MS/MS in silico subtraction-based proteomic profiling as an approach to facilitate disease gene discovery: application to lens development and cataract

• Published in: Human genetics Vol. 139; no. 2; pp. 151 - 184
• Main Authors: Aryal, Sandeep, Anand, Deepti, Hernandez, Francisco G., Weatherbee, Bailey A. T., Huang, Hongzhan, Reddy, Ashok P., Wilmarth, Phillip A., David, Larry L., Lachke, Salil A.
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Springer Berlin Heidelberg 01.02.2020; Springer Nature B.V
• Subjects: Animals; Bioinformatics; Biomarkers - metabolism; Biomedical and Life Sciences; Biomedicine; Cataract - genetics; Cataract - metabolism; Cataract - pathology; Cataracts; Comparative analysis; Computational Biology; Computer Simulation; Embryos; Eye Proteins - genetics; Eye Proteins - metabolism; Gene expression; Gene Expression Profiling; Gene Function; Genes; Homeostasis; Human Genetics; Humans; Lens, Crystalline - embryology; Lens, Crystalline - metabolism; Mass spectroscopy; Metabolic Diseases; Mice; Mice, Inbred C57BL; Molecular Medicine; Original Investigation; Proteins; Proteome - analysis; Proteome - metabolism; Proteomes; Tandem Mass Spectrometry - methods; Transcriptome
• ISSN: 0340-6717; 1432-1203
• DOI: 10.1007/s00439-019-02095-5

While the bioinformatics resource-tool iSyTE (integrated Systems Tool for Eye gene discovery) effectively identifies human cataract-associated genes, it is currently based on just transcriptome data, and thus, it is necessary to include protein-level information to gain greater confidence in gene prioritization. Here, we expand iSyTE through development of a novel proteome-based resource on the lens and demonstrate its utility in cataract gene discovery. We applied high-throughput tandem mass spectrometry (MS/MS) to generate a global protein expression profile of mouse lens at embryonic day (E)14.5, which identified 2371 lens-expressed proteins. A major challenge of high-throughput expression profiling is identification of high-priority candidates among the thousands of expressed proteins. To address this problem, we generated new MS/MS proteome data on mouse whole embryonic body (WB). WB proteome was then used as a reference dataset for performing “in silico WB-subtraction” comparative analysis with the lens proteome, which effectively identified 422 proteins with lens-enriched expression at ≥ 2.5 average spectral counts, ≥ 2.0 fold enrichment (FDR < 0.01) cut-off. These top 20% candidates represent a rich pool of high-priority proteins in the lens including known human cataract-linked genes and many new potential regulators of lens development and homeostasis. This rich information is made publicly accessible through iSyTE ( https://research.bioinformatics.udel.edu/iSyTE/ ), which enables user-friendly visualization of promising candidates, thus making iSyTE a comprehensive tool for cataract gene discovery.