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

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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., Carr, Steven A.·2022·Nature Reviews Cancer

DOI 10.1038/s41568-022-00446-5PMC PMC12404316

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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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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.
ORCID: Mani, D. R.
Krug, Karsten
Zhang, Bing
Satpathy, Shankha
Clauser, Karl R.
Ding, Li
Ellis, Matthew
Gillette, Michael A.
Carr, Steven A.
Venue: Nature Reviews Cancer
Publisher: Springer Science and Business Media LLC
Published: 2022-03-02
Volume: 22
Issue: 5
Pages: 298-313
ISSN: 1474-175X (ISSN-L)
1474-1768
DOI: 10.1038/s41568-022-00446-5
PMC: PMC12404316
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: green
pmc.ncbi.nlm.nih.gov
Licence: www.springer.com/tdm (tdm)
www.springer.com/tdm (vor)
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
Life Sciences › Biochemistry, Genetics and Molecular Biology › Cancer Research › 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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