER-371

High compared with PER-371 Low xenografted mice.

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Fireplicated in vitro. Pre-B ALL cell lines were cultured for 48 hours in presence of conditioned media and proliferation was measured by tritiated 3[ H]thymidine uptake. a. Proliferation of PER-371 Low cells in the presence of conditioned media from stromal cells (HS5) co-cultured with PER-371 High or Low cells. b. Proliferation of PER-278 Low cells in the presence of conditioned media from stromal cells (HS5) co-cultured with PER-371 High or Low cells. Data are expressed as the mean isotope count per minute (n=3). Vertical bars show standard error of the mean.

gure 6.14. Decreased survival of PER-371 High xenografts was not

a.

b.

Cell line

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 170

6.3.7 Changes to secreted protein expression from BM cell co-culture with PER-371 High compared with PER-371 Low cells To investigate the mechanism by which CTGF was increased leukaemia cell

progression in PER-371 xenografted mice, a protein array was performed to

detect proteins being secreted as a result of stromal and leukaemia cell

interaction. HS5 stromal cells were cultured in low serum media (HS5) or in

culture with PER-371 High (HS5:PER-371 High) or PER-371 Low cells

(HS5:PER-371 Low) for 48 hours. Conditioned media was filtered to remove

cells and used in a commercial protein array to detect the expression of 1,000

human proteins (a full protein list is described in Supplementary Table S3). Raw

intensity signals were normalised to background and then to internal loading/

positive controls on the membrane to create adjusted intensity signals (raw

signals from array membrane exposures are presented in Supplementary

Figure S2). Secreted proteins present in the top 1% of adjusted intensity signals

from HS5 control membranes found high expression of common stromal-

associated proteins including; Interleukin 8 (IL8), Interleukin 6 (IL6), Matrix

metalloproteinase 1 (MMP1) and Fibronectin (FN) (Roecklein & Torok-Storb,

1995a). Presence of these proteins confirmed protein array results fitted with

previously reported secreted proteins in HS5 cells.

Altered secreted protein expression due to leukaemia cells

Changes in secreted proteins due to stromal cell interaction with leukaemia

cells was assessed with PER-371 leukaemia cells and HS5 protein secretion.

To achieve this the effect of was evaluated as follows. All HS5 adjusted

intensity signals were procured that had a greater than 2-fold change difference

in expression compared with HS5:PER-371 High and HS5:PER-371 Low

adjusted intensity signals. Differences in protein expression were included as a

positive or negative fold change if the protein intensity was increased/

decreased in the mean fold change (of FC1 and FC2) greater than 2 –fold.

Seventeen secreted proteins were found differentially expressed and the

majority of were underexpressed due to leukaemia cell interaction compared

with stromal cells alone (Table 6.2).

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Tableafter co-culture. Continued next page.

6.2. Leukaemia cells alter secreted proteins from HS5 stromal cells

FADD

CA19-9

fas-associated protein with death domain

cancer antigen 19-90.27

0.17

HS5

b.t.

b.t.

HS5:PER-371 Low

- FC

Adj. Signal .

Mean

FC

- FC

Protein

IGFBP6

CXCL1

insulin-like growth factor, binding protein 6

chemokine (C-X-C motif) ligand 1

0.50

0.36 b.t.

b.t. - FC

- FC

CA15-3cancer antigen 15-3

0.36 b.t. - FC

CXCL2chemokine (C-X-C

motif) ligand 20.54 0.23 - 3.4

CXCL5

GPC5

chemokine (C-X-C motif) ligand 5

glypican 50.15

0.55 0.15

b.t. - FC

- 2.9

SFRP4secreted frizzled-related protein 4

0.80 0.32 - 2.1

SPARCsecreted protein,

acidic, cysteine rich0.97 0.57 - 2.0

- FC

- FC

FC 1

- FC

- FC

- FC

- 2.35

- 3.7

- FC

- 2.5

- 1.7

1.16 0.28 - 2.7TBSP1

thrombospondin 1- 4.1

1.11 0.39 - 2.1IGFBP7

insulin-like growth factor, binding protein 7

- 2.9

EDARectodysplasin A

receptor1.02 b.t. - FC- FC

b.t.

b.t.

HS5:PER-371 High

b.t.

b.t.

b.t.

0.12

0.27

b.t.

0.48

0.41

0.96

0.86

b.t.

- FC

- FC

FC 2

- FC

- FC

- FC

- 4.5

- 2.0

- FC

- 1.7

- 2.4

-1.3

-1.3

- FC

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TPM1tropomyosin 1

b.t.

HS5

0.11

HS5:PER-371 Low

+ FC

Adj. Signal .

Mean

FCProtein

TGFB5

SMAC/ DIABLO

transforming growth factor, beta 5

IAP-binding mitochondrial protein

b.t.

b.t. 0.19

0.13 + FC

+ FC

ITLN1omentin

b.t. 0.17 + FC

+ FC

FC 1

+ FC

+ FC

+ FC

PLGplasminogen

b.t. 0.41 + FC+ FC

0.17

HS5:PER-371 High

0.12

0.18

0.13

0.38

+ FC

FC 2

+ FC

+ FC

+ FC

+ FC

Tableleukaemia-stromal cell co-culture. Low-serum conditioned media from HS5 stromal cells or from HS5 cells co-cultured with PER-371 High or Low cells for 48 hours was used on a human protein array membrane detecting 1000 proteins (Human Array L-1000, Ray Biotech). Raw signal intensity data were normalised to background and then to internal positive control values (adj. signal). Altered expression was analysed as the fold change between HS5:PER-371 Low compared with HS5 adjusted signals (FC1) and HS5:PER-371 High compared with HS5 adjusted signals (FC2). The mean fold change was calculated as the average between FC1 and FC2, and included all secrted proteins with a mean FC≥2. Data are represented as the average adj. signal intensity for the duplicated antibody dots. FC, fold change, b.t., adjusted signal <0.01 and below threshold cut-off.

6.2. Leukaemia cells alter expression of secreted proteins after

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CXCL2chemokine (C-X-C

motif) ligand 20.54

HS5

0.23

HS5:PER-371 Low

Adj. Signal .

Mean

FC

- 3.2

Protein

CCR2

TF

chemokine (C-C motif) receptor 2

transferrinb.t.

b.t. b.t.

b.t. + FC

+ FC

CCR3chemokine (C-C motif)

receptor 3b.t. b.t. + FC

activin-a/ INHBA

inhibin, beta A0.51 0.42 - 3.1

TIMP1

VEGF

TIMP metalloprotease inhibitor 1

vascular endothelial growth factor

0.46

0.94 0.89

0.48 - 3.0

- 3.8

TIMP2TIMP metalloprotease

inhibitor 20.53 0.71 - FC

TIMP3TIMP metalloprotease

inhibitor 30.24 0.35 - FC

- 4.5

FC 1

+ FC

+ FC

+ FC

- 3.4

- 3.9

- 2.9

- FC

- FC

CXCR2chemokine (C-X-C motif) receptor 2

b.t. b.t. + FC+ FC

0.12

HS5:PER-371 High

0.11

0.20

0.12

0.15

0.24

0.16

b.t.

b.t.

0.37

- 1.9

FC 2

+ FC

+ FC

+ FC

- 2.8

- 3.7

- 3.0

- FC

- FC

+ FC

Tablecultures. Low-serum conditioned media from HS5 stromal cells or from stromal cells co-cultured for 48 hours with PER-371 High or Low cells was used on a human protein array membrane detecting 1000 proteins (Human Array L-1000, Ray Biotech). Raw signal intensity data were normalised to background and then to positive control values (adj. signal). Altered expression was analysed as the fold change between HS5:PER-371 High compared with HS5 adjusted signals (FC1) and HS5:PER-371 High compared with HS5:PER-371 Low adjusted signals (FC2). The mean fold change was calculated as the average between FC1 and FC2, and included all secreted proteins with a mean FC≥2. Data are represented as the average adj. signal intensity for the duplicated antibody dots. FC, fold change, b.t., adjusted

6.3. CTGF alters secreted proteins from stromal-leukaemia cell co-

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 174

Altered secreted protein expression due to CTGF

The differential expression of secreted proteins after leukaemia-stromal

interaction was assessed due to increased CTGF expression. The adjusted

signal intensity for PER-371 High cells cultured with HS5 cells was compared

with HS5:PER-371 Low and HS5 adjusted intensity signals using the same

parameters outlined for detecting differences due to leukaemia cell interaction

with HS5 cells. Mainly, the final calculated fold change was the average of the

individual fold changes between HS5:PER-371 High adjusted signal intensities

and HS5:PER-371 Low and HS5 adjusted signal intensitites. Eleven secreted

proteins were deregulated by more than 2-fold in HS5:PER-371 High cultured

medium compared with in HS5:PER-371 Low or HS5 media (Table 6.3).

