Identification of primary genes in glomeruli compartment of immunoglobulin A nephropathy by bioinformatic analysis

Mohammed Khamis Miraji; Yichun Cheng; Shuwang Ge; Gang Xu

doi:10.7717/peerj.7067

Identification of primary genes in glomeruli compartment of immunoglobulin A nephropathy by bioinformatic analysis

PeerJ. 2019 Jul 19:7:e7067. doi: 10.7717/peerj.7067. eCollection 2019.

Authors

Mohammed Khamis Miraji^#¹, Yichun Cheng^#¹, Shuwang Ge¹, Gang Xu¹

Affiliation

¹ Department of Nephrology, Tongji Hospital affiliated to Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, China.

^# Contributed equally.

Abstract

The current study is aimed to explore the specific genes which are responsible for the manifestation of Immunoglobulin A nephropathy (IgAN). Gene expression profiles GSE37460, GSE93798 and GSE104948 were analyzed using biological informatics methods to identify differentially expressed genes (DEGs) in IgAN glomeruli samples which were then compared to normal control samples. Subsequently, the DEGs were overlapped to explore genes with significant expression in at least two profiles. Finally, the enrichment analysis was conducted and the protein-protein interaction (PPI) network was constructed for the overlapping DEGs. A total of 28 genes were up-regulated and 10 genes were down-regulated. The up-regulated genes including CD44 and FN1 were chiefly involved in extracellular matrix receptors interaction pathway. In addition, CX3CR1 and CCL4 were associated with chemokine signaling pathway. ITGB2, PTPRC, FN1, and FCER1G were hub genes with a high degree of interaction in the PPI network. Therefore, this study identified many significant genes associated with extracellular matrix expansion and inflammatory mechanism which may be the novel biomarker and target candidates in IgAN.

Keywords: Down-regulation; Gene expression profiling; Immunoglobulin A Nephropathy; Protein–protein interaction; Up-regulation.

Grants and funding

This work was financially supported by the Major Research plan of the National Natural Science Foundation of China (Grant No. 91742204), international (regional) cooperation and exchange projects, (NSFC-DFG, Grant No. 81761138041), the National Natural Science Foundation of China (Grants 81470948, 81670633, 81570667), the National Key Research and Development Program (Grants 2016YFC0906103) and the National Key Technology R&D Program (Grant 2013BAI09B06, 2015BAI12B07). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.