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 Städler & 9 others Lauren A. Byers, Funda Meric-Bernstam, John N. Weinstein, Bradley M. Broom, Roeland G W Verhaak, Han Liang, Sach Mukherjee, Yiling Lu, Gordon B. Mills

Research output: Contribution to journalArticle

187 Citations (Scopus)

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

Fingerprint

genome
Atlases
Proteomics
Genes
cancer
Genome
proteins
proteome
Tumors
tumors
Proteome
Neoplasms
Proteins
commonality
biomarkers
Biomarkers
Protein Array Analysis
antibodies
biology
complement

ASJC Scopus subject areas

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

Cite this

Akbani, R., Ng, P. K. S., Werner, H. M. J., Shahmoradgoli, M., Zhang, F., Ju, Z., ... Mills, G. B. (2014). A pan-cancer proteomic perspective on the cancer genome atlas. Nature Communications, 5, [3887]. https://doi.org/10.1038/ncomms4887

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

In: Nature Communications, Vol. 5, 3887, 29.05.2014.

Research output: Contribution to journalArticle

Akbani, R, Ng, PKS, Werner, HMJ, Shahmoradgoli, M, Zhang, F, Ju, Z, Liu, W, Yang, JY, Yoshihara, K, Li, J, Ling, S, Seviour, EG, Ram, PT, Minna, JD, Diao, L, Tong, P, Heymach, JV, Hill, SM, Dondelinger, F, Städler, N, Byers, LA, Meric-Bernstam, F, Weinstein, JN, Broom, BM, Verhaak, RGW, Liang, H, Mukherjee, S, Lu, Y & Mills, GB 2014, 'A pan-cancer proteomic perspective on the cancer genome atlas', Nature Communications, vol. 5, 3887. https://doi.org/10.1038/ncomms4887
Akbani R, Ng PKS, Werner HMJ, Shahmoradgoli M, Zhang F, Ju Z et al. A pan-cancer proteomic perspective on the cancer genome atlas. Nature Communications. 2014 May 29;5. 3887. https://doi.org/10.1038/ncomms4887
Akbani, Rehan ; Ng, Patrick Kwok Shing ; Werner, Henrica M J ; Shahmoradgoli, Maria ; Zhang, Fan ; Ju, Zhenlin ; Liu, Wenbin ; Yang, Ji Yeon ; Yoshihara, Kosuke ; Li, Jun ; Ling, Shiyun ; Seviour, Elena G. ; Ram, Prahlad T. ; Minna, John D. ; Diao, Lixia ; Tong, Pan ; Heymach, John V. ; Hill, Steven M. ; Dondelinger, Frank ; Städler, Nicolas ; Byers, Lauren A. ; Meric-Bernstam, Funda ; Weinstein, John N. ; Broom, Bradley M. ; Verhaak, Roeland G W ; Liang, Han ; Mukherjee, Sach ; Lu, Yiling ; Mills, Gordon B. / A pan-cancer proteomic perspective on the cancer genome atlas. In: Nature Communications. 2014 ; Vol. 5.
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