Standard Operating Pre-Analytical Procedures for Protein … · Protein Profiling and DNA Studies:...
Transcript of Standard Operating Pre-Analytical Procedures for Protein … · Protein Profiling and DNA Studies:...
Fiorella Guadagni, M.D., Ph.D.Department of Laboratory Medicine & Advanced BiotechnologiesIRCCS San Raffaele Pisana, Rome, [email protected]
Standard Operating Pre-Analytical Procedures for Protein Profiling and DNA Studies: the Experience of
the Interinstitutional Multidisciplinary BioBank (BioBIM)
3rd Annual Biospecimen Research Network (BRN) Symposium:Advancing Cancer Research Through Biospecimen Science
March 24-25, 2010, Bethesda, Maryland, USA
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
The BioBIM is an organized collection of biological samples obtained from individuals attending several Italian Institutions. The BioBIM operates under the auspices of the IRCCS San Raffaele, Rome, Italy, a private Scientific Institution certified by the Italian Minister of Health.
The BioBIM is ISO certified.
BioBIM - Interinstitutional Multidisciplinary BioBank
AIMSThe Inter-Institutional Multidisciplinary BioBank will operate with the aims of:
• collecting and analyzing high-quality biological specimens from all participating Units, in an efficient, organized and accessible manner using leading-edge technologies.
• connecting professionals with each other across traditional hospital or laboratory departments to provide a multidisciplinary research structure properly embedded into European ethical and legal frameworks.
• facilitating translational research enabling us to apply biomarker discovery to clinical outcome studies and novel targets for therapy.
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
Five different disease-based biorepositories have been structured, devoted to:
1. Cancer diseases2. Cardiovascular and respiratory diseases3. Neurodegenerative diseases4. Developmental disabilities5. Rare diseases
Healthy volunteers are also recruited
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
IRCCS San Raffaele Romeand Cassino
Italian network ACISMOM
San Camillo Hospital, Rome
Unità Sanitaria Locale 2 Salerno
San Giovanni Addolorata Hospital, Rome
University of Rome Tor Vergata
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
clinicaldata
records
Lab-1data
dev1 dev2 dev3
repo
rtin
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OLA
P
data
min
ing
DatawarehouseDatamart-1 Datamart-2 Datamart-3
Lab-2data
devA devB devC
externalsystem-A
externalsystem-B
patientdata
samplecollection
Hospitals/Institutions
externalsystem-1
externalsystem-2
exte
rnal
ser
vice
s
quality control& active
monitoring
ETL – data integration
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
Clinical Center Network
Check-in Biological Samples
Automation
Pre-Analytical Phase
BioBIM TLA Diagnostic areaAutomation
Research activities
Genomics
Proteomics
Metabolomics
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010\
BIOMARKERS DISCOVERY
Key point - Pre-analytical phases:Sample Processing and Storage Procedures
Possible approach:Total Lab Automation
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
All blood samples are initially identified by the Tecan FE500 robot that sorts samples for diagnostic routine and samples dedicated to the BioBIM
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
Total Lab AutomationSample distribution
Robotic Station TECAN FE500
Robotic S
tation Freedom E
vo 1503rd Annual BRN SymposiumBethesda, 24-25 March, 2010
Total Lab AutomationSample identification and recording
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
Total Lab Automation
Blood storage for biological bank
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
BiospecimensBlood, Serum, Plasma, Urine, Tissues, Cells
PROTEOMICS- Protein identification- Post-translational modification- Protein Profiling- Molecular MS-Imaging
GENOMICS- Mutational Analysis- Gene Expression- Real Time PCR- SNPs
Biobank- Storage Biological Samples
BIOMARKERS DISCOVERY
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
Laboratory Robotization for proteomics highthroughput analysis
Protein extraction, purification and MS analysisProtein extraction
Protein purification
Protein profiling
Protein caracterization
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
Methodological Approach
• Comparison between manual vs robotized analytical processing for protein profiling (Low Molecular Weight proteins)
Pre-analytical conditions • Addition of protease inhibitors • Time before processing• Storage temperature
A
C
E
Automated ProcedureAutomated Procedure(peaks 68, average CV 14.1 %)
B
D
F
Manual ProcedureManual Procedure(peaks 57, average CV 18.2 %)
CV> 50% 0% 1.75%
CV 30-50% 5.90% 19.30%
CV 10-30% 45.60% 40.35%
CV< 10% 48.50% 38.60%
0%
10%
20%
30%
40%
50%
60%
70%
AutomatedProcedure
ManualProcedure
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
24 to 42 years, 3 males and 3 females
Four blood samples were treated with protease inhibitor-EDTA free
Protease inhibitor were added in some serum samples
LMW serum proteome purification by C18 magnetic beads
The average peak intensity, SD and CV (%) for each corresponding peak was calculated.
