Cancer proteogenomics: current impact and future prospects

Cancer proteogenomics: current impact and future prospects

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...

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Published in:Nature reviews. Cancer Vol. 22; no. 5; pp. 298 - 313
Main Authors: Mani, D. R., Krug, Karsten, Zhang, Bing, Satpathy, Shankha, Clauser, Karl R., Ding, Li, Ellis, Matthew, Gillette, Michael A., Carr, Steven A.
Format: Journal Article
Language:English
Published: London Nature Publishing Group UK 01-05-2022
Nature Publishing Group
Subjects:
631/114/1305
631/1647/296
631/61/475
631/67/1059
631/67/69
Biomedical and Life Sciences
Biomedicine
Cancer immunotherapy
Cancer Research
Clinical trials
Copy number
DNA Copy Number Variations
Genomic analysis
Genomics
Humans
Integration
Mass spectroscopy
Mutation
Neoplasms - metabolism
Oncology
Post-translation
Proteogenomics - methods
Proteomics
Review Article
Transcriptomics
Translation
Tumors
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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. This Review examines recent developments in proteogenomics, key findings from the proteogenomic analyses of a wide range of cancers and emerging applications of proteogenomics to translational studies and immuno-oncology, as well as discussing future prospects regarding integration into clinical trials and patient care.
AbstractList 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.
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.This Review examines recent developments in proteogenomics, key findings from the proteogenomic analyses of a wide range of cancers and emerging applications of proteogenomics to translational studies and immuno-oncology, as well as discussing future prospects regarding integration into clinical trials and patient care.
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. This Review examines recent developments in proteogenomics, key findings from the proteogenomic analyses of a wide range of cancers and emerging applications of proteogenomics to translational studies and immuno-oncology, as well as discussing future prospects regarding integration into clinical trials and patient care.
Author Satpathy, Shankha
Ellis, Matthew
Gillette, Michael A.
Carr, Steven A.
Zhang, Bing
Krug, Karsten
Clauser, Karl R.
Ding, Li
Mani, D. R.
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Snippet Genomic analyses in cancer have been enormously impactful, leading to the identification of driver mutations and development of targeted therapies. But the...
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SubjectTerms 631/114/1305
631/1647/296
631/61/475
631/67/1059
631/67/69
Biomedical and Life Sciences
Biomedicine
Cancer immunotherapy
Cancer Research
Clinical trials
Copy number
DNA Copy Number Variations
Genomic analysis
Genomics
Humans
Integration
Mass spectroscopy
Mutation
Neoplasms - metabolism
Oncology
Post-translation
Proteogenomics - methods
Proteomics
Review Article
Transcriptomics
Translation
Tumors
Title Cancer proteogenomics: current impact and future prospects
URI https://link.springer.com/article/10.1038/s41568-022-00446-5
https://www.ncbi.nlm.nih.gov/pubmed/35236940
https://www.proquest.com/docview/2656448106
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