DN remains end - stage renal disease worldwide because of its complicated molecular mechanisms and cellular heterogeneity, and its prevalence rise every year [28]. Therefore, recognition of DN may offer clinicians novel tools that can be used to treat the disease. Extensive genomic investigations showing the effects of genes have accepted noticeable attention. Many potential and valuable genes must be identified to develop the clinical outcome for DN patients. However, the number of specific molecular biomarkers that can be used to show therapeutic effects is still limited, and prognostic factors are essential for the treatment of DN patients. Therefore, to diminish mortality and develop DN prognosis, there is a critical demand for the screening of molecular biomarkers of DN.
To better understand the genetic modifications occurring during DN advancement, bioinformatics methods were used to extract data from the GSE7803 and GSE142025 expression profiling by high throughput sequencing. In this investigation, we identified 549 DEGs (275 up regulated and 274 down regulated) between DN and normal control. Xie et al [29] and Zhou et al [30] demonstrate that increased activity of polymorphic CFHR1 and RGS1 genes play a key role in nephropathy progression. Previous investigations report that polymorphic GREM1 gene plays an essential role in progression of DN [31]. Sun et al [32] find that CCL19 is responsible for renal inflammation and fibrosis in DN. Martinelli-Boneschi et al [33] revealed that polymorphic COL6A5 gene is involved in neuropathic chronic itch, but this gene might be liable for progression of DN. Hall et al [34] observed that the expression of CIDEC (cell death inducing DFFA like effector c) play key role in obesity, but this gene might be involved in DN progression. NR4A1 drives DN growth through mitochondrial fission and mitophagy [35]. Recent study has reported that low expression of NR4A2 is associated with myocardial infarction [36], but this gene might be linked with progression of DN. EGR1 is required for fibrosis and inflammatory response in DN [37]. ATF3 expression has been implicated in DN [38]. Polymorphic NR4A3 gene may contribute to type 2 diabetes progression [39], but this gene might be associated with development of DN. KLK1 functions in DN progression can be used for predicting the progression and prognosis of the disease [40].
A series of DEGs were discovered to be enriched in the GO functions and pathways. SERPINA3 [41], IKZF1 [42], BTK (Bruton tyrosine kinase) [43], C1QA [44], CD1C [45] and CCL13 [46] have a key role in lupus nephritis, but these genes might be liable for advancement of DN. TNFSF14 [47], ITGAL (integrin subunit alpha L) [48], PLAC8 [49], ADRA2A [50], CCL21 [51], ALOX5 [52], CNR2 [53], COL1A1 [54], WNT7A [55], SLAMF1 [56], CD3D [57], LTF (lactotransferrin) [58], MIR27B [59], PDK4 [60], UCN3 [61], PCK1 [62], CEL (carboxyl ester lipase) [63], TRPM6 [64], MTTP (microsomal triglyceride transfer protein) [65], CYP2C8 [66] and CYP3A4 [67] have important role in the progression of type 2 diabetes via inflammation , but these genes might be crucial role in DN progression. Zhang et al [68], Ellenbroek et al [69], Guo et al [70] and Tillmanns et al [71] have shown that MZB1, LAIR1, MIR142 and FAP (fibroblast activation protein alpha) modulating mitochondrial function and alleviating inflammation in myocardial infarction, but these genes might be involved in progression of DN. IRF4 plays a key role in the obesity-induced insulin resistance [72], but this gene might be responsible for development of DN. MDK (midkine) [73], CCR2 [74], SAA1 [75], C3 [76], CD19 [77], CCR5 [78], CXCR3 [79], FABP4 [80], GDF15 [81], IGF2 [82], IGFBP1 [83] and IL6 [84] are important in the progression of DN through inflammation. A previous study has shown that UBASH3A [85], SIRPG (signal regulatory protein gamma) [86], IKZF3 [87], CD1D [88], CD2 [89], CD48 [90], CD247 [91] and CYP27B1 [92] are liable for progression of type 1 diabetes through inflammation, but these