Cited by 229Advanced Proteomics Techniques and ApplicationsCancer Genomics and DiagnosticsProstate Cancer Treatment and Research

Cancer proteogenomics: current impact and future prospects

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Mani, D. R., Krug, Karsten, Zhang, Bing, Satpathy, Shankha, Clauser, Karl R., Ding, Li, Ellis, Matthew, Gillette, Michael A. +1 more·2022·Nature Reviews Cancer

Abstract

Genomic analyses in cancer have been enormously impactful, leading to the identification of driver mutations and development of targeted therapies. But the functions of the vast majority of somatic mutations and copy number variants in tumours remain unknown, and the causes of resistance to targeted therapies and methods to overcome them are poorly defined. Recent improvements in mass spectrometry-based proteomics now enable direct examination of the consequences of genomic aberrations, providing deep and quantitative characterization of tumour tissues. Integration of proteins and their post-translational modifications with genomic, epigenomic and transcriptomic data constitutes the new field of proteogenomics, and is already leading to new biological and diagnostic knowledge with the potential to improve our understanding of malignant transformation and therapeutic outcomes. In this Review we describe recent developments in proteogenomics and key findings from the proteogenomic analysis of a wide range of cancers. Considerations relevant to the selection and use of samples for proteogenomics and the current technologies used to generate, analyse and integrate proteomic with genomic data are described. Applications of proteogenomics in translational studies and immuno-oncology are rapidly emerging, and the prospect for their full integration into therapeutic trials and clinical care seems bright.

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  • Recent advances in proteomics through the maturation of several MS techniques have enabled the introduction of proteogenomic approaches that can integrate genomic data with proteomics and information on post-translational modifications.

    “Recent advances in proteomics through the maturation of several MS techniques have enabled the introduction of proteogenomic approaches that can integrate genomic data with proteomics and information on post-translational modifications [89].”

    From Bioinformatics Analysis and Validation of Potential Markers Associated with Prediction and Prognosis of Gastric Cancer (2024) · cites this paper as [89]

    The Abstract (page unavailable) describes LC-MS/MS-based proteomics measuring proteins and post-translational modifications and relating them to genomic changes; Computational methods and tools describes linking genomic and proteomic data. The cited passages do not establish the more specific historical claim that maturation of several MS techniques enabled the introduction of proteogenomic approaches. (LLM, conf=0.83)

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  1. [92]Rudnick PA A description of the Clinical Proteomic Tumor Analysis Consortium (CPTAC) common data analysis pipeline. J. Proteome Res 15, 1023– 1032 (2016). 26860878 PMC5117628

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Authors
Mani, D. R., Krug, K., Zhang, B., Satpathy, S., Clauser, K. R., Ding, L., Ellis, M., Gillette, M. A., & Carr, S. A.
Affiliations
  • Broad Institute (US)
  • Baylor College of Medicine (US)
  • Washington University in St. Louis (US)
Corresponding author
  • Mani, D. R.
  • Carr, Steven A.
Venue
Nature Reviews Cancer
Published
2022-03-02
Volume
22
Issue
5
Pages
298-313
ISSN
  • 1474-175X (ISSN-L)
  • 1474-1768
OpenAlex
W4214929667
Cited by
229
References
173
Citations by year
2026: 47 · 2025: 56 · 2024: 51 · 2023: 59 · 2022: 16
FWCI
5.32
Type
journal article
Language
en
Open access
Locations
  • Nature reviews. Cancer (publishedVersion)
  • PubMed (publishedVersion)
  • PubMed Central (publishedVersion)
  • Europe PMC (PubMed Central) (acceptedVersion)
Funders
  • National Human Genome Research Institute (R01HG009711)
  • National Cancer Institute (U24CA210972, P50CA186784, U24CA210954, U24CA210986, U01CA214125, U2CCA233303, U24CA211006, U24CA160034, U24CA210979, U54CA224083)
Topics
  • Physical Sciences › Chemistry › Spectroscopy › Advanced Proteomics Techniques and Applications
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › Cancer Genomics and Diagnostics
  • Health Sciences › Medicine › Pulmonary and Respiratory Medicine › Prostate Cancer Treatment and Research
Keywords
somatic mutations, copy number variation, post-translational modification, targeted therapy resistance, mass spectrometry-based proteomics, cancer immunotherapy, translational oncology
MeSH terms
Proteogenomics, Humans, Neoplasms, Genomics, Proteomics, DNA Copy Number Variations

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