An integrated in silico prediction and in vivo approach identifies NF-κB as master regulator in the rat model of chronic kidney disease

To find the novel genes/proteins and their cross talk leading to chronic kidney injury employing integrated in silico and in vivo approach. National Centre for Biotechnology Information data were used as the initial source for the chronic kidney disease (CKD) genes. Hub genes were analyzed through Cytoscape employing three centrality methods viz. degree, between-ness centrality, and maximum neighborhood centrality. Additionally, a master regulator of these genes was also identified through ingenuity pathway analysis. All these molecular entities were further experimentally validated in-vivo in rat unilateral ureter obstruction (UUO) model of CKD, by gene and protein expression studies by employing real time polymerase chain reaction and immunohistochemistry analysis. The study exploits in-silico and in-vivo approach for hub gens identification underlining CKD through UUO rat model. The bioinformatics approach scrutinized 10 hub genes and Nuclear factor kappa-light-chain-enhancer of activated B cells (NF-?B) as the master regulator of these screened hub genes. Amongst these, 3 top-ranked genes viz. Transforming growth factor beta, transforming growth factor alpha , and STAT-3 were found to be highly upregulated genes in CKD as signified by the coloring pattern of the software. Furthermore, the in vivo analysis employing the UUO rat model reiterated the mechanistic role being played by these hub genes in CKD as demonstrated by the upregulated gene and protein expression of the genes, with higher elevation at day 18 than at day 14 post surgery. NF-?B has been ascertained as a major participant in various forms of kidney diseases and the observations from the present study lend support that NF-?B has a much more complicated role, being the major regulator of genes participating in the manifestation of CKD and thus can be restrained by therapeutic manoeuvres.