Development of antibody colocalization microarrays: A new chip format for large scale, high throughput protein profiling

Transcription

1 Micro & Nanobioengineering Lab Biomedical Engineering Department McGill University Development of antibody colocalization microarrays: A new chip format for large scale, high throughput protein profiling David Juncker david.juncker@mcgill.ca McGill, Nov IBM Corporation

2 Outline Goal: Chip for profiling biomarkers for diagnosis and prognosis of breast cancer using serum as sample Biological challenge: Single biomarkers lack sensitivity and specificity Need a biomarker panel Technological challenge: Multiplexed analytical technologies lack sensitivity and specificity when measuring multiple proteins in small (serum) samples Technological goal: Design and develop a proteomics platform for accurate protein profiling Strategy: Use microtechnologies and microfluidics to design a scalable proteomics platform 2Proposal for a scalable

3 Genomics advances Genome sequencing: the third generation Nature, 457, 768 (2009) 3

4 4

5 Key: Small and Scalable Moore s law Sequencer (sequences/run) DNA microarray (number of spots) Microwell plate (number of wells) Miniaturized, scalable technologies drive Genomics Protein profiling has progressed at a much slower pace 5

6 MS identified many biomarker candidates A search strategy combining literature search, extraction from microarray data, and a review of existing clinical tests, followed by manual curation, provided a list of 1261 candidate protein biomarkers Polanski, M. & Anderson, N. L. A List of Candidate Cancer Biomarkers for Targeted Proteomics. Biomarker Insights 2, 1-48 (2006). 6

7 Biomarker sensitivity & specificity Polanski and Anderson, A List of Candidate Cancer Biomarker for Targeted ProteomicsBiomarker Insights 2006:

8 Biomarkers publications vs validation Joseph A. Ludwig and John N. Weinstein* Nature Rev. Cancer

9 Challenge: sensitivity and selectivity in protein assays Source: Anderson & Anderson, The plasma proteome 9

10 Case study for multiplexing: Ovarian cancer Number of biomarkers Biomarker Cut off Sensitivity Specificity Reference 1 CA u/ml ~83 % 20-95% (Bast et al, 1983, Moss et al 2008) 4 Leptin, prolactin OPN, IGF-II NA 95% 95% (Mor et al. 2005) [3] 6 Leptin, prolactin OPN, IGF-II, MIF, CA125 NA 95.3% 99.4% (Visintin et al.) 2008 [4] 10

11 Sandwich assays (such as ELISAs) F G AD EC BH Deliver Rinse secondary Deliver Rinse Measure Rinse antibody capture sample fluorescence blockingab solution Rinse specific binding Proteins bound of detection antibody non capture specifically Ab no Target protein specifically Blocking non-specific agent captured (BSA) binding of detection target protein antibody Dual binding (sandwich) is key to specificity

12 Antibody microarrays with sandwich assay 12

13 Interference in Sandwich immunoassays Interference scenarios: 1. Non-specific binding of a non-target protein to the substrate surface 2. Non-specific binding of analyte (target protein) to the substrate surface 3. Cross-reactive binding between non-target protein and capture antibody 4. Cross-reactive binding between analyte and capture antibody 5. Complex formation between analyte and non-target proteins 6. Complex-formation between different analytes 7. Cross-reactive binding between analyte and detection antibody Affinity and selectivity of antibodies is limited 13

14 Colocalization antibody microarrays Interference scenarios: 1. Non-specific binding of a non-target protein to the substrate surface 2. Non-specific binding of analyte (target protein) to the substrate surface 3. Cross-reactive binding between non-target protein and capture antibody 4. Cross-reactive binding between analyte and capture antibody 5. Complex formation between analyte and non-target proteins 6. Complex-formation between different analytes 7. Cross-reactive binding between analyte and detection antibody 14

15 Colocalization microarray 7. Cocktail antibody application 15

16 Microfluidics: Capillary liquid transfer 16

17 Challenges ahead Basic challenges Mask Fabrication engineering, chemistry Alignment engineering Liquid transfer physics, chemistry, engineering Assay optimization biochemistry, engineering Scaling challenges Target selection biology, bioinformatics Cost grantsmanship Handling/storage Standardization Data acquisition & analysis 17 Serum Qualitative Quantitative Time-to-result

