RCC: Molecular Pathways and Novel Therapies Kidney Cancer
Transcript of RCC: Molecular Pathways and Novel Therapies Kidney Cancer
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James Brugarolas, M.D., Ph.D.Kidney Cancer Program Leader
Virginia Murchison Linthicum Endowed ScholarAssociate Professor of Internal Medicine
University of Texas Southwestern Medical Center
http://www.utsouthwestern.edu/kidneycancer
RCC: Molecular Pathways and Novel Therapies
Brugarolas Lab
Research Funding: Peloton Therapeutics, Inc.
I will discuss investigational use of a HIF-2 inhibitorSiegel et al., CA Cancer J Clin 2015
Kidney Cancer
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https://www.dshs.state.tx.us/tcr/data.shtm
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Sunitinib SorafenibPazopanibAxitinib
Temsirolimus Everolimus
Biological understanding leads to new therapies
Bevacizumab
Shen, C. and Kaelin, W.G. Sem. Can. Biol. 2013
Adapted from Brugarolas J. N Engl J Med 2007
Nivolumab
How do we advance the field?
New targetsNew pathways
HIF‐2
VEGF Myc/Cyclin D1 Oct4 p53
ANGIOGENESIS CELL PROLIFERATION PLURIPOTENCY APOPTOSIS
BevacizumabSunitinibSorafenibPazopanib
Axitinib
HIF2-I
Scheuermann et al. PNAS 2009
B
A
B
A
HRE (DNA)
HIF-2 HIF-1
HRE (DNA)
HIF-1HIF-2
Scheuermann et al. Nat Chem Biol 2013
High-Throughput Screen
HIF2-I
Development of a HIF-2 inhibitor (HIF2-I)
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Testing HIF2-I in kidney cancer
Human tumors in mice do they reproduce: Histological appearance?
Gene expression?
Mutations?
DNA copy number alterations?
Treatment responsiveness?
Sivanand et al., Sci Transl Med 2012Adapted from Sivanand et al., Sci Transl Med 2012
Unsupervised hierarchical clustering of gene expression shows similarities between tumors and corresponding tumorgrafts
HIF2-I is active against human ccRCC transplants in mice
Days
Tum
or v
olum
e (m
m3 )
Vehicle
Sunitinib
HIF2-I
HIF2-I is active in 50% of ccRCC
Inte
rmed
.Se
nsiti
veR
esis
tant
VehicleSunitinibHIF2-I
267 mice from 22 independently derived TG lines
Chen et al., Submitted – do not reproduce
HIF2-I inhibits proliferation and angiogenesis in sensitive ccRCC
XP164
XP469
XP454
XP373
HIF2-Ivehicle
V4239 P4244
P3297V3294
V5407 P5399
V4921 P4924
HIF2-Iveh
XP373
XP144
CD
31H
&E
XP373
Ki67
veh HIF2-I
XP16
4XP
490
XP16
9XP
373
vehicle HIF2‐I
V4237
V5239 V5229 P5231 P5240
V4236 V4241V4234
V3290 V3294 V3287 V3281
V3212 V3224 V3210 V3214
VehicleHIF2-ISunitinib
Chen et al., Submitted – do not reproduce
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HIF2-I dissociates HIF-2 in sensitive & resistant tumors
RE
SIS
TAN
T
S
EN
SIT
IVE
Chen et al., Submitted – do not reproduce
Reformation of HIF-2 dimers with acquired resistance
Input
IP HIF-1
V3290
V3294
V3298
P3283
P3288
P3297
V3290
V3294
V3298
P3283
P3297
Tubulin
post-resistance
HIF‐2
HIF‐1
P3288
pre-resistance
0500100015002000250030003500400045005000
‐20 0 20 40 60 80 100 120 140 160 180 200
Tum
or V
olum
e (m
m3 )
XP164
3283
3288
3296
3295
3299
3286 Veh
Sunitinib
HIF2-I
Chen et al., Submitted – do not reproduce
Phase I Clinical Trial of HIF2-I
Photo, courtesy of Brian Coats
Conclusions (Part I) RCC tumorgrafts reproduce the biological properties of patient
tumors.
