Proteomics

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Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer


ABSTRACT: Explore This Study at the NCI Proteomic Data Commons

Zhang H, Liu T, Zhang Z, Payne SH, Zhang B, McDermott JE et al., Cell (2016), DOI: 10.1016/j.cell.2016.05.069, Published online June 29, 2016.

To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass-spectrometry-based proteomic characterization of 174 ovarian tumors previously analyzed by The Cancer Genome Atlas (TCGA), of which 169 were high-grade serous carcinomas (HGSCs). Integrating our proteomic measurements with the genomic data yielded a number of insights into disease, such as how different copy-number alternations influence the proteome, the proteins associated with chromosomal instability, the sets of signaling pathways that diverse genome rearrangements converge on, and the ones most associated with short overall survival. Specific protein acetylations associated with homologous recombination deficiency suggest a potential means for stratifying patients for therapy. In addition to providing a valuable resource, these findings provide a view of how the somatic genome drives the cancer proteome and associations between protein and post-translational modification levels and clinical outcomes in HGSC.

Information on the complete TCGA Ovarian Serous Cystadenocarcinoma (OV) cohort can be found here.
The Cancer Genome Atlas Research Network published on the Genomic characterization of the OV cohort in Nature on June 30, 2011

Genomic data for the 174 TCGA samples used in the CPTAC Proteome study can be downloaded from here.

Peptide-Spectrum-Matches and Protein Reports from the CPTAC Common Data Analysis Pipeline (CDAP) can be downloaded from here.

INSTRUMENT(S): LTQ Orbitrap Velos, Q Exactive

ORGANISM(S): Homo Sapiens (ncbitaxon:9606)

SUBMITTER: Richard Smith   Hui Zhang  

PROVIDER: MSV000084246 | MassIVE | Wed Aug 28 15:07:00 BST 2019

SECONDARY ACCESSION(S): PXD015908

REPOSITORIES: MassIVE

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Integrated Proteogenomic Characterization of Human High-Grade Serous Ovarian Cancer.

Zhang Hui H   Liu Tao T   Zhang Zhen Z   Payne Samuel H SH   Zhang Bai B   McDermott Jason E JE   Zhou Jian-Ying JY   Petyuk Vladislav A VA   Chen Li L   Ray Debjit D   Sun Shisheng S   Yang Feng F   Chen Lijun L   Wang Jing J   Shah Punit P   Cha Seong Won SW   Aiyetan Paul P   Woo Sunghee S   Tian Yuan Y   Gritsenko Marina A MA   Clauss Therese R TR   Choi Caitlin C   Monroe Matthew E ME   Thomas Stefani S   Nie Song S   Wu Chaochao C   Moore Ronald J RJ   Yu Kun-Hsing KH   Tabb David L DL   Fenyƶ David D   Bafna Vineet V   Wang Yue Y   Rodriguez Henry H   Boja Emily S ES   Hiltke Tara T   Rivers Robert C RC   Sokoll Lori L   Zhu Heng H   Shih Ie-Ming IM   Cope Leslie L   Pandey Akhilesh A   Zhang Bing B   Snyder Michael P MP   Levine Douglas A DA   Smith Richard D RD   Chan Daniel W DW   Rodland Karin D KD  

Cell 20160629 3


To provide a detailed analysis of the molecular components and underlying mechanisms associated with ovarian cancer, we performed a comprehensive mass-spectrometry-based proteomic characterization of 174 ovarian tumors previously analyzed by The Cancer Genome Atlas (TCGA), of which 169 were high-grade serous carcinomas (HGSCs). Integrating our proteomic measurements with the genomic data yielded a number of insights into disease, such as how different copy-number alternations influence the prote  ...[more]

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