Technische Universität München Cancer biomarker discovery by chemical and quantitative proteomics Sebastian Berger, B. Sc., Center of Life and Food Sciences Weihenstephan Chair of Proteomics and Bioanalytics Master Kolloquium
Content Introduction Methods Results Discussion
Einführung Cancer: A major cause of death Lung Cancer (85% NSCLC) Cancer establishment: 6 hallmarks of cancer No exact pathway
Einführung Biomarkers: Since antiquity DNA biomarker Protein biomarker –e.g. Kinase Discovery: Needle in the haystack
Einführung Aim: Kinase as biomarker To-Do: Healthy vs. Cancer Kinase enrichment Quantification
Methods Workflow: Tissue lysis Affinity pulldown LC-MS/MS Quantification Identification Statistical analysis Kinome enrichment
Methods Affinity pulldown: Kinobeads –Kinase inhibitors Protein Quantification Progenesis LC-MS –Intensity based quantification
Results
Quantification method comparison
Ergebnisse Reproducibility Correlation Coefficient All identified kinases Kinases with >3 peptides for quantification Higher reproducibility in the higher intensity part SampleCorrelation [1/2]Correlation [1/2] > ,
Results Data Evaluation Progenesis data VSN normalized data QQ-Plots –Straight line indicates normal distribution Scatter plots Progenesis VSN data
Results Progenesis VSN
Results PCA Analysis Progenesis data
Results PCA Analysis VSN data
Results Kinase Clustering ProgenesisVSN
Results Ingenuity Pathway
Results Kinase profiling
Results Patient profiling
Discussion Quantification Only „Chemical labeling“ or label-free Sample Exclusion Cancer Sample 33 Cancer Sample 36 Control Sample kD C 33 E 33C 36E 36 C 56 C 33 E 33C 36 E 36 C 56 E 56 HOP 62 E kD 50 kD SampleCorrelation [1/2]Correlation [1/2] >
Discussion Kinase profiling Overall expression Patient profiling Stratification IPA Pathway prediction
Discussion Sample type Biopsy Blood
Outlook Further screening Not yet diseased Smokers vs. Non- smokers Therapy context Blood sample
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