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批量和单细胞转录组分析揭示糖尿病足溃疡中线粒体相关程序性细胞死亡的基因特征

Bulk and Single-Cell Transcriptome Analyses Unravel Gene Signatures of Mitochondria-Associated Programmed Cell Death in Diabetic Foot Ulcer.

作者信息

Luo Wenqiang, Li Ning, Liu Jin, Li Duoyu, Li Yongheng, Ma Qing, Lin Chuangxin, Lu Liang, Lin Sipeng

机构信息

Department of Orthopedics, The First Affiliated Hospital of USTC, Division of Life Sciences and Medicine, University of Science and Technology of China, Hefei, Anhui, P. R. China.

Department of Orthopedics, Shenshan Medical Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Shanwei, Guangdong, P. R. China.

出版信息

J Cell Mol Med. 2024 Dec;28(24):e70319. doi: 10.1111/jcmm.70319.

DOI:10.1111/jcmm.70319
PMID:39730319
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC11680196/
Abstract

Mitochondrial programmed cell death (PCD) plays a critical role in the pathogenesis of diabetic foot ulcers (DFU). In this study, we performed a comprehensive transcriptome analysis to identify potential hub genes and key cell types associated with PCD and mitochondria in DFU. Using intersection analysis of PCD- and mitochondria-related genes, we identified candidate hub genes through protein-protein interaction and random forest analysis. At the single-cell level, key cell types were further validated based on the expression of hub genes. Additionally, we explored the transcription factors (TFs) regulating hub gene expression and the cellular heterogeneity of DFU. Finally, the expression of key hub genes and TFs was validated in clinical specimens. Our results identified BCL2 and LIPT1 as significantly downregulated hub genes in DFU, with Keratinocytes, as the key cell type. Immunohistochemistry confirmed downregulation of BCL2 and LIPT1 in DFU samples (p < 0.05). Additionally, TFs CEBPD and IRF1 were significantly upregulated in DFU, as confirmed by real-time polymerase chain reaction analysis (p < 0.05).

摘要

线粒体程序性细胞死亡（PCD）在糖尿病足溃疡（DFU）的发病机制中起关键作用。在本研究中，我们进行了全面的转录组分析，以鉴定与DFU中PCD和线粒体相关的潜在枢纽基因和关键细胞类型。通过对PCD和线粒体相关基因的交集分析，我们通过蛋白质-蛋白质相互作用和随机森林分析鉴定了候选枢纽基因。在单细胞水平上，基于枢纽基因的表达进一步验证了关键细胞类型。此外，我们探索了调节枢纽基因表达的转录因子（TFs）以及DFU的细胞异质性。最后，在临床标本中验证了关键枢纽基因和TFs的表达。我们的结果确定BCL2和LIPT1为DFU中显著下调的枢纽基因，角质形成细胞为关键细胞类型。免疫组织化学证实DFU样本中BCL2和LIPT1下调（p<0.05）。此外，实时聚合酶链反应分析证实TFs CEBPD和IRF1在DFU中显著上调（p<0.05）。

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