6.4 Discussion Overexpression of CTGF in PER-371 xenografted mice resulted in a more

aggressive leukaemia expansion. Reduced survival in PER-371 High compared

with PER-371 Low xenografted mice is evidence of a functional role for CTGF in

disease outcome. Differences in leukaemia cell engraftment in the BM at late

stage disease were confirmed by multiple methods. Increased engraftment of

PER-371 High compared with PER-371 Low cells was found by flow cytometry

and immunohistochemical methods of leukaemia cell detection in the BM

space. The effects of CTGF appear to be either not relevant until a significant

population of leukaemia cells has amounted or require a substantial amount of

time to establish an influence over tumour progression. With late stage disease

the first time where differences in leukaemia cell behaviour are observed in

response to increased CTGF.

Mechanisms of CTGF action were investigated in PER-371 xenografted mice.

Functional experiments were performed and were successful in outlining a

mechanism of action for CTGF within BCP ALL. Differences in engraftment

between PER-371 High and Low xenografted mice at late stage disease

occurred independently to any overt changes in leukaemia cell proliferation.

Similarly, conditioned media from leukaemia and BM stromal cell interactions

was insufficient in altering proliferation in leukaemia cells in vitro.

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However, a trend for reduced apoptosis in PER-371 High compared with PER-

371 Low leukaemia cells could explain one potential pathway by which PER-

371 High xenografted mice increase engraftment in the BM.

Evidence that CTGF influences leukaemia cells indirectly through the

microenvironment include increased Ki67+ proliferation in PER-371 High

xenografted mice at early stage disease, before differences in leukaemia

engraftment can be detected and in a larger population of cells than Pax5+

staining accounts for, these proliferating cells are therefore most likely stromal

cells. CTGF has been shown to increase proliferation of mesenchymal stem

cells and contribute to both to osteogenic and fibroblastic differentiation (Lee, et

al., 2010; Wang, et al., 2009a). In PER-371 cells there is evidence that CTGF

requires a complex microenvironment to indirectly facilitate leukaemia cell

progression.

Immunostaining of BM sections supported a relationship between reticulin fibre

deposition and PER-371 High leukaemia engraftment. CTGF is known to be

involved in inducing deposition of collagen fibres in wound healing and in organ

repair in humans (Leask, 2002; Sonnylal, et al., 2010). Increased reticulin

deposition seen in PER-371 High BM sections, at late stage disease in

particular, could be induced directly by CTGF binding to ECM or binding to

stromal cells with known associations with reticulin deposition such as CAR

cells or fibroblasts within the BM space. Reticulin fibre density at time of

diagnosis in human cases has been associated with worse disease outcome in

one study of BCP ALL (Noren-Nystrom, et al., 2007) and BM fibrosis has also

been shown to correlate with worse overall survival and worse progression-free

survival after autologous haematopoietic stem cell transplantation (Suyani, et

al., 2010). However, in other retrospective studies of childhood and adult ALL,

BM fibrosis had no correlation to disease outcome (Bharos, et al., 2010;

Thomas, et al., 2002). Whether BM fibrosis influences BCP ALL clinical

outcome, is not yet clearly defined. Use of the PER-371 NOD/SCID xenografted

model could prove valuable in the study of the effects of BM reticulin fibrosis.

Differences in secreted proteins from stromal-leukaemia cell interactions

indicated several potential important secreted proteins supporting leukaemia

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 176

infiltration or survival. A larger list of deregulated proteins were decreased in

expression due to PER-371 Low and HS5 incubation. Many of these proteins

have associations as tumour suppressors including: TSP1, IGFBP6, IGFBP7,

GPC5, SFRP4 and SPARC (Bach, et al., 2013; Giefing, et al., 2008; Jacob, et

al., 2012; Mok, et al., 1996; Rodriguez-Manzaneque, et al., 2001; Said, et al.,

2013; Wajapeyee, et al., 2008; Yang, et al., 2013). Many inhibited proteins have

also been identified as involved in ECM remodelling. SPARC has been shown

to act in similar ways to CTGF, by inducing COL3A1 and COL1A2 expression

and driving a fibrotic response in cells (Wang, et al., 2010b). Therefore

suppression of SPARC in PER 371 High with HS5 indicates different

mechanism are involved in BM fibrosis. Downregulated chemokines CXCL1,

CXCL2 and CXCL5 attract neutrophils to tumour sites and their suppression is

associated with primary tumour cell metastasis (Toh, et al., 2011). Additionally,

increased expression of these chemokines has been associated with fibrosis

and tissue remodelling in myeloid neoplasia and liver fibrosis (Jen Chin, 2005).

PER-371 High or Low incubations with HS5 cells increased expression of a

smaller number but diverse range of proteins including; an enzyme precursors

for ECM degradation (PLG), positive apoptotic regulator (SMAC/ DIABLO),

adipokine (ITLN1), cytokine (TGFB5) and an actin-binding contractile protein

(TPM1). No relationship between upregulated-secreted proteins was evident in

the literature, though all genes have been associated with cancer in various

ways. Leukaemia cells were found to have a significant effect on protein

secretion from BM stromal cells and these findings concur with the reported

literature that the microenvironment response facilitates leukaemia cell survival

and progression.

Protein arrays also found reduced secreted proteins due to CTGF expression

by PER-371 cells. Reduced expression of tissue remodelling proteins included

activin-a, VEGF and TIMP1,2 and 3. Deregulated secreted proteins from

stromal-leukaemia cell interactions due to CTGF expression suggest a role in

ECM modification and tie in with immunohistochemical findings reported in this

chapter and previously discussed findings of altered HS5 gene expression due

to rhCTGF in Chapter 4, this is discussed in further detail in the General

Discussion (Chapter 7).

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The NOD/SCID xenograft model allowed us to investigate some fundamental

biological aspects of leukaemia survival and expansion in the BM. Both

monocytic and lymphoblastic leukaemias are clinically associated with a

gradual eviction of normal haematopietic cells from the BM. The specific

movement of megakaryocytes have not been addressed. In PER-371

xenografted mice, megakaryocytes were found diminished in number as

leukaemia engraftment was increased. Additionally, megakaryocytes were

present at the invading tumour edge in PER-371 xenografted mice, which

supports a possible role for megakaryocytes as tumour modulators.

Megakaryocytes have been reported as functional immune cell types in

NOD/SCID mice with evidence that they phagocytose human erythroid cells

and platelets (Psaila, et al., 2012). Psaila et al. indicate an important role for

megakaryocytes in modifying angiogenesis and osteogenesis during tumour

development by secretion of integral proteins. Follow-up studies will evaluate

spleen megakaryocyte numbers in PER-371 xenografts, to determine if the

spleen compensates for the loss of megakaryocytes in the bone marrow.

CTGF was found to not contribute to ARAC drug sensitivity in PER-371

xenografted mice. PER-371 High xenografted mice were sensitive to low-dose

ARAC, while survival analysis suggests PER-371 Low xenografted mice did not

respond to low-dose ARAC. However, as the survival curves of PER-371 High

and Low ARAC treated mice are not different this suggests the drug behaves

similarly on both cell lines. Timing of ARAC delivery in treated mice had the last

ARAC dose coincide with end stage disease in untreated PER-371 Low

xenografted mice. If the data reveals anything it is that low-dose ARAC is only

effective during the course of treatment and expansion of leukaemia resumes

immediately after the drug is withdrawn. The need for high-dose ARAC regimes

to achieve complete remission has been noted in human AML and refractory

ALL adult clinical trials (Kern & Estey, 2006; Willemze, et al., 1983). The

response found to low and high-dose ARAC in the PER-371 NOD/SCID

xenograft model supports the need for high-dose ARAC for drug efficacy.

However, the two doses used in the current study leave a large middle ground

and it is likely optimisation of ARAC dose would be required to determine if

higher doses of ARAC would improve leukaemic blast reduction beyond the

treatment phase in the NOD/SCID model.

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The various roles of CTGF throughout the body have supported a multitude of

mechanistic pathways. Despite broad CTGF overexpression across a range of

BCP ALL subtypes and associations with worse clinical outcome, a functional

role for CTGF in BCP ALL has been lacking.

This study outlines a role for CTGF using the PER-371 NOD/SCID xenograft

model, with an internalised CTGF transgene responsible for differential

expression. High CTGF expression was found to decrease survival in PER-371

xenografted mice compared with low-expressing control groups. Observable

changes in engraftment were only evident from late stage disease in the BM,

and suggested a time-dependent component of CTGF function. Investigations

into leukaemia cell interactions with the BM microenvironment and in particular

the ECM, confirmed increased secretion of ECM remodelling proteins due to

CTGF overexpression in PER-371 High cells. This data together with observed

increases in stromal cell proliferation at early stage disease and increased

reticulin fibre density at late stage disease. Taken together, CTGF is postulated

to indirectly enhance the progression of PER-371 cells by modifications to the

ECM.

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General Discussion

Intellectually we stand on an island in the midst of an illimitable ocean of inexplicability. Our business in every generation is to reclaim

a little more land.