Inhibition of arguably the most important driver of ccRCC, the HIF-2 transcription factor, abrogates tumor growth in 56% of ccRCC tumorgrafts, including tumors resistant to sunitinib.
HIF2-I effectively (and specifically) dissociates HIF-2 from HIF-1in human ccRCC implanted in mice.
HIF-2 inhibition results in the downregulation of HIF-2 target genes and decreased circulating levels of tumor-produced VEGF.
Primary resistance occurs despite dissociation of the HIF-2 complex in tumors.
A Phase I clinical trial at UTSW (and elsewhere) with a first-in-class HIF-2 inhibitor has completed accrual.
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Sunitinib SorafenibPazopanibAxitinib
Temsirolimus Everolimus
Bevacizumab
Biological understanding leads to new therapies
How do we go forward?
New targetsNew pathways
Adapted from Brugarolas J. N Engl J Med 2007
PBRM1 mutations in ~50% of ccRCC.
PBRM1 is a two-hit tumor suppressor gene located on chromosome 3p.
Encodes BAF180, a component of a nucleosome remodeling complex - SWI/SNF family (PBAF complex).
Thought to regulate DNA packing and accessibility.
BAP1 is mutated in ~15% of sporadic ccRCC.
BAP1 is a two-hit tumor suppressor gene located on chromosome 3p and mutations abrogate protein expression.
BAP1 is a nuclear DUB of the UCH family implicated in cell cycle regulation, DNA replication and DNA damage repair.
BAP1-mutant tumors tend to be of high grade and associated with mTOR complex 1 activation.
Tumors with simultaneous BAP1 and PBRM1 mutations are underrepresented
p = 0.00003
Pena-Llopis et al., Nat Genet 2012
What are these data telling us?
, deletionI, insertion*, non-senseS, splice site†, missense*L, stop codon lost
Mutation
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Under-representation of tumors with simultaneous BAP1 & PBRM1 in meta-analysis
Pena-Llopis et al., Can Res 2013
Study n PBRM1 BAP1 BAP1/ PBRM1
Expecteddouble mutants p value
Odds Ratio
(95% CI)
Peña-Llopis et al. 176 89 21 3 13 (9-16) 0.00003 0.10 (0.03 - 0.35)
Guo et al. 98 21 8 0 2 (0-4) 0.2 0.19 (0.01 - 3.43)
Hakimi et al. 185 53 10 1 3 (1-5) 0.18 0.23 (0.03 - 1.83)
TCGA 293 101 22 5 10 (7-13) 0.058 0.37 (0.14 - 1.01)
Total 576 175 40 6 14 (11-18) 0.004 0.29 (0.12 - 0.70)
A foundation for a molecular genetic classification of ccRCC
Pena-Llopis et al., Nature Genet 2012
High grade(q = 0.0005)
Low grade(q = 0.025)
Pena-Llopis et al., Can Res 2013
BAP1 and PBRM1 genes are on chromosome 3p and one allele is frequently co-deleted with VHL in ccRCC
Chr 3
VH
L
BA
P1
PB
RM
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VHL intragenic mutation
VH
L
BA
P1
PB
RM
1
Loss of 3p
VH
L
BA
P1
PB
RM
1Brugarolas J. JCO 2014
VH
L
BA
P1
PB
RM
1 BAP1 mutation
High grade Low grade
VH
L
BA
P1
PB
RM
1PBRM1 mutation
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May explain why VHL+/- humans but not Vhl+/- mice develop renal cancer
Chr 6
Vhl Bap1Pbrm1
Chr 14
In the mice:
To test this hypothesis: We inactivated Vhl and one allele of Bap1 in nephron progenitor cells. (Loss of both copies of Bap1 causes renal failure and perinatal death).
