Search for sarcoidosis candidate genes by integration of data from genomic, transcriptomic and proteomic studies
Ales Maver, Igor Medica, Borut Peterlin
Med Sci Monit 2009; 15(12): SR22-28
Available online: 2009-12-01
The search for gene candidates in multifactorial diseases such as sarcoidosis can be based on the integration of linkage association data, gene expression data, and protein profile data from genomic, transcriptomic and proteomic studies, respectively.
Material and Method: In this study we performed a literature-based search for studies reporting such data, followed by integration of collected information. Different databases were examined--Medline, HugGE Navigator, ArrayExpress and Gene Expression Omnibus (GEO). Candidate genes were defined as genes which were reported in at least 2 different types of omics studies. Genes previously investigated in sarcoidosis were excluded from further analyses.
Results: We identified 177 genes associated with sarcoidosis as potential new candidate genes. Subsequently, 9 gene candidates identified to overlap in 2 different types of studies (genomic, transcriptomic and/or proteomic) were consistently reported in at least 3 studies: SERPINB1, FABP4, S100A8, HBEGF, IL7R, LRIG1, PTPN23, DPM2 and NUP214. These genes are involved in regulation of immune response, cellular proliferation, apoptosis, inhibition of protease activity, lipid metabolism. Exact biological functions of HBEGF, LRIG1, PTPN23, DPM2 and NUP214 remain to be completely elucidated.
Conclusions: We propose 9 candidate genes: SERPINB1, FABP4, S100A8, HBEGF, IL7R, LRIG1, PTPN23, DPM2 and NUP214, as genes with high potential for association with sarcoidosis.
Keywords: Sarcoidosis - genetics, Proteomics, Receptors, Interleukin-7 - genetics, Protein Tyrosine Phosphatases, Non-Receptor - genetics, Protein Array Analysis, Nuclear Pore Complex Proteins - genetics, Membrane Glycoproteins - genetics, Mannosyltransferases - genetics, Intercellular Signaling Peptides and Proteins - genetics, Genomics, Genetic Predisposition to Disease, Genome-Wide Association Study, Gene Expression Profiling, Fatty Acid-Binding Proteins - genetics, Databases, Genetic, Calgranulin A - genetics, Serpins - genetics