Proteogenomics in Nephrology: A New Frontier in Nephrological Research

Abstract

Proteogenomics represents a transformative intersection in nephrology, uniting genomics, transcriptomics, and proteomics to unravel the molecular intricacies of kidney diseases. This review encapsulates the methodological essence of proteogenomics and its profound implications in chronic kidney disease (CKD) research. We explore the proteogenomic pipeline, highlighting the integrated analysis of genomic, transcriptomic, and proteomic data and its pivotal role in enhancing our understanding of kidney pathologies. Through case studies, we showcase the application of proteogenomics in clear cell renal cell carcinoma (ccRCC) and Autosomal Recessive Polycystic Kidney Disease (ARPKD), emphasizing its potential in personalized treatment strategies and biomarker discovery. The review also addresses the challenges in proteogenomic analysis, including data integration complexities and bioinformatics limitations, and proposes solutions for advancing the field. Ultimately, this review underscores the prospective future of proteogenomics in nephrology, particularly in advancing personalized medicine and providing novel therapeutic insights.

Keywords: biomarkers; kidney cancer; nephrology; proteogenomics; proteomics.

Figure 1

In proteogenomics, a blend of genomic and transcriptomic information is utilized to create custom protein databases, enhancing the interpretation of proteomic data. This method allows for the validation of gene expression at the protein level and aids in refining gene models. Improved gene models, in turn, contribute to the advancement of protein sequence databases used in traditional proteomic analyses. This cyclical process enhances the overall accuracy and efficiency of proteomic research (Created with BioRender.com, accessed on 1 April 2024).