A large number of studies have confirmed that BMI, hypertension, proteinuria and renal function contribute to the progression of IgAN, however, the genetic mechanism of these clinical characteristics leading to IgAN progression is not clear. The relationship and association between factors and IgAN also require more research and evidence of biological processes at the molecular level. Diseases involve thousands of gene expression changes with a huge and complex gene regulated network, which means research for a single gene is superficial and insufficient, it is hard to explain the mechanism of a disease. WGCNA is an advanced, successful and comprehensive algorithm for co-expression analysis, and it was not only used to construct gene co-expression network and screen gene modules. It served as a powerful tool to identify hub genes associated external information, clinical characteristics especially, and help researchers to understand the mechanism of the disease, providing a theoretical basis for the diagnosis and treatment of the disease.
Genes sets, which associated with GFR in glomeruli, enriched in immune response, cellular response to chemical stimulus and PI3K-Akt signaling pathway, indicated that immune response and IgA stimulus were dominant in impaction of glomerular filtration. It is known that glycosylated IgA has a transferrin receptor on the surface of mesangial cells4 and abnormal glycosylated IgA immune complexes are specifically recognized and deposited in the mesangium, causing proinflammatory cytokines and angiotensinⅡto be released5. Tumor necrosis factor alpha, derived from IgAN patients podocytes cells autocrine synthesis, caused TNF receptor 1, TNF receptor 2 and IL-6 to be up-regulated. Elevated expression of TNF receptor 1 leads to podocyte apoptosis and up-regulation of TNF receptor 2 expression, leading to chronic inflammation6; PI3K-Akt is an important intracellular pathway involved in cell metabolism, apoptosis, proliferation and differentiation7, 8. A study by Cox et al. reported that PI3K-Akt signaling pathway was hyperactive in IgAN patients and played an important role in IgAN9. Therefore, based on the results of WGCNA, we believed that PI3K-Akt signaling pathway specificity impacts the renal function in IgAN. For proteinuria, hub genes in glomeruli were enriched in the extracellular matrix organization, extracellular structure organization and PI3K-Akt signaling pathway, this means that these genes may play an important role in changing the extracellular matrix and potentially leading to proteinuria.
In tubulointerstitium group, there were 480 DEGs between IgAN and health control group. Among 480 DEGs, 6 hub genes associated with age, 15 hub genesassociated with sex, 35 hub genes associated with Bp enriched in positive regulation of apoptotic process, cellular response to nutrient levels and regeneration. Moreover, 87 hub genes associated with GFR in tubulointerstitium enriched in negative regulation of macromolecule metabolic process, negative regulation of metabolic process and RNA transport, and 33 hub genes associated with proteinuria enriched in the regulation of apoptotic process, regulation of programmed cell death and FoxO signaling pathway. Proteinuria is closely associated with poor cardiovascular outcomes and progression of ESRD in patients with CKD10, 11. It is worth noting that since the expression pattern of genes is very similar, WGCNA only screens one turquoise module in the IgAN tubulointerstitium group and genes that cannot be clustered into one of the modules are assigned to the grey module which represents background genes outside of the modules. Thus, genes in the grey module could possibly be related to GFR or Scr but not belong to WGCNA modules.