Pan-cancer Molecular Subtypes Revealed by Mass-spectrometry-based Proteomic Characterization of More Than 500 Human Cancers

Overview

Journal Nat Commun

Specialty Biology

Date 2019 Dec 14

PMID 31831737

Citations 301

Authors

Fengju Chen

Darshan S Chandrashekar

Sooryanarayana Varambally

Chad J Creighton

Affiliations

Soon will be listed here.

Abstract

Mass-spectrometry-based proteomic profiling of human cancers has the potential for pan-cancer analyses to identify molecular subtypes and associated pathway features that might be otherwise missed using transcriptomics. Here, we classify 532 cancers, representing six tissue-based types (breast, colon, ovarian, renal, uterine), into ten proteome-based, pan-cancer subtypes that cut across tumor lineages. The proteome-based subtypes are observable in external cancer proteomic datasets surveyed. Gene signatures of oncogenic or metabolic pathways can further distinguish between the subtypes. Two distinct subtypes both involve the immune system, one associated with the adaptive immune response and T-cell activation, and the other associated with the humoral immune response. Two additional subtypes each involve the tumor stroma, one of these including the collagen VI interacting network. Three additional proteome-based subtypes-respectively involving proteins related to Golgi apparatus, hemoglobin complex, and endoplasmic reticulum-were not reflected in previous transcriptomics analyses. A data portal is available at UALCAN website.

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