Abstract 3890: NCI's Clinical Proteomic Tumor Analysis Consortium

Abstract

Abstract The NCI Clinical Proteomic Tumor Analysis Consortium (CPTAC) constitutes a network of Proteome Characterization Centers (PCCs), which coordinate and conduct research and data sharing activities to comprehensively interrogate genomically characterized cancer biospecimens. Such integrated proteogenomics approach brings key insights into genomic abnormalities manifested at the protein network and pathway level. Established in late 2011, CPTAC works closely with genomics initiatives such as The Cancer Genome Atlas (TCGA) to systematically identify proteins that derive from alterations in cancer genomes and related biological processes, and provide this data with accompanying assays and protocols to the public. CPTAC investigators conducted the first in-depth comprehensive proteome (global, phosphoproteome and N-glycoproteome) study on understanding the impact of cold ischemia that has resulted in the development of an ischemic signature database and best practice procedures for biospecimen (tissue) sample collection/processing. The PCCs have deeply characterized three cancer types (colorectal, ovarian and breast tumors) previously analyzed by TCGA and additional tissue collections, all of which are accompanied by genomic datasets. Scientific findings examining 95 TCGA colon and rectal tumors using deep proteomic analysis include: a) five proteomic subtypes were identified, with the TCGA MSI/CIMP transcriptomic subtype separated into distinct proteomic subtypes including one subtype (subtype C) that displayed protein network features characteristic of epithelial-mesenchymal transition (EMT); b) copy number alterations (CNAs) on mRNA abundance analysis showed strong cis- and trans-effects; but few extending to the protein level; and c) chromosome 20q amplicon was shown to contain the largest global changes in both mRNA and protein levels, allowing for prioritizing driver genes. In addition to the publicly available proteomic datasets (https://cptac-data-portal.georgetown.edu/cptacPublic), proteomic targeted assays developed by the consortium are available at CPTAC's Assay Portal (http://assays.cancer.gov). This is a public resource of mass spectrometry-based quantitative targeted proteomic assays for measuring proteins of interest from the program. Lastly, monoclonal antibodies targeting cancer specific proteins and peptides are made available at CPTAC's Antibody Portal (http://antibodies.cancer.gov). Citation Format: Mehdi Mesri, Emily Boja, Tara Hiltke, Chris Kinsinger, Jerry Lee, Henry Rodriguez. NCI's Clinical Proteomic Tumor Analysis Consortium. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 3890.