Identification of Key Biomarkers and Immune Infiltration in Sciatic Nerve of Diabetic Neuropathy BKS-db/db Mice by Bioinformatics Analysis.

Yixuan Lin,Zhaohui Fang,Lianzhi Cheng,Guoming Shen,Fanjing Wang

doi:10.3389/fphar.2021.682005

Yixuan Lin, Zhaohui Fang + Show 3 more

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https://doi.org/10.3389/fphar.2021.682005

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Abstract

Diabetic neuropathy (DN) is one of the chronic complications of diabetes which can cause severe harm to patients. In order to determine the key genes and pathways related to the pathogenesis of DN, we downloaded the microarray data set GSE27382 from Gene Expression Omnibus (GEO) and adopted bioinformatics methods for comprehensive analysis, including functional enrichment, construction of PPI networks, central genes screening, TFs-target interaction analysis, and evaluation of immune infiltration characteristics. Finally, we examined quantitative real- time PCR (qPCR) to validate the expression of hub genes. A total of 318 differentially expressed genes (DEGs) were identified, among which 125 upregulated DEGs were enriched in the mitotic nuclear division, extracellular region, immunoglobulin receptor binding, and p53 signaling pathway, while 193 downregulated DEGs were enriched in ion transport, membrane, synapse, sodium channel activity, and retrograde endocannabinoid signaling. GSEA plots showed that condensed nuclear chromosome kinetochore were the most significant enriched gene set positively correlated with the DN group. Importantly, we identified five central genes (Birc5, Bub1, Cdk1, Ccnb2, and Ccnb1), and KEGG pathway analysis showed that the five hub genes were focused on progesterone-mediated oocyte maturation, cell cycle, and p53 signaling pathway. The proportion of immune cells from DN tissue and normal group showed significant individual differences. In DN samples, T cells CD4 memory resting and dendritic cells resting accounted for a higher proportion, and macrophage M2 accounted for a lower proportion. In addition, all five central genes showed consistent correlation with immune cell infiltration levels. qPCR showed the same expression trend of five central genes as in our analysis. Our research identified key genes related to differential genes and immune infiltration related to the pathogenesis of DN and provided new diagnostic and potential therapeutic targets for DN.

Highlights

Diabetic neuropathy (DN) is one of the most common and serious chronic complications of diabetic mellitus (DM) (Barrett et al, 2017; Iqbal et al, 2018), which is characterized by pain, paresthesia, and sensory loss (Pinzur, 2011)
In the Gene Ontology (GO) enrichment analysis, the upregulated differentially expressed genes (DEGs) in biological pathways (BP) were mainly enriched in mitotic nuclear division, cell division, inflammatory response, cell cycle, chromosome segregation, and innate immune response, while the downregulated DEGs in BP were enriched in ion transport, transport, sodium ion transport, synaptic vesicle exocytosis, retinal ganglion cell axon guidance, and learning
cellular components (CC) analysis showed that the upregulated DEGs were significantly enriched in the extracellular region, extracellular space, condensed chromosome kinetochore, kinetochore, chromosome, centromeric region, and external side of plasma membrane, while the downregulated DEGs were enriched in the membrane, synapse, axon, neuronal cell body, perikaryon, and synaptic vesicle

Summary

Introduction

Diabetic neuropathy (DN) is one of the most common and serious chronic complications of diabetic mellitus (DM) (Barrett et al, 2017; Iqbal et al, 2018), which is characterized by pain, paresthesia, and sensory loss (Pinzur, 2011). The principal pathological process of DN includes axonal degeneration and segmental demyelination (Vinik et al, 2000). Studies have identified persistently impaired insulin function and hyperglycemia to cause a series of downstream abnormalities that eventually lead to axon loss (Malik et al, 2001; Sima and Zhang, 2014). Several biological pathways including oxidative stress, inflammation, apoptosis, and autophagy are involved in the development of diabetic neuropathy (Fernyhough and McGavock, 2014; Roman-Pintos et al, 2016; Chung et al, 2018). The process is still controversial due to its complexity

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