Eight Vacutainer tubes with clot activator from each subject.
Blood samples from six consenting healthy donors
1 our of clotting time HIL test of serum samples on an Architect c8000 system (Abbott,
Irving TX USA)
The tests confirmed the absence of haemolysis in serum samples
Automated serum Low Molecular Weight protein/peptides (LMW) purification
MALDI/MS analisys of LMW
ClinProt system
ClinProTools software analysis
-80ºC -80ºC +4ºC+4ºCRT RT
1, 2, 3, 6, 12 and 24hrsRPC18
1, 3, 6 months, 1 yearRPC18
1, 2,3, 6, 12 and 24hrsRPC18
t=0
1, 2, 3, 6, 12 and 24hrsRPC18 1, 2, 3, 6, 12 and 24hrs
RPC18
Whole blood with protease inhibitors
Serum with protease inhibitors **
Serum without protease inhibitorst=0
1, 3, 6 months, 1 yearRPC18
* Complete EDTA-free protease inhibitor cocktail tablets from Roche (Mannheim, Germany) containing: D-mannitol, polivinylpyrrolidone, polyethylene glycol and AEBSF
** Complete protease inhibitor cocktail tablets from Roche (Mannheim, Germany) containing: D-mannitol, polivinylpyrrolidone, polyethylene glycol, AEBSF and EDTA
-80ºC -80ºC +4ºC+4ºCRT RT
1, 2, 3, 6, 12 and 24hrsRPC18
1, 2,3, 6, 12 and 24hrsRPC18
t=0
1, 2, 3, 6, 12 and 24hrsRPC18
1, 2, 3, 6, 12 and 24hrsRPC18
Whole blood without protease inhibitors
Serum with protease inhibitors **
Serum without protease inhibitorst=0
1, 3, 6 months,1 yearRPC18
1, 3, 6 months, 1 yearRPC18
** Complete protease inhibitor cocktail tablets from Roche (Mannheim, Germany) containing: D-mannitol, polivinylpyrrolidone, polyethylene glycol, AEBSF and EDTA
Ave. CV 32.81%
Ave. CV 18.35%
Ave. CV 28.38%
1 3 4 9 . 9 8 5
2 0 2 2 . 6 1 2
0
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5x 1 0
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a.u.
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2 0 0 0 4 0 0 0 6 0 0 0 8 0 0 0 1 0 0 0 0m / z
2 0 2 0 . 6 4 2
1 3 5 0 . 3 9 9
0
1
2
3
5x 1 0
Inte
ns. [
a.u.
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2 0 0 0 4 0 0 0 6 0 0 0 8 0 0 0 1 0 0 0 0m / z
2 0 2 2 . 8 3 2
1 3 4 9 . 9 6 4
0
1
2
3
5x 1 0
Inte
ns. [
a.u.
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2 0 0 0 4 0 0 0 6 0 0 0 8 0 0 0 1 0 0 0 0m / z
0 . 0
0 . 5
1 . 0
1 . 5
2 . 0
2 . 5
5x 1 0
Inte
ns. [
a.u.
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2 0 0 0 4 0 0 0 6 0 0 0 8 0 0 0 1 0 0 0 0m / z
28 Peaks
38 Peaks
35 Peaks
25 Peaks
Clotting Time Clotting Time 30 min. 30 min.
Clotting Time Clotting Time 60 min. 60 min.
Clotting Time Clotting Time 120 min. 120 min.
Clotting Time Clotting Time 240 min. 240 min.
Clotting times
LMW protein profiles from serum (w/o PI addition on whole blood)stored at +4 C up to 24 hrs
2020.656 * 30 min camp 1-5 T0\0_B1\1\1SLin, "Baseline subt."
0
1
2
3
4
5x10
Inte
ns. [
a.u.
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1349.985
2022.612 * camp 1-5 T1+ camp 2-6 T0\0_B3\1\1SLin, "Baseline subt."
0
1
2
3
5x10
Inte
ns. [
a.u.
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2021.034 * camp 1-5 T1+ camp 2-6 T0\0_A3\1\1SLin, "Baseline subt."
0
1
2
3
5x10
Inte
ns. [
a.u.
]
2000 4000 6000 8000 10000m/z
T 0
1h
2h
Ave. CV < 16%
Ave. CV < 26%
2 0 2 2 . 6 5 5
0 . 0
0 . 5
1 . 0
1 . 5
2 . 0
2 . 5
5x 1 0
Inte
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a.u.