Wang et al., PNAS 2014
Six2-Cre induces the loss of Bap1 in renal tubular cells normally expressing Bap1
R26RtdT/-gal/DAPI-galR26RtdT
LTL -gal merge
Bap1expressionloxPFRT
55
413
loxPFRT5 -gal5 6neo 4 4
12 13Gene-trap line
-gal
Reporter line Lineagetracing
+ Six2-Cre
Stopcassette tdTomatotdTomato tdTomato
Knockout line+ Six2-Cre Bap1
knockout
loxPFRT4 5
3 4 5 6
loxP
3 6
Wang et al., PNAS 2014
Targeting Vhl and Bap1 in the mouse kidney causes ccRCC
Ki6
7
CA
IX
Wang et al., PNAS 2014
Chr 3
VH
L
BA
P1
PB
RM
1
VHL intragenic mutation
VH
L
BA
P1
PB
RM
1
Loss of 3p
VH
L
BA
P1
PB
RM
1Brugarolas J. JCO 2014
VH
L
BA
P1
PB
RM
1 BAP1 mutation
High grade Low grade
VH
L
BA
P1
PB
RM
1PBRM1 mutation
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BAP1- and PBRM1-mutant tumors are associated with different outcomes
Time from surgery (years)0 2 4 6 8 10 12
Ove
rall
Surv
ival
0.0
0.2
0.4
0.6
0.8
1.0
PBRM1BAP1
HR, 2.7 (95% CI 0.99-7.6)Log-rank p = 0.044
UTSW cohort
Kapur et al., Lancet Oncology 2013
Time from surgery (years)0 2 4 6 8
Ove
rall
Surv
ival
0.0
0.2
0.4
0.6
0.8
1.0
PBRM1BAP1
HR, 2.8 (95% CI 1.4-5.9)Log-rank p = 0.004
TCGA cohort
Development of a BAP1 IHC test for broader analyses
Pena-Llopis et al., Nat Genet 2012
ID M IHC ID M IHC ID M IHC ID M IHC ID M IHC ID M IHC40 X - 9 + 322 + 9478 + T79 + T157 +63 - 14 + 324 + 9563 + T80 + T158 +78 - 19 + 325 + 9812 + T83 + T160 +
162 - 23 + 425 + 9964 + T84 + T161 +209 - 26 + 572 + 10038 + T91 + T162 +
3397 S - 31 + 619 + 10162 + T92 + T164 +3575 I - 32 + 974 + 10305 + T94 + T165 +9145 XL - 37 + 981 + 13425 + T97 + T170 +9575 X - 39 + 1014 + T4 + T98 + T171 +T16 ¶ - 42 + 1393 + T5 + T106 + T173 +T25 - 44 + 1524 + T6 + T107 + T175 +T26 - 45 + 1637 + T7 + T110 + T183 +T55 - 52 + 1677 + T9 + T116 + T191 +T69 ¶ - 74 + 1791 + T11 + T118 + T192 +T70 X - 75 + 1793 + T15 + T125 + T193 +
T114 - 76 + 2038 + T18 + T126 + T194 +T115 ¶ - 83 + 2077 + T20 + T127 + T197 +T149 - 111 + 2154 + T21 + T128 + T199 +T163 - 113 + 2827 + T22 + T130 + T202 +T166 ¶ - 115 + 3246 + T24 + T131 + T204 +T184 X - 131 + 3483 + T28 + T133 + T205 +T211 X - 139 + 3570 + T37 + T136 + T209 +T145 ¶ + 222 + 3604 + T39 + T142 + T210 +T212 ¶ + 233 + 3750 + T41 + T143 + T213 +
312 - 239 + 3801 + T42 + T144 + T214 +1732 - 240 + 3907 + T52 + T146 + T216 +T195 - 260 + 4077 + T65 + T150 +2368 ? 262 + 4301 + T73 + T151 +
1 + 265 + 4505 + T75 + T153 +4 + 275 + 8885 + T76 + T155 +
BAP1 deficient BAP1 wild-type
Evaluation of BAP1 in 1,400 patients with resectable ccRCC from Mayo Registry
BAP1 loss is associated with reduced RCC-specific survival in the Mayo Registry
RC
C-s
peci
fic s
urvi
val (
%)
Time from surgery (yrs)
BAP1 pos (n=1,196)
BAP1 neg (n=148)
HR: 3.06; 95% CI (2.28 - 4.10)P = 6·10-14
Joseph, R.* and Kapur, P.* et al., Cancer 2013
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BAP1 and PBRM1 loss in different tumors regions
