Proteogenomic data and resources for pan-cancer analysis

Yize Li; Yongchao Dou; Felipe Da Veiga Leprevost; Yifat Geffen; Anna P Calinawan; François Aguet; Yo Akiyama; Shankara Anand; Chet Birger; Song Cao; Rekha Chaudhary; Padmini Chilappagari; Marcin Cieslik; Antonio Colaprico; Daniel Cui Zhou; Corbin Day; Marcin J Domagalski; Myvizhi Esai Selvan; David Fenyö; Steven M Foltz; Alicia Francis; Tania Gonzalez-Robles; Zeynep H Gümüş; David Heiman; Michael Holck; Runyu Hong; Yingwei Hu; Eric J Jaehnig; Jiayi Ji; Wen Jiang; Lizabeth Katsnelson; Karen A Ketchum; Robert J Klein; Jonathan T Lei; Wen-Wei Liang; Yuxing Liao; Caleb M Lindgren; Weiping Ma; Lei Ma; Michael J MacCoss; Fernanda Martins Rodrigues; Wilson McKerrow; Ngoc Nguyen; Robert Oldroyd; Alexander Pilozzi; Pietro Pugliese; Boris Reva; Paul Rudnick; Kelly V Ruggles; Dmitry Rykunov; Sara R Savage; Michael Schnaubelt; Tobias Schraink; Zhiao Shi; Deepak Singhal; Xiaoyu Song; Erik Storrs; Nadezhda V Terekhanova; Ratna R Thangudu; Mathangi Thiagarajan; Liang-Bo Wang; Joshua M Wang; Ying Wang; Bo Wen; Yige Wu; Matthew A Wyczalkowski; Yi Xin; Lijun Yao; Xinpei Yi; Hui Zhang; Qing Zhang; Maya Zuhl; Gad Getz; Li Ding; Alexey I Nesvizhskii; Pei Wang; Ana I Robles; Bing Zhang; Samuel H Payne; Clinical Proteomic Tumor Analysis Consortium

doi:10.1016/j.ccell.2023.06.009

Proteogenomic data and resources for pan-cancer analysis

Cancer Cell. 2023 Aug 14;41(8):1397-1406. doi: 10.1016/j.ccell.2023.06.009.

Authors

Yize Li¹, Yongchao Dou², Felipe Da Veiga Leprevost³, Yifat Geffen⁴, Anna P Calinawan⁵, François Aguet⁴, Yo Akiyama⁴, Shankara Anand⁴, Chet Birger⁴, Song Cao¹, Rekha Chaudhary⁶, Padmini Chilappagari⁶, Marcin Cieslik⁷, Antonio Colaprico⁸, Daniel Cui Zhou¹, Corbin Day⁹, Marcin J Domagalski⁶, Myvizhi Esai Selvan⁵, David Fenyö¹⁰, Steven M Foltz¹, Alicia Francis⁶, Tania Gonzalez-Robles¹¹, Zeynep H Gümüş⁵, David Heiman⁴, Michael Holck⁶, Runyu Hong¹⁰, Yingwei Hu¹², Eric J Jaehnig², Jiayi Ji¹³, Wen Jiang², Lizabeth Katsnelson¹⁰, Karen A Ketchum⁶, Robert J Klein⁵, Jonathan T Lei², Wen-Wei Liang¹, Yuxing Liao², Caleb M Lindgren⁹, Weiping Ma⁵, Lei Ma⁶, Michael J MacCoss¹⁴, Fernanda Martins Rodrigues¹, Wilson McKerrow¹⁰, Ngoc Nguyen⁶, Robert Oldroyd⁹, Alexander Pilozzi⁶, Pietro Pugliese¹⁵, Boris Reva⁵, Paul Rudnick¹⁶, Kelly V Ruggles¹⁷, Dmitry Rykunov⁵, Sara R Savage², Michael Schnaubelt¹², Tobias Schraink¹¹, Zhiao Shi², Deepak Singhal⁶, Xiaoyu Song¹³, Erik Storrs¹, Nadezhda V Terekhanova¹, Ratna R Thangudu⁶, Mathangi Thiagarajan¹⁸, Liang-Bo Wang¹, Joshua M Wang¹⁰, Ying Wang¹⁰, Bo Wen², Yige Wu¹, Matthew A Wyczalkowski¹, Yi Xin⁶, Lijun Yao¹, Xinpei Yi², Hui Zhang¹², Qing Zhang⁴, Maya Zuhl⁶, Gad Getz¹⁹, Li Ding²⁰, Alexey I Nesvizhskii³, Pei Wang⁵, Ana I Robles²¹, Bing Zhang²², Samuel H Payne²³; Clinical Proteomic Tumor Analysis Consortium