Thomas Huxley

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Chapter 7 General Discussion

 

7.1 Introduction The overall Aim of this thesis was to discover potential mechanisms of action of

CTGF in childhood B-precursor ALL. Previous studies have highlighted its

significance as an overexpressed gene in the majority of childhood B-precursor

ALL sub-types and its association with poor clinical outcome (Boag, et al., 2007;

Kang, et al., 2010). In order to clarify the importance of CTGF in driving disease

outcome, it was necessary to define any mechanism by which it could alter B-

precursor ALL cell function. The overall Aim was achieved through three smaller

Aims:

Firstly, engineering two B-precursor ALL cell lines to overexpress CTGF 3-fold

above a baseline detectable level was found to have minimal impact on the

behaviour of the cell in vitro. In particular, proliferation and sensitivity to ARAC

and VCR were found to be similar between CTGF High and Low cell lines in

both PER-278 and PER-371. Though no differences were found due to CTGF

expression, PER-278 cells exhibited a 25-fold reduced ARAC sensitivity

compared with PER-371 cells. Similarly, though no genes were commonly

deregulated due to CTGF overexpression by microarray, PER-278 and PER-

371 show distinct global gene expression profiles though primary material was

from patients with common ages, genders and E2A-PBX1 translocations. The

overall findings from Aim 1 indicate mechanisms of action of CTGF are

consequent to its role as a matricellular protein and not due to direct autocrine

or intracrine changes to the cell.

Secondly, the role of CTGF in extracellular signalling and communication was

explored. The presence of recombinant CTGF was found capable of changing

gene expression in the HS5 human BM stromal cell line, in a pronounced and

time dependent manner. Following 8 hours CTGF exposure, genes involved in

the cell cycle and activation of PI3K/AKT and IGF1 pathway signalling were

altered. Among altered secreted genes, the greatest number were involved in

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ECM remodelling. The overall findings of Aim 2 verified CTGF is capable of

communication with human BM stromal cells and affects genes involved in

important downstream functions.

Thirdly, mechanisms of CTGF action in B-precursor ALL were explored within

the context of the murine BM microenvironment using NOD/SCID xenograft

models that closely intimate the human disease. In PER-278 xenografted mice,

CTGF overexpression had no effect on leukaemia growth but was found to

reduce sensitivity to low dose ARAC, with no effect on VCR senisitivity. In PER-

371 xenografted mice CTGF overexpression caused a more aggressive

expansion of leukaemia resulting in reduced survival, while sensitivity to ARAC

was unaltered. The different responses of the two cell lines due to CTGF were

considered separately.

Mechanisms by which CTGF altered PER-278 ARAC sensitivity were not fully

determined. Compared to PER-371 cells, reduced ARAC sensitivity in vitro was

found for both PER-278 High and Low cells suggesting that PER-278 cell lines

would be expected to be less sensitive to ARAC in vivo. However in PER-278

Low mice the low ARAC dose resulted in a small but significantly prolonged

survival and only PER-278 High mice proved to be insensitive to low dose

ARAC. Mechanisms by which CTGF altered PER-278 ARAC sensitivity in the

BM were not determined and remain a potential avenue of exploration.

In PER-371 xenografts, CTGF was found to reduce survival by inciting a more

aggressive progression of leukaemic cells in the BM and to a lesser extent in

the extramedullary organs. CTGF mechanisms of action included increasing

stromal cell proliferation and reticulin connective tissue deposition indirectly

affecting leukaemia cell expansion in the BM. The overall findings of Aim 3

conclusively proved a functional role for CTGF in B-precursor ALL, which was

dependent on the expression of cooperating genes by the leukaemia cell and

interaction with the microenvironment.

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7.2 Limitations of the current research

Immune-compromised mouse model and importance of immune response The NOD/SCID mouse model has a severely depleted immune response. While

there is residual NK cell activity and macrophage function, it is a subset of the

full range of immune elements that would be relevant in human BM (Shultz, et

al., 1995a). While the other cells types in the BM stromal compartment are not

affected by the strain, this limitation is important to consider when defining

responses within the microenvironment, no model system of leukaemia is

currently available that allows engraftment of a large number of foreign cells

while maintaining a complete innate and adaptive immune response. The

NOD/SCID mouse was the most suitable strain for the presented studies, which

focused on growth of leukaemia cells within the BM, as this strain has a greater

immune response compared with the other immune-compromised mouse

strains and therefore a more biologically similar microenvironment to human

BM.

CTGF affected ARAC drug sensitivity only in restricted conditions

CTGF-induced ARAC resistance in PER-278 cells was found only at low dose

in female xenografted mice. The response of PER-278 High cells to ARAC at

higher doses and at 24 hours after a single dose was administered was no

different to PER-278 Low cells. The ARAC snapshot did not highlight

differences in proliferation or apoptosis due to CTGF with resistance to ARAC

not evident due to the 24-hour window missing the effects of drug activity or the

use of larger male mice with differences in the onset of 1% engraftment and

timing of drug administration. The restricted conditions under which CTGF was

found to effect ARAC sensitivity in PER-278 cells, particularly re-sensitisation at

higher doses, diminishes its likely importance in the clinical setting, where high

dose regimens of ARAC are more commonly used. The finding does provide

further insight into the variety of responses enabled by CTGF activity in B-

precursor ALL.

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7.3 Critical findings

The microenvironment is essential for CTGF function in B-precursor ALL The inability to recapitulate in vitro the responses observed due to CTGF in vivo

in B-precursor ALL cells, highlighted the importance of the BM in CTGF

function. Neither CTGF overexpression alone nor secreted proteins from co-

incubations of leukaemia cells with stromal cells could replicate in vitro the

resistance of PER-278 cells to ARAC or the increased proliferation of PER-371

cells seen in xenograft mice. These results indicate that CTGF does not act

directly on B-precursor ALL cells and physical interaction with components of

the ECM is required. Tumour-associated fibroblasts are known to influence

tumour invasiveness and survival (Egeblad, et al., 2010). Further, in other

human cancers CTGF expression is commonly associated with increased

fibrosis in the surrounding tumour parenchyma (Birgersdotter, et al., 2010;

Cunningham, et al., 2010). In B-precursor ALL it is possible the effects of CTGF

are due solely to changes induced in BM stromal cells resulting in ECM

restructuring and increased BM fibrosis. Whether CTGF-mediated crosstalk with

the BM modifies leukaemia cell gene expression in turn, remains to be

determined.

The individual responses observed in PER-278 and PER-371 are dependent on

intrinsic differences in gene expression. The distinct responses highlight that

CTGF acts in cooperation with other genes expressed by leukaemia cells in

microenvironment interactions. It is also possible that the effect of CTGF on BM

stromal cells is threshold dependent and the slightly higher level of baseline

CTGF in PER-278 Low cells may diminish the response to lentiviral-induced

CTGF overexpression. It is possible a greater fold-change difference in CTGF

expression may also have led to a greater survival differential in PER-371

CTGF Low and High xenograft mice. However, the expression level caused by

lentiviral transfection in PER-278 and PER-371 fell within the range seen in

patient samples by qRT-PCR (Welch, et al., 2013) and therefore corresponds

with real observations made in the human disease.

CTGF mediates communication between B-precursor ALL cells and BM stromal cells

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The role of CTGF in leukaemia and BM stromal cell communication was

outlined in two ways: firstly by changes to HS5 gene expression due to

recombinant CTGF and secondly changes to secreted proteins in co-cultures of

HS5 cells with PER-371 High and Low. Several genes and their corresponding

proteins were deregulated in both the microarray and protein array. These

included the chemokines; CCL2, CCL7 and CCL8, with upregulated gene

expression in HS5 cells. The receptor for all 3 ligands, CCR2, was upregulated

in the secreted protein from HS5 and PER-371 High. Similarly, increased gene

expression of CXCL1 and CXCL5 accompanied increased protein levels of

CXCR2, their known chemokine receptor. Whereas, downregulation of VEGF,

TIMP1 and TIMP2 were found concurrently at the gene expression and

secreted protein level due to overexpression of CTGF. The potential effects of

these genes are varied. Chemokines are responsible for immune cell trafficking,

cell survival and proliferation (Proudfoot, 2002). The receptors CCR2, CCR3

and CXCL2 have been associated with inflammation in disease and

chemokines have shown involvement in tumour growth, immune evasion,

metastasis and angiogenesis (Bendall, 2005). The TIMP proteins and VEGF

are associated with ECM remodelling, both capable of altering HSC niches

within the BM (Shen, et al., 2010). Beyond their MMP-inhibitory activity, the

TIMPS also act in cooperation or opposition to VEGF in establishing neo-

angiogenesis (Qi, et al., 2003; Stetler-Stevenson & Seo, 2005; Yamada, et al.,

2001). As all four proteins are downregulated they could function separately

from their known role in angiogenesis in the B-precursor ALL BM. These

deregulated genes are evidence of CTGF mediating communication between B-

precursor ALL cells and BM stromal cells, as HS5 and PER-371 High

interactions have increased CTGF protein due to PER-371 High cells and

secreted protein deregulation from HS5 cells.

Additionally, CTGF increased proliferation of stromal cells at early stages of

leukaemia cell engraftment, as evidenced by increased Ki67-positive

immunostaining in PER-371 CTGF High xenografted mice unaccompanied by

an increased percentage of Pax-5-positive leukaemia cells in the BM. Increased

stromal cell proliferation in BM sections is consistent with the changes in HS5

gene expression after 8 hours in the presence of rhCTGF, as the most altered

genes were associated with the cell cycle. While the stromal cell type

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undergoing proliferation has not been qualified, it is clear that through CTGF,

PER-371 leukaemia cells directly communicate with components of the BM

microenvironment.

