Proteogenomics connects somatic mutations to signalling in breast cancer.

Philipp Mertins,Zhidong Tu,David Fenyö,Venkata Yellapantula,Henry Rodriguez,D R Mani,Karsten Krug,Michael A Gillette,Amanda G Paulovich,Kelly V Ruggles,Filip Mundt,Bing Zhang,Jonathan T Lei,R Reid Townsend,Francesca Petralia,Song Cao,Mehdi Mesri,Jing Wang,Steven J Skates,Xianlong Wang,Matthew J Ellis,Ping Yan,Michael L Gatza,Charles M Perou,Emily Kawaler,Michael D Mclellan,Chenwei Lin,Li Ding,Steven A Carr,Sherri R Davies,Karl R Clauser,Christopher R Kinsinger,Pei Wang,Kuan Lin Huang ,Matthew D Wilkerson ,Jana Qiao

doi:10.1038/nature18003

Abstract

SummarySomatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. We describe quantitative mass spectrometry-based proteomic and phosphoproteomic analyses of 105 genomically annotated breast cancers of which 77 provided high-quality data. Integrated analyses allowed insights into the somatic cancer genome including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. The 5q trans effects were interrogated against the Library of Integrated Network-based Cellular Signatures, thereby connecting CETN3 and SKP1 loss to elevated expression of EGFR, and SKP1 loss also to increased SRC. Global proteomic data confirmed a stromal-enriched group in addition to basal and luminal clusters and pathway analysis of the phosphoproteome identified a G Protein-coupled receptor cluster that was not readily identified at the mRNA level. Besides ERBB2, other amplicon-associated, highly phosphorylated kinases were identified, including CDK12, PAK1, PTK2, RIPK2 and TLK2. We demonstrate that proteogenomic analysis of breast cancer elucidates functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies therapeutic targets.

Highlights

A central deficiency in our knowledge of cancer concerns how genomic changes drive the proteome and phosphoproteome to execute phenotypic characteristics[1,2,3,4]
Samples were analyzed by high-resolution, accurate mass, tandem mass spectrometry (MS) that included extensive peptide fractionation and phosphopeptide enrichment (Extended Data Fig. 1a)
Due to the heterogeneous nature of breast tumors[11,12,13], and because proteomic analyses were performed on tumor fragments that were different from those used in the genomic analyses, rigorous pre-specified sample and data QC metrics were implemented[14,15] (Supplementary Discussion and Extended Data Figures 2, 3)

Summary

Somatic mutations have been extensively characterized in breast cancer, but the effects of these genetic alterations on the proteomic landscape remain poorly understood. We describe quantitative mass spectrometry-based proteomic and phosphoproteomic analyses of 105 genomically annotated breast cancers of which 77 provided high-quality data. Integrated analyses allowed insights into the somatic cancer genome including the consequences of chromosomal loss, such as the 5q deletion characteristic of basal-like breast cancer. Global proteomic data confirmed a stromal-enriched group in addition to basal and luminal clusters and pathway analysis of the phosphoproteome identified a G Protein-coupled receptor cluster that was not readily identified at the mRNA level. We demonstrate that proteogenomic analysis of breast cancer elucidates functional consequences of somatic mutations, narrows candidate nominations for driver genes within large deletions and amplified regions, and identifies therapeutic targets

Findings

Introduction

Discussion