18 Self-sealing, reusable masks 18

19 Colocalization in nanocompartment arrays 2592 Nanocompartments, 112 μm diameter, ~ 1 nl 19

20 Automation 20

21 Polymer pins with low capillary pressure

22 Double-compartmentalization Slides with 2592 nanocompartments 8 partitions Partitions are useful for controls, reference samples and dilution series for quantitative profiling

23 Quantitative analysis of arrays Without TSA With TSA 23

24 Signal amplification for ELISA on microarray 60 fluorescece intensity (x10 3 ) CA15-3 concentration (ng/ml) w/o TSA w/ TSA Detection of CA15-3 with and without using tyramide signal amplification (TSA) system. 24

25 Assay optimization Detection of CA15 3 with TSA Intensity Detection Ab 1000ng/ml ng/ml Intensity Detection Ab 200ng/ml ng/ml Detection Ab 40ng/ml Detection Ab 8ng/ml Intensity Intensity Rendez-vous ng/ml Protéomique ng/ml

26 Cross-reactivity of multiplexed immunoassay 1e+5 Antigen cocktail & Detection CEA 1e+5 Antigen PSA & Detection PSA Fluorescence intensity 1e+4 1e+3 Fluorescence intensity CEA PSA HER2 CA e+4 1e+3 CEA PSA HER2 CA15-3 CEA PSA HER2 CA15-3 1e+2 CEA PSA HER2 CA15-3 1e+2 CEA PSA HER2 CA15-3 mabs mabs 1e+5 Antigen cocktail & Detection PSA Fluorescence intensity 1e+4 1e+3 Support for compartmentalization and colocalization 1e+2 CEA PSA HER2 CA15-3 mabs

27 Antibody pairs R&D matched antibody pairs Invitrogen ELISA Cytosets other providers Human IL-11 Human VCAM Human CA15.3 Human Angiopoietin-1 Human IFN gamma Human CEA Human Angiopoietin-2 Human CCL2/MCP-1 Human Erb2 Human CCL3/MIP-1 alpha Human CCL3/MIP-1 alpha Human CCL4/MIP-1 beta Human CCL4/MIP-1 beta Human CXCL10/IP-10 Human VEGF Human EGF Human IL 12 [P40/P70] Human EGF Receptor Human TNF alpha Human Endoglin/CD105 Human IL 2 Human ErbB2 Human IL 4 Human FGF basic Human IL 8 Human GM-CSF Human GM CSF Human IL-6 Human IL 6 Human Leptin Human IL 10 Human MMP-9 Human Osteopontin Human E-Selectin/CD62E Human Serpin E1/PAI-1 Human u-plasminogen Activator Human u-pa Receptor Human CCL2/MCP-1 27

28 Storage of slides with capture antibodies Fluorescent intensity (10 3 ) Fresh slide 8 week old, -20 C w. glycerol 3 days at 4 C CEA concentration (ng/ml) Only 10% loss after 8 week storage, most likely due to freeze-thaw cycle 28

29 Comparison of bindin curves for cytokines Fluorescent intensity IL-4 IL-6 IL-8 IL-10 MIP IL-12 MCP VEGF TNF IFN Concentration (pg/ml)

30 Conclusion Colocalization antibody microarrays chips can be scaled without trade-off in sensitivity or selectivity Applications of colocalization microarrays: Scientific discovery: profiling of up to proteins corresponding to each human gene ( > 6000 antibodies available) NCI Ab intitiative may provide new targets Cost and availability of pairs of antibodies is a bottleneck Validation of biomarker candidates individually and in combination for disease diagnosis, prognosis and monitoring 30

31 Acknowledgments Group members: Mateu Pla-Roca Emmanuel Moreau Wen Luo Saule Tourekhanova Rym Leulmi Collaborators: John Bergeron Mike Hallett Maryam Tabrizian Paul Charette Teodor Veres Andrew Kirk Morag Park Peter Siegel Judith Marcoux

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