CTGF enables a more aggressive expansion of PER-371 cells in xenograft mice In PER-371 xenografted mice, overexpression of CTGF resulted in reduced

survival compared with PER-371 Low mice. Reduced survival was the result of

a faster spread of disease with a greater percentage of engraftment at late

stage disease in the BM, spleen, liver and lymph node in PER-371 High

compared with PER-371 Low cells. PER-371 High and Low xenografted mice

had similar levels of proliferation and apoptosis in the BM at late stage disease

indicating CTGF does not exert a sustained effect on leukaemia cell growth

throughout disease progression. Evidence from microarray studies found CTGF

affected a significant human BM stromal cell response and supports the notion

that a probable mechanism of CTGF action in PER-371 xenografts is through

microenvironment interactions. As reduced survival was specific to PER-371

xenografted mice, CTGF must interact with components of the BM

microenvironment in cooperation with genes expressed specifically in PER-371

cells and not PER-278.

CTGF alters drug sensitivity in PER-278 cells In PER-278 xenografts, overexpression of CTGF reduced the sensitivity of

leukaemia cells to low dose ARAC. The resistance was peculiar to the low

ARAC concentration and proximal to the time of ARAC injection as no

differences due to CTGF were found using a maximum-tolerated ARAC dose or

24 hours after a low dose ARAC bolus injection. The cellular changes enacted

by CTGF that confer tumour cell resistance were not identified; though they

appear dependent on the physical interaction with the microenvironment, as

secreted proteins from leukaemia cell-stroma interactions could not replicate

ARAC resistance in vitro. Potentially CTGF could provide protection from ARAC

in PER-278 cells by activating signalling pathways by adhesion of leukaemia

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and stromal cells or by creating a physical barrier through increased fibrotic

deposition around the leukaemia cells. Stromal cell adhesion has previously

been shown to suppress apoptosis in B-lineage ALL cell lines after exposure to

ARAC and etoposide, acting via expression of the vascular cell adhesion

molecule 1 (VCAM1) (Mudry, et al., 2000). In these experiments soluble factors

were unable to attain the same level of drug resistance as adhesion to stromal

cells. Nor was adhesion to fibronectin alone, in contrast to chronic myelogenous

leukaemia were adhesion to fibronectin was sufficient to induce drug resistance

(Damiano, et al., 2001). In multiple cancer types tumour cell adhesion to stroma

via integrins or cell adhesion molecules has proven to be a potent mediator of

multidrug resistance (Aoudjit & Vuori, 2012; Correia & Bissell, 2012). However,

mechanisms of stromal-induced drug resistance are not completely understood,

in colon cancer adhesion to ECM components increased expression of anti-

apoptotic proteins, bcl-2 and bcl-x(L), but their expression did not correlate to

the protective effect induced by ECM contact suggesting differences in other

apoptotic or unidentified mechanisms were involved (Kouniavsky, et al., 2002).

The ECM can also affect drug resistance indirectly; collagen deposition in

ovarian cancer created increased interstitial pressure inside the tumour mass

and thereby reduced the accessibility of antibodies after intraperitoneal injection

(Choi, et al., 2006). Defining a mechanism by which CTGF alters cell sensitivity

to nucleoside analogues such as ARAC would extend our knowledge of drug

resistance mechanisms in B-precursor ALL.

In B-precursor ALL, the overall phenotype that results from the complex

regulation of cells by CTGF appears to depend on tumour genotype. In

oesophageal cancer CTGF has differential effects between squamous and

adenocarcinoma histological subtypes. Increased CTGF was associated with

better survival in squamous cell cancers, correlated with increased formation of

fibrotic capsules surrounding the tumour, and worse survival with

adenocarcinoma with no change to fibrosis and therefore postulated to directly

mediate apoptosis of tumour cells (Koliopanos, et al., 2002).

CTGF increases deposition of reticular connective tissue in B-precursor ALL BM microenvironment

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Overexpression of CTGF in PER-371 xenografts was associated with increased

reticulin fibre deposition at early and late stage disease, reaching a significant

difference in mean reticulin score at late stage disease in the diaphysis.

Reticulin fibres are mainly composed of type 3 collagen and associated with

adventitial reticular cells in the BM (Cattoretti, et al., 1993; Gelse, et al., 2003;

Ushiki, 2002). ECM-associated genes COL3A1 and COL1A2 were found

upregulated in HS5 cells after an 8 hour exposure to rhCTGF, along with lysyl

oxidase (LOX), integrin, alpha V (ITGAV), fibronectin 1 (FN1), pentraxin 3

(PTX3), transforming growth factor beta 2 (TGFB2) and the proteoglycan

decorin (DCN). These genes are capable of contributing to the observed ECM

modifications and possibly play other associated roles in promoting leukaemia

cell growth via the microenvironment. Two ECM related genes were verified by

qRT-PCR as being upregulated by CTGF in HS5 cells: LOX (upregulated 5.4-

fold) and ITGAV (upregulated 1.8-fold). ITGAV may act as the transmembrane

receptor for CTGF when binding to stromal cells and LOX is implicated in cross-

linking collagen fibres. LOX has been postulated as a target for therapy in

many solid tumours (Barker, et al., 2012). In breast cancer, collagen cross-

linking by LOX was essential for collagen fibrosis and the resulting increased

tumour stiffness and focal adhesion signalling led to increased tumour invasion

into surrounding epithelium (Levental, et al., 2009).

With evidence that acute leukaemia exists as a closely associated population of

cells and are not dispersed throughout the BM space, has led to the recent

appreciation of leukaemia and stromal cell interactions in the disease. Fibrosis

accounts for a third of natural death globally and includes a chronic loss of

organ function in BM, heart, intestine, kidney, liver, lung, skin and more solid

tumours (Zeisberg & Kalluri, 2013). TGFβ overexpression is common among all

fibrotic tissues and has been extensively studied in bone marrow fibrosis, where

it is largely expressed by megakaryocytes and platelets (Kuter, et al., 2007). B-

precursor ALL cell expression of CTGF, may activate the same pathways and

cellular responses as megakaryocyte-expressed TGFβ.

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7.4 Proposed mechanism of CTGF action

ECM remodelling by CTGF, was reported in this thesis to indirectly support

leukaemic growth and expansion in a NOD/SCID xenograft mouse model of B-

precursor ALL. It is unknown how CTGF modifies the deregulated ECM-

interacting genes presented in Chapter 4 and also how they specifically

implement the observed phenotype. We hypothesise, that in the early stages of

disease development CTGF acts to increase proliferation of adventitial reticular

cells. These cells increase production of COL3A1, LOX and other important

ECM-interacting genes to set up new niches tailored for expansion of leukaemia

cells. Production of reticulin connective tissue may modify the number of normal

cells, such as megakaryocytes, within the newly created space and can also

control the sequester and release of certain growth factors. The fibrotic reticular

connective tissue may act as a physical barrier to chemotherapy drugs,

however reticulin fibre density would be unique to each patient. Plasma CTGF

or LOX levels may act as a biomarker for fibrotic connective tissue and guide

concomitant delivery of ECM-degrading drugs.

7.5 Future directions

Further study will be essential to validate the proposed mechanism of action by

which CTGF alters disease progression in childhood B-precursor ALL.

Delineation of the mechanism by which CTGF increases fibrotic reticulin

connective tissue in the BM will increase our understanding of the clinical

impact of CTGF. Studies using B-precursor ALL cell lines with downregulation

of CTGF by shRNAs have already been initiated in our laboratory and will act to

validate the mechanisms presented in this thesis.

Use of the NOD/SCID xenograft model to test further cell lines with lentiviral-

induced CTGF overexpression or primary patient cell samples, would contribute

toward understanding how prevalent the effects of CTGF might be among

childhood B-precursor ALL cases. While this thesis successfully identifies a

mechanism of action for CTGF in B-precursor ALL, extrapolation of the findings

would help define how prolific or specific this CTGF-initiated phenotype is

among B-precursor ALL patients. Further, identifying the differences in gene

expression between PER-278 and PER-371 responsible for the dissimilar

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outcomes in vivo will uncover important genetic traits currently overlooked in the

clinical profile of patients.

In order to confirm a causative role for CTGF in deposition of reticulin

connective tissue, an ECM inhibitor can be used, such as β–aminopropionitrile

(BAPN) an irreversible LOX inhibitor (Levental, et al., 2009). If CTGF is

causative for inducing reticulin deposition in the PER-371 NOD/SCID xenograft

model, and in turn increasing progression of leukaemia engraftment, then

preventing deposition of ECM should reverse the observed differences in

survival between PER-371 High and Low xenografted mice.

Further experimental opportunities include determining the effect of CTGF on

neo-angiogenesis, with possible links between CTGF as a proangiogenic

modulator and increased angiogenesis being associated with acute leukaemias

(Hussong, et al., 2000; Perez-Atayde, et al., 1997; Shimo, et al., 1999; Shimo,

et al., 2001). Studies to identify adventitial reticular cells as the stromal cell

population undergoing proliferation in early stage disease would provide further

substance to the argument that CTGF plays a direct role in reticulin deposition.

