A pan-cancer proteomic perspective on the cancer genome atlas

Rehan Akbani, Patrick Kwok Shing Ng, Henrica M J Werner, Maria Shahmoradgoli, Fan Zhang, Zhenlin Ju, Wenbin Liu, Ji Yeon Yang, Kosuke Yoshihara, Jun Li, Shiyun Ling, Elena G. Seviour, Prahlad T. Ram, John D. Minna, Lixia Diao, Pan Tong, John V. Heymach, Steven M. Hill, Frank Dondelinger, Nicolas StädlerLauren A. Byers, Funda Meric-Bernstam, John N. Weinstein, Bradley M. Broom, Roeland G W Verhaak, Han Liang, Sach Mukherjee, Yiling Lu, Gordon B. Mills

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221 Scopus citations

Abstract

Protein levels and function are poorly predicted by genomic and transcriptomic analysis of patient tumours. Therefore, direct study of the functional proteome has the potential to provide a wealth of information that complements and extends genomic, epigenomic and transcriptomic analysis in The Cancer Genome Atlas (TCGA) projects. Here we use reverse-phase protein arrays to analyse 3,467 patient samples from 11 TCGA 'Pan-Cancer' diseases, using 181 high-quality antibodies that target 128 total proteins and 53 post-translationally modified proteins. The resultant proteomic data are integrated with genomic and transcriptomic analyses of the same samples to identify commonalities, differences, emergent pathways and network biology within and across tumour lineages. In addition, tissue-specific signals are reduced computationally to enhance biomarker and target discovery spanning multiple tumour lineages. This integrative analysis, with an emphasis on pathways and potentially actionable proteins, provides a framework for determining the prognostic, predictive and therapeutic relevance of the functional proteome.

Original languageEnglish (US)
Article number3887
JournalNature communications
Volume5
DOIs
StatePublished - May 29 2014

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ASJC Scopus subject areas

  • Chemistry(all)
  • Biochemistry, Genetics and Molecular Biology(all)
  • Physics and Astronomy(all)

Cite this

Akbani, R., Ng, P. K. S., Werner, H. M. J., Shahmoradgoli, M., Zhang, F., Ju, Z., Liu, W., Yang, J. Y., Yoshihara, K., Li, J., Ling, S., Seviour, E. G., Ram, P. T., Minna, J. D., Diao, L., Tong, P., Heymach, J. V., Hill, S. M., Dondelinger, F., ... Mills, G. B. (2014). A pan-cancer proteomic perspective on the cancer genome atlas. Nature communications, 5, [3887]. https://doi.org/10.1038/ncomms4887