Proteogenomics for understanding oncology: recent advances and future prospects

Area of Science:

• Biochemistry
• Genomics
• Proteomics

Background:

• Proteogenomics combines mass spectrometry-based proteomic data with genomic and transcriptomic information.
• It enhances the discovery of potential biomarkers, therapeutic targets, and novel proteins in biological processes and diseases.
• This integrated approach has been instrumental in identifying novel genes and refining gene annotations.

Purpose of the Study:

• To review the application of proteogenomics in unraveling the complexities of cancer biology.
• To highlight the role of proteogenomics in identifying cancer-specific peptides, including those from mutant proteins, splice variants, and fusion proteins.
• To discuss the potential of proteogenomics-derived findings as diagnostic, prognostic, and therapeutic biomarkers.

Main Methods:

• Integration of mass spectrometry-derived proteomic data with genomic and transcriptomic data.
• Utilizing proteogenomic strategies to analyze tumor genomes and proteomes.
• Employing standard proteomics workflows on translated cancer genomes and transcriptomes.

Main Results:

• Successful identification of novel genes and improved annotation of existing gene models across various genomes.
• Identification of peptides from mutant proteins, splice variants, and fusion proteins within the tumor proteome.
• Potential for discovering new diagnostic and prognostic biomarkers, as well as therapeutic targets in cancer.

Conclusions:

• Proteogenomics is a powerful strategy for understanding cancer biology by integrating multi-omics data.
• It offers significant potential for identifying novel biomarkers and therapeutic targets, complementing existing panels.
• The continued application of proteogenomics is vital for advancing cancer research and clinical applications.