Lastly, elucidating undiscovered CTGF-induced changes to drug sensitivity by

testing of further chemotherapies could be performed in combination with

different ECM inhibitors. A recent study using a NOD/SCID xenograft model of

B-cell ALL found a monoclonal antibody against CTGF increased survival when

mice were co-treated with conventional chemotherapy drugs: vincristine, L-

asparaginase and dexamethasone (Lu, et al., 2013). Comparatively, in

pancreatic ductal adenocarcinoma CTGF was largely secreted from cancer-

associated fibroblasts and a CTGF monoclonal antibody given in combination

with single agent chemotherapy induced tumour cell apoptosis. Apoptosis was

induced without altering microenvironment composition, angiogenesis or

chemotherapy drug uptake but instead by down-regulating expression of

prosurvival genes in the tumour cells (Neesse, et al., 2013). Defining the

mechanism by which CTGF acts would lead to a better understanding of ECM

deposition in B-precursor ALL and allow the identification of the best ECM

inhibitor to counteract increased reticulin deposition and maximize synergy with

standard chemotherapeutic drugs. The results of which could potentially lead to

a personalised course of therapy for children with high CTGF expression,

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preventing the worse clinical outcomes associated with CTGF expression in

childhood B-precursor ALL.

7.6 Final conclusions

This thesis provides the first evidence of a mechanism of action for CTGF in B-

precursor ALL. In PER-371 cells CTGF acts on BM stromal cells to increase the

deposition of reticular fibres forming fibrotic reticular connective tissue that

potentially provides space for B-precursor ALL cells to grow and expand within

the BM, contributing to the deregulation of normal haematological and immune

cell functions. Further understanding of other important elements in the fibrotic

response will aid in establishing drug targets and expanding current knowledge

of the networks of protein interactions that contribute to leukaemia progression

and survival. This thesis has provided strong evidence for CTGF initiating a

series of interactions that influence disease outcome in childhood B-precursor

ALL.

 

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Appendix: Supplementary Figures

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Tabl

e S1

. Ing

enui

ty p

athw

ay a

naly

sis

(IPA)

for d

iffer

entia

lly re

gula

ted

gene

s be

twee

n st

rom

al c

ells

(HS5

) tre

ated

with

rhCT

GF

(100

ng/m

l) or

con

trol b

uffe

r for

16

hour

s . T

he IP

A ge

ne lis

t com

prise

s ge

nes

iden

tifie

d sig

nific

antly

diff

eren

t by

LIM

MA

and

with

an

expr

essio

n di

ffere

nce

grea

ter t

han

two-

fold

com

pare

d to

unt

reat

ed c

ontro

l cel

ls (B

enja

min

i and

Hoc

hber

g-ad

just

ed p

-val

ue <

0.05

, fol

d ch

ange

>2

and

<2).

Num

ber o

f upr

egul

ated

(·) and

dow

nreg

ulat

ed (‚) g

enes

indi

cate

d we

re u

sed

to g

ener

ate

IPA

signi

fican

t net

work

, ca

noni

cal p

athw

ay a

nd k

nown

bio

logi

cal f

unct

ion

asso

ciatio

ns.

Cellu

lar A

ssem

bly

and

Org

aniza

tion

Cellu

lar F

unct

ion

and

Mai

nten

ance

Amin

oacy

l-tRN

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osyn

thes

is

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ine,

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ine

and

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onin

e M

etab

olism

1.Re

nal a

nd U

rolo

gica

l Dise

ase,

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etic

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rder

, Sk

elet

al a

nd M

uscu

lar D

isord

ers

2. N

ervo

us S

yste

m D

evel

opm

ent a

nd F

unct

ion,

Ti

ssue

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phol

ogy,

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o Ac

id M

etab

olism

·136 ‚23

Cellu

lar M

ovem

ent

Amyo

troph

ic La

tera

l Scle

rosis

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gnal

ing

3.

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ctio

n M

echa

nism

, Inf

ectio

us D

iseas

e, C

ell

Mor

phol

ogy

Cell M

orph

olog

y M

ethi

onin

e M

etab

olism

Amin

o Ac

id M

etab

olism

Mito

chon

dria

l Dys

func

tion

IPA

Netw

ork

# G

enes

Top

Biol

ogic

al F

unct

ions

IPA

Cano

nica

l

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Page 241: The Bone Marrow Microenvironment is Essential for the ... · iv! ! overexpressing cell lines 2.3.5 Global gene expression to determine effect of recombinant human CTGF on stromal

Tabl

e S2

. Ing

enui

ty p

athw

ay a

naly

sis

(IPA)

for d

iffer

entia

lly re

gula

ted

gene

s be

twee

n st

rom

al c

ells

(HS5

) tre

ated

with

rhCT

GF

(100

ng/m

l) or

con

trol b

uffe

r for

48

hour

s . T

he IP

A ge

ne lis

t com

prise

s ge

nes

iden

tifie

d sig

nific

antly

diff

eren

t by

LIM

MA

and

with

an

expr

essio

n di

ffere

nce

grea

ter t

han

two-

fold

com

pare

d to

unt

reat

ed c

ontro

l cel

ls (B

enja

min

i and

Hoc

hber

g-ad

just

ed p

-val

ue <

0.05

, fol

d ch

ange

>2

and

<2).

Num

ber o

f upr

egul

ated

(·) and

dow

nreg

ulat

ed (‚) g

enes

indi

cate

d we

re u

sed

to g

ener

ate

IPA

signi

fican

t net

work

, ca

noni

cal p

athw

ay a

nd k

nown

bio

logi

cal f

unct

ion

asso

ciatio

ns.

Cellu

lar A

ssem

bly

and

Org

aniza

tion

Cellu

lar F

unct

ion

and

Mai

nten

ance

Hepa

tic F

ibro

sis /

Hepa

tic

Stel

late

Cel

l Act

ivatio

n

Coag

ulat

ion

Syst

em

1. L

ipid

Met

abol

ism, S

mal

l Mol

ecul

e Bi

oche

mist

ry,

Cellu

lar D

evel

opm

ent

2. G

enet

ic Di

sord

er, H

emat

olog

ical D

iseas

e,

Ce

ll Dea

th

·89 ‚180Ce

llula

r Mov

emen

t Pr

opan

oate

Met

abol

ism3.

Cel

l-To-

Cell S

igna

ling

and

Inte

ract

ion,

Hep

atic

Syst

em D

iseas

e, In

flam

mat

ory

Dise

ase

Post

-Tra

nsla

tiona

l Mod

ificat

ion

Intri

nsic

Prot

hrom

bin

Activ

atio

n Pa

thwa

y

Cellu

lar D

evel

opm

ent

p53

Sign

alin

g

IPA

Netw

ork

# G

enes

Top

Biol

ogic

al F

unct

ions

IPA

Cano

nica

l

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secreted genes upregulated at 8 hours

Gene

Symbol Aliases & Descriptions

Fold

change

COL3A1 collagen, type 3, alpha 1 15.07LOX lysyl oxidase 7.08PLCB4 phospholipase C, beta 4 6.99PAPPA pregnacy-associated plasma protein A 6.26EFEMP1 EGF-containing fibulin-like extracellular matrix protein 1 5.42CYP51A1 cytochrome P450, family 51, subfamily A, polypeptide 1 5.35LUM lumican 4.81DPP4 dipeptidyl-peptidase 4 4.44MATN2 matrilin 2 4.30COL1A2 collagen, type 1, alpha 2 4.23FN1 fibronectin 1 4.00ROBO1 roundabout homolog 1 3.88NUCB2 nucleobindin 2 3.83NPTX2 neuronal pentraxin 2 3.68LAMB1 laminin subunit beta 1 3.66CCL2 chemokine (C-C motif) ligand 2 3.60TGFBR3 transforming growth factor beta receptor type 3 3.55NID2 nidogen 2 3.36COL5A1 collagen, type 5, alpha 1 3.33GALC Galactosylceramidase 3.26FBN2 fibrillin 2 3.26SEMA3C semaphorin-3C 3.21CALU calumenin 3.10PTX3 pentraxin 3 3.05SEC24A SEC24 related gene family, member A 3.05TNFAIP6 tumor necrosis factor alpha-inducible protein 6 3.01DCN decorin 2.95C5orf13 chromosome 5 open reading frame 13 2.94

TMEFF1transmembrane protein with EGF-like and two follistatin-like domains 1 2.87

PSG1 pregnancy specific beta-1-glycoprotein 1 2.82CCL7 chemokine (C-C motif) ligand 7 2.77TGFB2 transforming growth factor beta 2 2.75COLEC12 collectin sub-family member 12 2.75IL1RAP interleukin 1 receptor accessory protein 2.67ASAH1 N-acylsphingosine amidohydrolase (acid ceramidase) 1 2.67TUFT1 tuftelin 1 2.67ZNF23 zinc finger protein 32 2.67RANBP9 ran-binding protein 9 2.60SYNJ1 synaptojanin 1 2.60GNS glucosamine (N-acetyl)-6-sulfatase 2.59

TFPItissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) 2.59

AGA aspartylglucosaminidase 2.59ADAM12 a disintegrin and metalloproteinase domain 12 (meltrin alpha) 2.55MATN3 matrilin 3 2.53CCL8 chemokine (C-C motif) ligand 8 2.50

