Faculty, Staff and Student Publications

Language

English

Publication Date

5-1-2025

Journal

Cell

DOI

10.1016/j.cell.2025.03.026

PMID

40233739

PMCID

PMC12326532

PubMedCentral® Posted Date

5-1-2026

PubMedCentral® Full Text Version

Author MSS

Abstract

We investigate the impact of germline variants on cancer patients' proteomes, encompassing 1,064 individuals across 10 cancer types. We introduced an approach, "precision peptidomics," mapping 337,469 coding germline variants onto peptides from patients' mass spectrometry data, revealing their potential impact on post-translational modifications, protein stability, allele-specific expression, and protein structure by leveraging the relevant protein databases. We identified rare pathogenic and common germline variants in cancer genes potentially affecting proteomic features, including variants altering protein abundance and structure and variants in kinases (ERBB2 and MAP2K2) impacting phosphorylation. Precision peptidome analysis predicted destabilizing events in signal-regulatory protein alpha (SIRPA) and glial fibrillary acid protein (GFAP), relevant to immunomodulation and glioblastoma diagnostics, respectively. Genome-wide association studies identified quantitative trait loci for gene expression and protein levels, spanning millions of SNPs and thousands of proteins. Polygenic risk scores correlated with distal effects from risk variants. Our findings emphasize the contribution of germline genetics to cancer heterogeneity and high-throughput precision peptidomics.

Keywords

Humans, Proteogenomics, Neoplasms, Germ-Line Mutation, Polymorphism, Single Nucleotide, Genome-Wide Association Study, Proteome, Quantitative Trait Loci, Protein Processing, Post-Translational, Erb-b2 Receptor Tyrosine Kinases, Pan-Cancer, germline, proteogenomics, precision peptidomics, CPTAC

Published Open-Access

yes

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