Proteogenomics for understanding oncology: recent advances and future prospects

Abstract

The concept of proteogenomics has emerged rapidly as a valuable approach to integrate mass spectrometry-derived proteomic data with genomic and transcriptomic data. It is used to harness the full potential of the former dataset in the discovery of potential biomarkers, therapeutic targets and novel proteins associated with various biological processes including diseases. Proteogenomic strategies have been successfully utilized to identify novel genes and redefine annotation of existing gene models in various genomes. In recent years, this approach has been extended to the field of cancer biology to unravel complexities in the tumor genomes and proteomes. Standard proteomics workflows employing translated cancer genomes and transcriptomes can potentially identify peptides from mutant proteins, splice variants and fusion proteins in the tumor proteome, which in addition to the currently available biomarker panels can serve as potential diagnostic and prognostic biomarkers, besides having therapeutic utility. This review focuses on the role of proteogenomics to understand cancer biology.

Dynamics of Dual Specificity Phosphatases and Their Interplay with Protein Kinases in Immune Signaling

“…Systems biology and integrative biology offer several approaches to identify molecular mechanisms operating behind biological processes in unprecedented detail. Integrated approaches such as Proteogenomics can provide macro-resolution snapshots to facilitate understanding of intricate molecular mechanisms in cancers [25,26] and infectious diseases [27,28]. Applying integrated approaches in the context of immunology can, therefore, offer unique insights into mechanisms of innate and adaptive immunity.…”

Systems medicine approaches for peptide array-based protein kinase profiling: progress and prospects

“…Likewise, mass-spec technologies are becoming very powerful for generating a snapshot of cellular metabolism and protein content, especially for the analysis of clinical material [25]. For now, however, array-like platforms remain the main mode of analysis of specific kinase activities in a mixture of different phosphorylating enzymes and highimpact papers employing this technology to address important clinical issues are regularly published.…”

Dynamics of dual specificity phosphatases and their interplay with protein kinases in immune signaling

“…Systems biology and integrative biology offer several approaches to identify molecular mechanisms operating behind biological processes in unprecedented detail. Integrated approaches such as Proteogenomics can provide macroresolution snapshots to facilitate understanding of intricate molecular mechanisms in cancers [25,26] and infectious diseases [27,28]. Applying integrated approaches in the context of immunology can therefore offer unique insights into mechanisms of innate and adaptive immunity.…”