ENPP2ectonucleotide pyrophosphatase/phosphodiesterase family member 2 2.49

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secreted genes upregulated at 8 hours

Gene

Symbol Aliases & Descriptions

Fold

change

WNT5A wingless-type MMTV integration site family, member 5A 2.49TGOLN2 trans-golgi network protein 2 2.48CLIC4 chloride intracellular channel protein 4 2.45

ALG5asparagine-linked glycosylation 5, dolichyl-phosphate beta-glucosyltransferase homolog (S. cerevisiae) 2.45

TTC3 tetratricopeptide repeat domain 3 2.43THOC2 THO complex 2 2.41INHBA inhibin beta A chain 2.39MYLK myosin light chain kinase 2.38BDNF brain-derived neurotrophic factor 2.36ENPP1 ectonucleotide pyrophosphatase/phosphodiesterase 1 2.36FBN1 fibrillin 1 2.35SHOX2 short stature homeobox protein 2 2.33

SERPINE2 serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 2.32

ITGBL1 integrin beta-like protein 1 2.31CHSY1 chondroitin synthase 1 2.27RBM3 RNA binding motif protein 3 2.21

B4GALT4beta-N-acetylglucosaminyl-glycolipid beta-1,4-galactosyltransferase 4 2.19

STAM2signal transducing adaptor molecule (SH3 domain and ITAM motif) 2 2.17

GALNT7 UDP-GalNAc:polypeptide N-acetylgalactosaminyltransferase 7 2.15CRIM1 cysteine-rich motor neuron 1 2.14FADS1 fatty acid desaturase 1 2.14C1S complement component 1, s subcomponent 2.12GRSF1 G-rich RNA sequence binding factor 1 2.11RDH11 retinol dehydrogenase 11 (all-trans/9-cis/11-cis) 2.10FAM3C family with sequence similarity 3, member C 2.08IL1R1 interleukin 1 receptor, type 1 2.07CYLD ubiquitin carboxyl-terminal hydrolase CYLD 2.05TFPI2 tissue factor pathway inhibitor 2 2.05TFRC transferrin receptor (p90, CD71) 2.05PDGFC platelet derived growth factor C 2.05

C1GALT1core 1 synthase, glycoprotein-N-acetylgalactosamine 3-beta-galactosyltransferase, 1 2.04

C1orf9 chromosome 1 open reading frame 9 2.03

Table S3(HS5) in the presence of CTGF. HS5 cells were incubated for 8 hours in the presence of rhCTGF (100ng/ml) or control buffer. RNA was used for microarray analysis. Gene list comprises secreted genes identified significantly upregulated by LIMMA (FDR-adjusted P-value <0.05, fold change >2) and present on the Secreted Protein Discovery Initiative (SPDI, Clarke et al., 2003).

. Significantly upregulated genes secreted from stromal cells

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secreted genes downregulated at 8 hours

Gene

Symbol Aliases & Descriptions

Fold

Change

CXCL5 neutrophil-activating peptide ENA-78 13.35

CXCL1chemokine (C-X-C motif) ligand 1 (melanoma growth stimulating activity, alpha) 8.85

COL6A2 collagen, type 6, alpha 2 8.09CALR calregulin 5.97

CXCL6chemokine (C-X-C motif) ligand 6 (granulocyte chemotactic protein 2) 5.83

PLAU plasminogen activator, urokinase 5.72GAL galanin peptides 5.28MIF macrophage migration inhibitory factor 4.91

CSF2 colony stimulating factor 2 (granulocyte-macrophage) 4.75COL6A1 collagen, type 6, alpha 1 4.51BMP2 bone morphogenetic protein 2 4.16CST3 cystatin 3 3.88

PLAUR urokinase plasminogen activator surface receptor 3.83STC1 stanniocalcin 1 3.78

PTPRF receptor-type tyrosine-protein phosphatase F 3.62

MCL1 myeloid cell leukemia sequence 1 (BCL2-related) 3.55TRIM28 transcription intermediary factor 1-beta 3.49SSR4 signal sequence receptor subunit delta 3.41SPRY4 sprouty homolog 4 (Drosophila) 3.40TGFB1 transforming growth factor, beta 1 3.39PRKCSH protein kinase C substrate, 80 Kda protein 3.28NMU neuromedin U 3.27FGF5 fibroblast growth factor 5 3.27

NDUFS8NADH dehydrogenase [ubiquinone] iron-sulfur protein 8, mitochondrial 3.16

MGAT4Balpha-1,3-mannosyl-glycoprotein beta-1,4-N-acetylglucosaminyltransferase 3.03

CD44 hematopoietic cell E- and L-selectin ligand 2.88

TIMP1tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) 2.77

CPNE1 copine 1 2.75COL1A1 collagen, type 1, alpha 1 2.73ADRM1 adhesion regulating molecule 1 2.71EMILIN1 elastin microfibril interfacer 1 2.58ANGPTL4 Angiopoietin-like protein 4 2.53AEBP1 adipocyte enhancer-binding protein 1 2.53CCL20 chemokine (C-C motif) ligand 20 2.53EREG proepiregulin 2.50LTBP3 latent-transforming growth factor beta-binding protein 3 2.50PGLS 6-phosphogluconolactonase 2.48GPX3 glutathione peroxidase 3 2.45GNAS guanine nucleotide regulatory protein 2.44ZNF185 zinc finger protein 185 (LIM domain) 2.41RCN3 reticulocalbin 3 2.41ESM1 endothelial cell-specific molecule 1 2.41

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Table S4. Significantly downregulated genes secreted from stromal cells (HS5) in the presence of CTGF. HS5 cells were incubated for 8 hours in the presence of rhCTGF (100ng/ml) or control buffer. RNA was used for microarray analysis. Gene list comprises secreted genes identified significantly downregulated by LIMMA (FDR-adjusted P-value <0.05, fold change >2) and present on the Secreted Protein Discovery Initiative (SPDI, Clarke et al., 2003).

secreted genes downregulated at 8 hours

Gene

Symbol Aliases & Descriptions

Fold

Change

C12orf10 chromosome 12 open reading frame 10 2.37G0S2 G0/G1 switch regulatory protein 2 2.34TIMP2 TIMP metallopeptidase inhibitor 2 2.34

CREB3 cyclic AMP response element (CRE)-binding protein 3 (luman) 2.33C12orf11 chromosome 12 open reading frame 11 2.32G0S3 G0/G1 switch regulatory protein 3 2.31TIMP3 TIMP metallopeptidase inhibitor 3 2.30

CREB4 cyclic AMP response element (CRE)-binding protein 3 (luman) 2.28MFAP2 microfibrillar-associated protein 2 2.21EPHA2 ephrin type-A receptor 2 2.20SFRP1 secreted apoptosis-related protein 2 2.16CS citrate synthase, mitochondrial 2.16MMP12 matrix metallopeptidase 12 (macrophage elastase) 2.14IGFBP7 insulin-like growth factor-binding protein 7 2.12VNN1 vascular non-inflammatory molecule 1 2.11MAZ myc-associated zinc finger protein 2.10IGFBP3 insulin-like growth factor-binding protein 3 2.09LAMC3 laminin subunit gamma-3 2.07ECM1 extracellular matrix protein 1 2.07

SERPINH1serine (or cysteine) proteinase inhibitor, clade H (heat shock protein 47), member 2, (collagen-binding protein 2) 2.07

LGALS3BP lectin, galactoside-binding, soluble, 3 binding protein 2.03CTSD cathepsin D (lysosomal aspartyl protease) 2.03TGFA protransforming growth factor alpha 2.01

PSMD2proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 2.00

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Figure S1.NOD/SCID xenografts treated with high dose ARAC. Mice were injected

5 6via the tail-vein with 2x10 PER-278 High and Low cells or 1x10 PER-371 High and Low cells. At 1% engraftment in peripheral blood ARAC treatment was started at 100mg/kg/day according to treatment protocol a. PER-278 Low, and b. PER-278 High injected mice were administered saline or ARAC. c. PER-371 Low, and d. PER-371 High xenografts were administered saline or ARAC. Data are expressed as the percent survival of mice against time. (n=5-7). (Log-Rank test: **, p<0.01, ***, p<0.001). Arrow indicates first and last ARAC injection, drug toxicity is responsible for treated mice sacrificed before last ARAC injection.

Kaplan Meier survival plots for PER-278 and PER-371

b.

c.

a.

d.

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Human L1000 Array, Membrane (AAH-BLM-1000)Detects 1000 Human Proteins.