Collaborators

Clinical Proteomic Tumor Analysis Consortium:
Alexander J Lazar, Amanda G Paulovich, Antonio Colaprico, Antonio Iavarone, Arul M Chinnaiyan, Brian J Druker, Chandan Kumar-Sinha, Chelsea J Newton, Chen Huang, D R Mani, Richard D Smith, Emily Huntsman, Eric E Schadt, Eunkyung An, Francesca Petralia, Galen Hostetter, Gilbert S Omenn, Hanbyul Cho, Henry Rodriguez, Hui Zhang, Iga Kolodziejczak, Jared L Johnson, Jasmin Bavarva, Jimin Tan, Karin D Rodland, Karl R Clauser, Karsten Krug, Lewis C Cantley, Maciej Wiznerowicz, Matthew J Ellis, Meenakshi Anurag, Mehdi Mesri, Michael A Gillette, Michael J Birrer, Michele Ceccarelli, Saravana M Dhanasekaran, Nathan Edwards, Nicole Tignor, Özgün Babur, Pietro Pugliese, Sara J C Gosline, Scott D Jewell, Shankha Satpathy, Shrabanti Chowdhury, Stephan Schürer, Steven A Carr, Tao Liu, Tara Hiltke, Tomer M Yaron, Vasileios Stathias, Wenke Liu, Xu Zhang, Yizhe Song, Zhen Zhang

Affiliations

¹ Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA.
² Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA.
³ Department of Pathology, University of Michigan, Ann Arbor, MI 48109, USA.
⁴ Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA.
⁵ Department of Genetic and Genomic Sciences, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
⁶ ICF, Rockville, MD 20850, USA.
⁷ Department of Computational Medicine & Bioinformatics, Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA.
⁸ Department of Public Health Sciences, University of Miami Miller School of Medicine, Miami, FL 33136, USA; Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136, USA.
⁹ Department of Biology, Brigham Young University, Provo, UT 84602, USA.
¹⁰ Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA.
¹¹ Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Biochemistry and Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA.
¹² Department of Pathology, Johns Hopkins University, Baltimore, MD 21231, USA.
¹³ Tisch Cancer Institute and Department of Population Health Science and Policy, Icahn School of Medicine at Mount Sinai, New York, NY 10029, USA.
¹⁴ Department of Genome Sciences, University of Washington, Seattle, WA 98195, USA.
¹⁵ Department of Sciences and Technologies, University of Sannio, Benevento 82100, Italy.
¹⁶ Spectragen Informatics, Bainbridge Island, WA 98110, USA.
¹⁷ Institute for Systems Genetics, NYU Grossman School of Medicine, New York, NY 10016, USA; Department of Medicine, NYU Grossman School of Medicine, New York, NY 10016, USA.
¹⁸ Frederick National Laboratory for Cancer Research, Frederick, MD 21702, USA.
¹⁹ Broad Institute of MIT and Harvard, Cambridge, MA 02141, USA; Cancer Center and Department of Pathology, Mass. General Hospital, Boston, MA 02114, USA; Harvard Medical School, Boston, MA 02115, USA.
²⁰ Department of Medicine, Washington University in St. Louis, St. Louis, MO 63130, USA; McDonnell Genome Institute, Washington University in St. Louis, St. Louis, MO 63130, USA; Siteman Cancer Center, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Genetics, Washington University in St. Louis, St. Louis, MO 63130, USA.
²¹ Office of Cancer Clinical Proteomics Research, National Cancer Institute, Rockville, MD 20850, USA. Electronic address: roblesa@mail.nih.gov.
²² Lester and Sue Smith Breast Center, Baylor College of Medicine, Houston, TX 77030, USA; Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA. Electronic address: bing.zhang@bcm.edu.
²³ Department of Biology, Brigham Young University, Provo, UT 84602, USA. Electronic address: sam_payne@byu.edu.

Abstract

The National Cancer Institute's Clinical Proteomic Tumor Analysis Consortium (CPTAC) investigates tumors from a proteogenomic perspective, creating rich multi-omics datasets connecting genomic aberrations to cancer phenotypes. To facilitate pan-cancer investigations, we have generated harmonized genomic, transcriptomic, proteomic, and clinical data for >1000 tumors in 10 cohorts to create a cohesive and powerful dataset for scientific discovery. We outline efforts by the CPTAC pan-cancer working group in data harmonization, data dissemination, and computational resources for aiding biological discoveries. We also discuss challenges for multi-omics data integration and analysis, specifically the unique challenges of working with both nucleotide sequencing and mass spectrometry proteomics data.

Keywords: CPTAC; data harmonization; multi-omics; open data; pan-cancer; proteogenomics.

Publication types

Review
Research Support, N.I.H., Extramural
Research Support, Non-U.S. Gov't

MeSH terms

Gene Expression Profiling
Genomics
Humans
Neoplasms* / genetics
Proteogenomics*
Proteomics

Abstract

Publication types

MeSH terms

Grants and funding