genes might be key for progression of DN. SIT1 [93], JAML (junction adhesion molecule like) [94], TIMP1 [95], PRKCB (protein kinase C beta) [96], MMP7 [97], WNT7B [98], WNT10A [99], DUSP1 [100], WT1 [101], APOC3 [102], ERRFI1 [103], HCN2 [104], MME (membrane metalloendopeptidase) [105], STRA6 [106], SLC12A3 [107] and GC (GC vitamin D binding protein) [108] expedites epithelial to mesenchymal transition and renal fibrosis in DN. Previous studies have found CFD (complement factor D) [109], DOCK2 [110], LYZ (lysozyme) [111], CD5L [112], SCARA5 [113], VCAN (versican) [114], GDF5 [115], SFRP2 [116], BTG2 [117], ZFP36 [118], GPR3 [119], OLR1 [120], PM20D1 [121] and UGT2B7 [122] to be expressed in obesity, but these genes might be liable for advancement of DN. Polymorphic FCRL3 [123], FCGR2B [124], COMP (cartilage oligomeric matrix protein) [125], ERFE (erythroferrone) [126] and NPHS1 [127] expression can be altered by inflammation, which might involved in nephropathy. The expression of COL1A2 [128], LCK (LCK proto-oncogene, Src family tyrosine kinase) [129], LCN2 [130] and APOB (apolipoprotein B) [131] are key for progression of diabetic retinopathy, but these genes might be essential for DN development. COL3A1 [132], PER1 [133], JUN (Jun proto-oncogene, AP-1 transcription factor subunit) [134], SLC26A4 [135], F2RL3 [136], CYP4A11 [137] and CYP4F2 [138] play an important role in the hypertension, but these genes might be involved in progression of DN.
Based on the PPI network and module analysis, we obtained top hub genes in the whole network. Onions et al. [139] showed that ALB (albumin) was potential biomarkers of DN and disease progression. Novel biomarkers such as MDFI (MyoD family inhibitor), FOS (Fos proto-oncogene, AP-1 transcription factor subunit), SH2D1A, SLA2, TRAT1, CD3E, JUNB and FOSB might play an important role in the development of DN.
Based on the miRNA-DEG regulatory network and TF-DEG regulatory network, we obtained target in the whole network. Recent investigation reported that the dysregulated activity of MYBL2 was associated with myocardial infarction progression [140], but this gene might be linked with progression of DN. Many investigation have reported the hsa-mir-637 [141] and NR3C1 [142] were linked with progression of hypertension, but these genes might be liable for advancement of DN. Wang et al. [143] noted that hsa-mir-1261 was associated with development of DN. Li et al [144] reported that hsa-mir-4458 expression was an independent marker of prognosis in myocardial infarction, but this gene might be involved in DN. Keller et al [145], Fujimoto et al [146] and Xu et al [147] demonstrated that expression of NFATC2, PDX1 and CREB1were involved in type 2 diabetes, but these genes might be key for progression of DN. Du et al. [148], Zhang et al. [149] and Zhao et al. [150] found that YY1, TP53 and SRF (serum-response factor) played a key role in DN through the epithelial–mesenchymal transition. Novel targets such as IL2RB, hsa-mir-4492, hsa-mir-4319, hsa-mir-4300, hsa-mir-3943, hsa-mir-548e-3p, hsa-mir-6077, hsa-mir-5586-5p, RET (ret proto-oncogene), MAP1LC3C, PTPRO (protein tyrosine phosphatase receptor type O), NR2C2, MAX (myc-associated factor X) and ARID3A might be responsible for progression of DN.
In the present investigation, the DEGs of DN and normal control samples were analyzed to achieve a better understanding of DN. GO and pathway enrichment analyses of DEGs were applied, and the protein-protein interaction (PPI) network, module and miRNA-DEG regulatory network and TF-DEG regulatory network of these DEGs were also constructed. ROC analysis and molecular docking experiments conducted. The aim of this investigation was to identify essential genes and pathways in DN using bioinformatics analysis, and then to explore the intrinsic mechanisms of DN and distinguish new potential diagnostic and therapeutic biomarkers of DN. We anticipated that these investigations will provide further insight of DN pathogenesis and advancement at the molecular level.