Proteogenomic Landscape Of Breast Cancer Tumorigenesis And Targeted Therapy
Ontology highlight
ABSTRACT: The integration of mass spectrometry-based proteomics with next-generation DNA and RNA sequencing profiles tumors more comprehensively. Herein this "proteogenomic" approach was applied to 122 treatment-naive primary breast cancers purposely accrued to preserve post-translational modifications, including protein phosphorylation and acetylation. Proteogenomics challenged standard breast cancer diagnoses, provided detailed analysis of the ERBB2 amplicon, defined tumor subsets that could benefit from immune checkpoint therapy and allowed more accurate assessment of Rb status for the prediction of CDK4/6 inhibitor responsiveness. Phosphoproteomic profiles uncovered novel associations between tumor suppressor loss and targetable kinases. Acetylproteome analysis highlighted acetylation on key nuclear proteins involved in the DNA damage response and revealed cross-talk between cytoplasmic and mitochondrial acetylation and metabolism. Our results underscore the potential of proteogenomics for the clinical investigation of breast cancer through more accurate annotation of targetable pathways and biological features of this remarkably heterogeneous malignancy. Genomic Data for Breast Cancer tumors is available from the NCI Genomic Data Commons (GDC), here
DOI: https://doi.org/10.1016/j.cell.2020.10.036
Gene Expression data in GCT file format is available under the metadata section below
Proteomic Data Analysis for Breast Cancer tumors (PSMs and Summary Reports) is available from the CPTAC Common Data Analysis Pipeline (Study S039 Early Data Release), here
INSTRUMENT(S): Orbitrap Fusion Lumos
ORGANISM(S): Homo Sapiens (ncbitaxon:9606)
SUBMITTER: 
D.R. Mani Steven A. Carr Michael A. Gillette Matthew J. Elliis
PROVIDER: MSV000087576 | MassIVE | Sat Jun 05 17:03:00 BST 2021
REPOSITORIES: MassIVE
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