11b-HSD1, 2B4, 4-1BB, 6Ckine, A1BG, A2M, ABL1, ACE, ACE-2, ACK1, ACPP, ACTH, Activin A, Activin B, Activin C, Activin RIA / ALK-2, Activin RIB / ALK-4, Activin RII A/B, Activin RIIA, ADAM-9, ADAMTS-1, ADAMTS-10, ADAMTS-13, ADAMTS-15, ADAMTS-17, ADAMTS-18, ADAMTS-19, ADAMTS-4 , ADAMTS-5, ADAMTS-L2, Adiponectin / Acrp30, Adipsin, Afamin, AFP, AgRP, ALBUMIN, ALCAM, Aldolase A, Aldolase B, Aldolase C, ALK, Alpha 1 AG, Alpha 1 Microglobulin, Alpha Lactalbumin, ALPP, AMICA, AMPKa1, Amylin, Angiogenin, Angiopoietin-1, Angiopoietin-2, Angiopoietin-4, Angiopoietin-like 1, Angiopoietin-like 2, Angiopoietin-like Factor, Angiostatin, ANGPTL3, ANGPTL4, Annexin A7, APC, APCS, Apelin, Apex1, APJ, APN, ApoA1, ApoA2, ApoA4, ApoB, ApoB100, ApoC1, ApoC2, ApoC3, ApoD, ApoE, ApoE3, ApoH, ApoM, APP, APRIL, AR (Amphiregulin), Artemin, ASPH, Attractin, Axl, B3GNT1, B7-1 /CD80, BAF57, BAFF, BAFF R / TNFRSF13C, BAI-1, BCAM, BCMA / TNFRSF17, BD-1, BDNF, Beta 2M, Beta Defensin 4, Beta IG-H3, beta-Catenin, beta-Defensin 2, beta-NGF, Biglycan, BIK, BLAME, BLC / BCA-1 / CXCL13, BMP-15, BMP-2, BMP-3, BMP-3b / GDF-10, BMP-4, BMP-5, BMP-6, BMP-7, BMP-8, BMP-9, BMPR-IA / ALK-3, BMPR-IB / ALK-6, BMPR-II, BMX, BNIP2, BNP, BTC, Btk, C2, C3a, C5/C5a, C7, C8B, C9, CA125, CA15-3, CA19-9, CA9, Cadherin-13, Calbindin, Calbindin D, Calcitonin, Calreticulin, Calsyntenin-1, Cardiotrophin-1 / CT-1, CART, Caspase-3, Caspase-8, Cathepsin B, Cathepsin D, Cathepsin L, Cathepsin S, CBP, CCK, CCL14 / HCC-1 / HCC-3, CCL28 / VIC, CCR1, CCR2, CCR3, CCR4, CCR5, CCR6, CCR7, CCR8, CCR9, CD 163, CD14, CD200, CD23, CD24, CD27 / TNFRSF7, CD30 / TNFRSF8, CD30 Ligand / TNFSF8, CD36, CD38, CD40 / TNFRSF5, CD40 Ligand / TNFSF5 /CD154, CD44, CD45, CD46, CD47, CD55, CD59, CD61, CD71, CD74, CD79 alpha, CD90, CD97, CEA, CEACAM-1, Cerberus 1, Ceruloplasmin, CFHR2, Chem R23, Chemerin, CHI3L1, Chordin-Like 1, Chordin-Like 2, Chromogranin A, Chymase, cIAP-2, Ck beta 8-1, CK-MB, Claudin-3, Claudin-4, CLC, CLEC3B, Clusterin, CNDP1, CNTF R alpha, CNTF, Coagulation Factor III / Tissue Factor, COCO, Complement factor H, Contactin-1, Contactin-2, Corticosteroid-binding globulin, COX-2, C-peptide, CPN2, Creatinine, CRIM 1, Cripto-1, CRP, CRTAM, CRTH-2, Cryptic, CSH1, Csk, CTACK / CCL27, CTGF / CCN2, CTLA-4 /CD152, cTnT / Troponin T, CutA, CV-2 / Crossveinless-2, CXCL14 / BRAK, CXCL16, CXCR1 / IL-8 RA, CXCR2 / IL-8 RB, CXCR3, CXCR4 (fusin), CXCR5 /BLR-1, CXCR6, Cyclin D1, Cystatin A, Cystatin B, Cystatin C, Cytochrome C, Cytokeratin 8, Cytokeratin18, Cytokeratin19, D6, DAN, DANCE, DBI, DCBLD2, DcR3 / TNFRSF6B, D-Dimer, Decorin, DEFA1/3, Defensin, Desmin, Dkk-1, Dkk-3, Dkk-4, DLL1, DLL4, DMP-1, DPPIV, DR3 / TNFRSF25, DR6 / TNFRSF21, Dtk, E-Cadherin, EDA-A2, EDAR, EDG-1, EGF, EGF R / ErbB1, EG-VEGF / PK1, EMAP-II, ENA-78, Endocan, Endoglin / CD105, Endorphin Beta, Endostatin, Endothelin, Endothelin Receptor A, Enolase 2, ENPP2, EN-RAGE, Eotaxin / CCL11, Eotaxin-2 / MPIF-2, Eotaxin-3 / CCL26, EpCAM, EphA1, EphA2, EphA3, EphA4, EphA5, EphA6, EphA7, EphA8, EphB1, EphB2, EphB3, EphB4, EphB6, Epiregulin, ErbB2, ErbB3, ErbB4, ERRa, Erythropoietin R, Erythropoietin, ESAM, E-Selectin, EV15L, EXTL2, FABP1, FABP2, FABP3, FABP4, Factor XIII A, Factor XIII B, FADD, FAK, FAM3B, FAP, Fas / TNFRSF6, Fas Ligand, Fc RIIB/C, Fen 1, FER, Ferritin, Fetuin A, Fetuin B, FGF Basic, FGF R3, FGF R4, FGF R5, FGF-10 / KGF-2, FGF-11, FGF-12, FGF-13 1B, FGF-16, FGF-17, FGF-18, FGF-19, FGF-20, FGF-21, FGF-23, FGF-4, FGF-5, FGF-6, FGF-7 / KGF, FGF-8, FGF-9, FGF-BP, FGFR1, FGFR1 alpha, FGFR2, Fibrinogen, Fibrinopeptide A, Fibronectin, Ficolin-3, FIH, FLRG, Flt-3 Ligand, Follistatin, Follistatin-like 1, FOLR1, FOXN3, FoxO1, FoxP3, Fractalkine, Frizzled-1, Frizzled-3, Frizzled-4, Frizzled-5, Frizzled-6, Frizzled-7, FRK, FSH, Furin, Fyn, GADD45A, Galanin, Galectin-1, Galectin-3, Galectin-3BP, Galectin-7, gamma-Thrombin, Gas1, GASP-1 / WFIKKNRP, GASP-2 / WFIKKN, Gastrin, GATA-3, GATA-4, GCP-2 / CXCL6, GCSF, G-CSF R / CD 114, GDF1, GDF11, GDF-15, GDF3, GDF5, GDF8, GDF9, GDNF, Gelsolin, GFR alpha-1, GFR alpha-2, GFR alpha-3, GFR alpha-4, Ghrelin, GITR / TNFRF18, GITR Ligand / TNFSF18, GLP-1, Glucagon, Glut1, Glut2, Glut3, Glut5, Glypican 3, Glypican 5, GM-CSF, GM-CSF R alpha, GMNN, GPBB, GPI, GPR-39, GPX1, GPX3, Granzyme A, GREMLIN, GRO, GRO-a, Growth Hormone (GH), Growth Hormone R (GHR), GRP, GRP75, GRP78, GSR, GST, HADHA, HAI-1, HAI-2, Haptoglobin, HB-EGF, HCC-4 / CCL16, hCG alpha, hCGb, Hck, HCR / CRAM-A/B, HE4, Hemopexin, Hepassocin, Hepcidin, Heregulin / NDF / GGF / Neuregulin, HGF, HGFR, HOXA10, HRG-alpha, HRG-beta 1, HSP10, HSP20, HSP27, HSP32, HSP40, HSP60, HSP70, HSP90, HSPA8, HTRA2, HVEM / TNFRSF14, I-309, IBSP, ICAM-1, ICAM-2, ICAM-3 (CD50), ICAM-5, IFN-alpha / beta R1, IFN-alpha / beta R2, IFN-beta, IFN-gamma, IFN-gamma R1, IGF2BP1, IGFBP-1, IGFBP-2, IGFBP-3, IGFBP-4, IGFBP-5, IGFBP-6, IGFBP-rp1 / IGFBP-7, IGF-I, IGF-I SR, IGF-II, IGF-II R, IL-1 alpha, IL-1 beta, IL-1 F10 / IL-1HY2, IL-1 F5 / FIL1delta, IL-1 F6 / FIL1 epsilon, IL-1 F7 / FIL1 zeta, IL-1 F8 / FIL1 eta, IL-1 F9 / IL-1 H1, IL-1 R3 / IL-1 R AcP, IL-1 R4 /ST2, IL-1 R6 / IL-1 Rrp2, IL-1 R8, IL-1 R9, IL-1 ra, IL-1 sRI, IL-1 sRII, IL-10, IL-10 R alpha, IL-10 R beta, IL-11, IL-12 p40, IL-12 p70, IL-12 R beta 1, IL-12 R beta 2, IL-13, IL-13 R alpha 1, IL-13 R alpha 2, IL15, IL-15 R alpha, IL-16, IL-

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Table S5membrane detecting 1000 proteins (Human Array L-1000, Ray Biotech). A combination of L-507 and L-493 arrays. For the simultaneous detection of the relative expression of 1000 human proteins in cell culture supernatants. Cat# AAH-BLM-1000-4.