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2 0 0 0 4 0 0 0 6 0 0 0 8 0 0 0 1 0 0 0 0m / z
3hAve. CV 30-36%
3, 6, 12, 24h
6hAve. CV 25-28%
12hAve. CV 25-27%
24hAve. CV 29-33%
BiospecimensBlood, Serum, Plasma, Urine, Tissues, Cells
PROTEOMICS- Protein identification- Post-translational modification- Protein Profiling- Molecular MS-Imaging
GENOMICS- Mutational Analysis- Gene Expression- Real Time PCR- SNPs
Biobank- Storage Biological Samples
BIOMARKERS DISCOVERY
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
Laboratory Automation for genomic high-throughput analysis
DNA extraction, purification and sequence analysis
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
Methodological Approach
• Comparison between manual vs robotized DNA extraction
Pre-analytical conditions • Different anticoagulants• Time before processing• Storage temperature
Automated - DNA Isolation Kit
DifferentDNA extraction methods
Manual QIAmp DNA Blood Mini Kit
In house Digestion Buffer / Proteinase K kit
DNA recovery ng/μl(Nanodrop spectrophotometric quantification 260 nm)
01020304050607080
0h 6h 24h 48h 72h 96h 168hStorage time at 4°C
ng/u
l
KIT QIAGEN
DIGESTION BUFFER/PK
AUTOMATED
0,00
5,00
10,00
15,00
20,00
25,00
30,00
35,00
0 h 6h 24h 48h 72h 96h 168h
Storage time
Cp
AUTOMATEDKIT QIAGENDIGESTION BUFFER/PK
Evaluation of DNA quality/integrity (Real –Time PCR, ex9a APC gene, 186bp)
Any temperature
Anticoagulant Closure color VolumeCTAD (Buffered sodium citrate theorphylline
adenosine dipyridamole) Light blue 4,5 ml
K3EDTA (K3 Ethylenediaminetetraacetic Acid) Lavender 3 ml
NaCit (Sodium Citrate, Silicone coated) Light blue 4,5 ml
LH 68 IU (Lithium Heparin 68 IU) Green 4 ml
LH 60 IU (Lithium Heparin 60 IU) Grey 3 ml
FX (Sodium Fluoride Oxalate) Light grey 2 ml
BD Vacutainer Venous Blood Collection Tubes
Anticoagulants
DNA recovery ng/μl(Automated extraction - Nanodrop spectrophotometry 260 nm)
0
10
20
30
40
50
60
70
80
CTAD K3EDTA NaCit LH 68 IU LH 60 IU FX
ng/u
l Fresh blood
96 hours RT
96 hours-80°C
Quantitative Real –Time PCR (ex9a APC gene, 186bp)
0,00
5,00
10,00
15,00
20,00
25,00
30,00
CTAD K3EDTA NaCit LH 68 IU LH 60 IU FX
cp
0h
24h
96h
96h, -80°C
These data were obtained also in all the other storage conditions
Conclusions
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
1. Automation allowed an increased LMW peak recovery of 16.2%, as well as a better reproducibility of results compared to manual procedure;
2. Clotting times up to 2 hours and serum storage (with or w/o PI addition) up to 2 hrs at +4 °C did not significantly modified the LMW protein profiling results;
3. Storage at −80 °C up to 1-year, without PI addition resulted in not significant changes in serum LMW profiling.
Automation of the pre-analytical phases of proteomics as well as genomic studies might be one approach to improve standardization and homogeneity of analytical results
LMW protein profiling
Conclusions (2)
3rd Annual BRN SymposiumBethesda, 24-25 March, 2010
1. Automation of DNA extraction allowed the best recovery and reproducibility of the results compared to manual procedures;
2. All six anticoagulant evaluated, with the exception of LH show similar results.
3. RT up to 168 hrs can be considered a good storage condition for samples to be used for DNA studies.
DNA analyses
In conclusion, preanalytical phases are crucial and require specific focus and traceability. However, we should not underestimate other parameters like, cellular population and the values of analytes that can be tested only on fresh samples. All these information should represent the package data linked to a sample stored in a biorepository.
Prof. Mario Roselli, Medical Oncology,Dept. of Internal Medicine, University of Rome Tor Vergata
Scientific CoordinatorDr.ssa Fiorella GuadagniDip. di Medicina di Laboratorio e Biotecnologie AvanzateIRCCS San Raffaele Pisana, Rome
Dr. Mauro Ragonese A.C.I.S.M.O.M. Associazione Italiana dei Cavalieri Italiani del Sovrano Militare Ordine di Malta, Rome
Prof. Umberto NanniFaculty of Engineering, Sapienza University of Rome
Ing. Angelo LiveraniNoemalife SpA, Bologna, Italy
Dr. Giuseppe Ettorre, Dept of Surgery,Azienda Ospedaliera San Camillo-Forlanini, Rome
Dr. Giuseppe De Cataldis, Dept. of Oncology,ASL Salerno 2,Da Procida Hospital, Salerno
Dr. Francesco Cavaliere Azienda Ospedaliera San Giovanni Addolorata, Rome