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

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机构: [1]Department of Endocrinology, Yunnan Province Clinical Medical Center for Endocrine and Metabolic Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, China. [2]Department of Geriatric Medicine, The First Affiliated Hospital of Kunming Medical University, Kunming, China.
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关键词: differentially expressed gene type 2 diabetes pyroptosis immune infiltration singlecell RNA

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Type 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.To 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.We 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.This 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.Copyright © 2023 Song, He, Jiang, Yang, Xu, Yuan, Zhang and Xu.

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大类 | 2 区 医学
小类 | 2 区 内分泌学与代谢
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出版当年[2023]版:
Q2 ENDOCRINOLOGY & METABOLISM
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Q2 ENDOCRINOLOGY & METABOLISM

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第一作者机构: [1]Department of Endocrinology, Yunnan Province Clinical Medical Center for Endocrine and Metabolic Disease, The First Affiliated Hospital of Kunming Medical University, Kunming, China.
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