Complete detectable protein list for human protein array

IL-15, IL-15 R alpha, IL-16, IL-17, IL-17B, IL-17B R, IL-17C, IL-17D, IL-17E, IL-17F, IL-17R, IL-17RC, IL-17RD, IL-18 BPa, IL-18 R alpha /IL-1 R5, IL-18 R beta /AcPL, IL-19, IL-2, IL-2 R alpha, IL-2 R beta /CD122, IL-2 R gamma, IL-20, IL-20 R alpha, IL-20 R beta, IL-21, IL-21 R, IL-22, IL-22 BP, IL-22 R, IL-23, IL-23 R, IL-23p19, IL-24, IL-26, IL-27, IL-28A, IL-29, IL-3, IL-3 R alpha, IL-31, IL-31 RA, IL-33, IL-34, IL36RN, IL-4, IL-4 R, IL-5, IL-5 R alpha, IL-6, IL-6 R, IL-7, IL-7 R alpha, IL-8, IL-9 , Inhibin A, Inhibin B, INSL3, INSRR, Insulin, Insulin R, Insulysin / IDE, Integrin alpha V, IP-10, I-TAC / CXCL11, Itk, ITM2B, Kallikrein 10, Kallikrein 11, Kallikrein 14, Kallikrein 2, Kallikrein 5, Kallikrein 6, Kallikrein 7, Kallikrein 8, KCC3, KCTD10, KIF3B, Kininostatin / kininogen, KLF4, Kremen-1, Kremen-2, LAG-3, Latent TGF-beta bp1, Layilin, LBP, Lck, LDL R, LECT2, Lefty - A, Legumain, Leptin (OB), Leptin R, LFA-1 alpha, LH, LIF R alpha, LIF, LIGHT / TNFSF14, LIMPII, LIN41, Lipocalin-1, Livin, LOX-1, LPS, LRG1, LRP-1, LRP-6, L-Selectin (CD62L), LTF, LTK, Luciferase, Lumican, Lymphotactin / XCL1, Lymphotoxin beta / TNFSF3, Lymphotoxin beta R / TNFRSF3, Lyn, LYRIC, LYVE-1, LZTS1, MAC-1, Mammaglobin A, Marapsin, MATK, MBL, MBL-2, MCP-1, MCP-2, MCP-3, MCP-4 / CCL13, M-CSF, M-CSF R, MDC, Mer, Mesothelin, MFG-E8, MFRP, MICB, Midkine, MIF, MIG, MINA, MIP 2, MIP-1a, MIP-1b, MIP-1d, MIP-3 alpha, MIP-3 beta, MMP-1, MMP-10, MMP-11 /Stromelysin-3, MMP-12, MMP-13, MMP-14, MMP-15, MMP-16 / MT3-MMP, MMP-19, MMP-2, MMP-20, MMP-24 / MT5-MMP, MMP-25 / MT6-MMP, MMP-3, MMP-7, MMP-8, MMP-9, MSHa, MSP alpha Chain, MSP beta-chain, MTUS1, Musk, Myoglobin, NAIP, Nanog, NAP-2, NCAM-1 / CD56, NELL2, NEP, Nesfatin, Nestin, NET1, Netrin G2, Netrin-4, Neuritin, NeuroD1, Neurokinin-A, Neuropeptide Y, Neuropilin-2, Neurturin, NF1, NGF R, NM23-H1/H2, Notch-1, NOV / CCN3, NPTX1, NPTXR, NR3C3, NRG1 Isoform GGF2, NRG1-alpha / HRG1-alpha, NRG1-beta1 / HRG1-beta1, NRG2, NRG3, NT-3, NT-4, Ntn1, OCT3/4, Omentin, Orexin A, Orexin B, OSM, Osteoactivin / GPNMB, Osteocalcin, Osteocrin, Osteopontin, Osteoprotegerin / TNFRSF11B, OX40, OX40 Ligand / TNFSF4, p21, p27, p53, PAI-1, PAK7, Pancreastatin, Pancreatic Polypeptide, Pappalysin-1, PARC / CCL18, PARK7, P-Cadherin, PCAF, PD-1, PD-ECGF, PDGF R alpha, PDGF R beta, PDGF-AA, PDGF-AB, PDGF-BB, PDGF-C, PDGF-D, PDX-1, PECAM-1 /CD31, PEDF , Pentraxin3 / TSG-14, PEPSINOGEN I, PEPSINOGEN II, Persephin, PF4 / CXCL4, PGRP-S, PI 16, PI 3Kinase p85 beta, PIM2, PKM2, Plasminogen, PlGF, PLUNC, Podocalyxin, POMC, PON1, PON2, PPARg2, PPP2R5C, Pref-1, Presenilin 1, Presenilin 2, Pro-BDNF, Procalcitonin, Pro-Cathepsin B, Progesterone, pro-Glucagon, Progranulin, Prohibitin, Prolactin, Pro-MMP-13, Pro-MMP-7, Pro-MMP-9, ProSAAS, Prostasin, Protein p65, PSA-Free, PSA-total, P-selectin, PSP, PTH, PTHLP, PTN, PTPRD, PYK2, PYY, RAGE, RANK / TNFRSF11A, RANTES, Ras, RBP4, RECK, RELM alpha, RELM beta, RELT / TNFRSF19L, Resistin, RET, RIP1, ROBO4, ROCK1, ROCK2, ROR1, ROR2, ROS, RYK, S100 A8/A9, S100A10, S100A4, S100A6, S100A8, S-100b, SAA, SART1, SART3, SCF, SCF R /CD117, SCG3, SDF-1 / CXCL12, Selenoprotein P, SEMA3A, Serotonin, Serpin 1, Serpin A1, Serpin A12, Serpin A3, Serpin A4, Serpin A5, Serpin A8, Serpin A9, Serpin B5, Serpin D1, Serpin I1, SERTAD2, sFRP-1, sFRP-3, sFRP-4, sgp130, SHBG, SIGIRR, Siglec-5/CD170, Siglec-9, SLPI, SMAC, Smad 1, Smad 4, Smad 5, Smad 7, Smad 8, SMDF / NRG1Isoform, SNCG, Soggy-1, Somatotropin, Sonic Hedgehog (Shh N-terminal), SOST, SOX17, SOX2, SPARC, SPARCL1, Spinesin, SPINK1, SRMS, SSEA-1, SSEA-4, SSTR2, SSTR5, Survivin, SYK, Syndecan-1, Syndecan-3, TACE, TACI / TNFRSF13B, TAF4, Tarc, TCCR / WSX-1, Tec, TECK / CCL25, TFF1, TFF3, TFPI, TGF-alpha, TGF-beta 1, TGF-beta 2, TGF-beta 3, TGF-beta 5, TGF-beta RI / ALK-5, TGF-beta RII, TGF-beta RIIb, TGF-beta RIII, Thrombin, Thrombomodulin, Thrombopoietin (TPO), Thrombospondin (TSP), Thrombospondin-1, Thrombospondin-2, Thrombospondin-4, Thymidine Kinase-1, Thymopoietin, Thyroglobulin, Tie-1, Tie-2, TIM-1, TIMP-1, TIMP-2, TIMP-3, TIMP-4, TL1A / TNFSF15, TLR1, TLR2, TLR3, TLR4, TMEFF1 / Tomoregulin-1, TMEFF2, TNF RI / TNFRSF1A, TNF RII / TNFRSF1B, TNF-alpha, TNF-beta, TNK1, TOPORS, TPA, TPM1, TRA-1-60, TRA-1-81, TRADD, TRAIL R1 / DR4 / TNFRSF10A, TRAIL R2 / DR5 / TNFRSF10B, TRAIL R3 / TNFRSF10C, TRAIL R4 / TNFRSF10D, TRAIL / TNFSF10, TRANCE, Transferrin, Trappin-2, TREM-1, TRKB, Troponin C, Troponin I, TROY / TNFRSF19, TRPC1, TRPC6, TRPM7, Trypsin 1, TSG-6, TSH, TSLP, TSLP, TWEAK / TNFSF12, TWEAK R / TNFRSF12, TXK, Tyk2, TYRO10, Ubiquitin+1, uPA, uPAR, Uromodulin, Vasopressin, Vasorin, VCAM-1 (CD106), VDUP-1, VE-Cadherin, VEGF, VEGF R1, VEGF R2 (KDR), VEGF R3, VEGF-B, VEGF-C, VEGF-D, VEGI / TNFSF15, VGF, VIP Receptor 2, Visfatin, Vitamin D Receptor, Vitamin D-BP, Vitamin K-dependent protein S, Vitronectin, VWF, WIF-1, Wilms Tumor 1, WISP-1 / CCN4, XEDAR, XIAP, ZAG, ZAP70

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c.

a.Membrane 1 (L-507) Membrane 2 (L-493)

b.

Figure S2proteins (Human Array L-1000, Ray Biotech). Protein expression was determined for secreted media from a. HS5 in low serum with red boxes indicating positive controls. b. HS5 co-incubated with PER-371 Low in low serum and c. HS5 co-incubated with PER-371 High in low serum. The left hand column depicts membrane 1 (L-507) and the right hand column depicts membrane 2 (L-493).

. Raw data for human protein array membrane detecting 1000

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