Bulk and single-cell transcriptome analyses of islet tissue unravel gene signatures associated with pyroptosis and immune infiltration in type 2 diabetes

Abstract

IntroductionType 2 diabetes (T2D) is a common chronic heterogeneous metabolic disorder. However, the roles of pyroptosis and infiltrating immune cells in islet dysfunction of patients with T2D have yet to be explored. In this study, we aimed to explore potential crucial genes and pathways associated with pyroptosis and immune infiltration in T2D.MethodsTo achieve this, we performed a conjoint analysis of three bulk RNA-seq datasets of islets to identify T2D-related differentially expressed genes (DEGs). After grouping the islet samples according to their ESTIMATE immune scores, we identified immune- and T2D-related DEGs. A clinical prediction model based on pyroptosis-related genes for T2D was constructed. Weighted gene co-expression network analysis was performed to identify genes positively correlated with pyroptosis-related pathways. A protein–protein interaction network was established to identify pyroptosis-related hub genes. We constructed miRNA and transcriptional networks based on the pyroptosis-related hub genes and performed functional analyses. Single-cell RNA-seq (scRNA-seq) was conducted using the GSE153885 dataset. Dimensionality was reduced using principal component analysis and t-distributed statistical neighbor embedding, and cells were clustered using Seurat. Different cell types were subjected to differential gene expression analysis and gene set enrichment analysis (GSEA). Cell–cell communication and pseudotime trajectory analyses were conducted using the samples from patients with T2D.ResultsWe identified 17 pyroptosis-related hub genes. We determined the abundance of 13 immune cell types in the merged matrix and found that these cell types were correlated with the 17 pyroptosis-related hub genes. Analysis of the scRNA-seq dataset of 1892 islet samples from patients with T2D and controls revealed 11 clusters. INS and IAPP were determined to be pyroptosis-related and candidate hub genes among the 11 clusters. GSEA of the 11 clusters demonstrated that the myc, G2M checkpoint, and E2F pathways were significantly upregulated in clusters with several differentially enriched pathways.DiscussionThis study elucidates the gene signatures associated with pyroptosis and immune infiltration in T2D and provides a critical resource for understanding of islet dysfunction and T2D pathogenesis.

The oxidative aging model integrated various risk factors in type 2 diabetes mellitus at system level

“…Chronic oxidative stress can also leads to decreased responsiveness to insulin, ultimately leading to diabetes reported by Alina Berdichevsky et al (p=0.01) ( 169 ). Besides, NFKBIA affects the wound healing in diabetic foot ulceration (DFU) (p=0.006) ( 170 ), MYC and SCD are related to pyroptosis and immune infiltration in T2DM (p=0.001) ( 171 ). The experiment of Parker C. Wilson et al using single-nucleus RNA sequencing has been revealed that GCH1 is associated with early-stage diabetic nephropathy (p=4.88e-09) ( 172 ) In short, our results also presented key clinical indices with the help of the integrated oxidative model.…”

The role of ncRNAs‐mediated pyroptosis in diabetes and its vascular complications

“…30 In addition, the inhibition of NLRP3-mediated pyroptosis can effectively alleviate VCD. [31][32][33][34] Human NLRP1 was identified as the first sensor capable of forming inflammasomes and may play a key role in the progression of diabetes. A recent single-cell transcriptomic analysis of islet tissue in type 2 diabetes revealed that GSDMD, GSDMB, CASP1, and NLRP1 were significantly increased in diabetic patients.…”

“…Studies have reported that the inhibition of podocyte pyroptosis could induce a protective effect against renal injury in DN 30 . In addition, the inhibition of NLRP3‐mediated pyroptosis can effectively alleviate VCD 31–34 …”

Single-cell RNA sequencing of peripheral blood mononuclear cells reveals complex cellular signalling signatures of metformin treatment type 2 diabetes mellitus

“…To date, the phenotypes and roles of T cells, NK cells, monocytes, macrophages and other immune cells have received less attention than other systems involved in diabetes mellitus [5][6]. In recent years, increasing evidence has shown that immune disorders are the main factors involved in the occurrence of T2DM [7][8][9]. Single-cell RNA sequencing (scRNA-seq) is a new technique that can be used to reveal cell heterogeneity and can be used to quantify the expression profile of each gene in each cell, which makes it easier to study genes.…”

“…To date, the phenotypes and roles of T cells, NK cells, monocytes, macrophages and other immune cells have received less attention than other systems involved in diabetes mellitus [5][6]. In recent years, increasing evidence has shown that immune disorders are the main factors involved in the occurrence of T2DM [7][8][9]. Single-cell RNA .…”