BAP1 and PBRM1 loss in same tumor regions
IHC identifies tumors with simultaneous inactivation of BAP1 and PBRM1
BAP1-
BAP1+
PBRM1+
PBRM1-
Joseph, R.* and Kapur, P.* et al., J. Urol. 2015
Four molecular subtypes of ccRCC with different outcomes (Mayo cohort)
PBRM1+ BAP1+
PBRM1- BAP1+
PBRM1+ BAP1-
PBRM1- BAP1-Expected double mutants: 5.3%Observed: 1.8%OR, 0.18; CI 0.11-0.28, p<0.00001
Joseph, R.* and Kapur, P.* et al., J. Urol. 2015
A foundation for the first molecular genetic classification of ccRCC
WT PBRM1 BAP1 BAP1/PBRM1
Deadliness
DR
UG
A
DR
UG
B
DR
UG
C
DR
UG
D
The Future:
Tumorgrafts tissue microarray:• 58 ccRCC
o 22 PBRM1-deficiento 7 BAP1-deficiento 3 BAP1/PBRM1-deficient
Integrated genomics (Exome, RNAseq) ~70 TG lines
TG: a platform for evaluation of BAP1 & PBRM1 pathway-targeting drugs
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Photo, courtesy of Brian Coats
BAP1 and PBRM1 mutations define 4 subtypes of renal cancer with different biology (gene expression) and prognosis.
These discoveries underlie the foundation for the first molecular genetic classification of sporadic ccRCC.
These findings pave the way for the development of subtype-specific treatments of previously unrecognized subtypes.
Co-linear arrangement of multiple ccRCC two-hit tumor suppressor genes on chromosome 3p may explain human predisposition to ccRCC.
More broadly, these findings provide a potential explanation for the differential tumor predisposition across species.
Conclusions (Part II)
http://www3.utsouthwestern.edu/brugarolaslab
http://www.utsouthwestern.edu/kidneycancer
Brugarolas LabYifeng GuHaley HillFarrah Homayoun Meghan KondaEric MaRenee McKay Andrea Pavia-JimenezNick C. WolffHui YeAnum Yousuf
Alana Christie Xian-Jin Xie
Wenfang ChenShannon CohnEboni Holloman Blanka KucejovaSamuel Peña-LlopisSharanya SivanandVanina ToffessiTram Anh T. TranSilvia Vega-Rubin de CelisShanshan WangToshinari Yamasaki
Deni Von Merveldt Vincy AlexDebbie Harvey
FundingVirginia Murchison Linthicum EndowmentCancer Prevention and Research Institute of TexasNIH, National Cancer Institute
Kidney Cancer ProgramUrologyJeff CadedduJeff GahanYair LotanVitaly MargulisGanesh RajArthur I. Sagalowsky
Medical OncologyYull ArriagaKevin CourtneyEugene Frenkel
Radiation OncologyRaquibul HannanNathan KimDavid PistenmaaRobert Timmerman
PathologyPayal KapurDinesh Rakheja
RadiologyIvan PedrosaLori Watumull
Clinical GeneticsMegan Farley
Illumina Inc. Arnold LiaoNan LengChristian HaudenschildMark RossDavid Bentley
Mayo ClinicRichard W. JosephDaniel J. SerieJeanette Eckel-PassowThai HoJohn C. ChevilleAlexander Parker
GenentechAnwesha DeySteffen DurinckEric W. StawiskiZora ModrusanSekar Seshagiri
NCILaura SchmidtMarston Linehan
Other CollaboratorsThomas CarrollRalph DeBerardinisRobert E. HammerTae Hyun Hwang Min KimBruce PosnerDipti RanganathanNoelle WilliamsYang XieJin YeYonghao Yu
GENENTECHPELOTON THERAPEUTICS