基于ceRNA网络的糖尿病足溃疡关键miRNA筛选及功能验证
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湖南师范大学附属第一医院(湖南省人民医院) 康复医学科,湖南 长沙 410016

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黄靓,湖南师范大学附属第一医院(湖南省人民医院)副主任医师,主要从事康复医学方面的研究。

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湖南省自然科学基金青年基金资助项目(2023JJ40374);湖南省研究生科研创新基金资助项目(CX20250810);湖南省人民医院(湖南师范大学附属第一医院)青年博士基金暨2023年国自培育基金资助项目(BSJJ202217);湖南省长沙市2024年度指导性科技计划基金资助项目(kzd2401003)。


Identification and functional validation of key miRNAs associated with diabetic foot ulcer based on the ceRNA network
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Department of Rehabilitation Medicine, the First Affiliated Hospital of Hu'nan Normal University (Hunan Provincial People's Hospital), Changsha 410005, China

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    摘要:

    背景与目的 糖尿病足溃疡(DFU)创面愈合障碍是导致患者截肢和死亡的重要原因,其分子调控机制尚未完全阐明。本研究基于竞争性内源性RNA(ceRNA)网络和加权基因共表达网络分析(WGCNA)筛选DFU创面愈合相关关键miRNA,并探讨其在DFU中的生物学功能。方法 从GEO数据库获取DFU相关circRNA、lncRNA、miRNA及mRNA表达谱数据,采用limma包筛选差异表达RNA,构建ceRNA调控网络;结合WGCNA筛选与DFU创面愈合相关的关键模块及枢纽基因,并构建关键ceRNA子网络。采用qRT-PCR检测DFU组织与对照组织中候选miRNA的表达水平。利用高糖培养的人脐静脉内皮细胞(HUVEC)建立体外模型,通过miRNA模拟物和抑制剂转染,检测hsa-miR-155-5p对细胞增殖、迁移、侵袭及血管生成能力的影响,并采用Western blot检测磷脂酰肌醇3-激酶/蛋白激酶B(PI3K/Akt)信号通路相关蛋白表达。结果 共筛选获得66个差异表达miRNA,并构建DFU相关ceRNA调控网络。WGCNA鉴定出与DFU创面愈合显著相关的关键模块及6个枢纽基因(PDE9A、PADI2、PRR15L、B3GALT5、TMPRSS2和NWD1)。结合ceRNA网络进一步筛选获得hsa-miR-155-5p、hsa-miR-204-5p和hsa-miR-302d-3p等候选miRNA。qRT-PCR结果显示,hsa-miR-155-5p在DFU组织中的表达显著低于对照组织(P<0.05)。体外实验表明,过表达hsa-miR-155-5p可显著促进高糖环境下HUVEC的增殖、迁移、侵袭及血管形成能力,同时上调p-PI3K和p-Akt蛋白表达水平(均P<0.05)。结论 基于ceRNA网络与WGCNA筛选出hsa-miR-155-5p是DFU愈合相关的关键miRNA。hsa-miR-155-5p可通过激活PI3K/Akt信号通路促进内皮细胞功能和血管生成,可能成为DFU治疗的潜在分子靶点。

    Abstract:

    Background and Aims Impaired wound healing in diabetic foot ulcers (DFUs) is a major cause of amputation and mortality in affected patients, and its underlying molecular regulatory mechanisms remain incompletely understood. This study aimed to identify key microRNAs (miRNAs) associated with DFU healing through the integration of a competing endogenous RNA (ceRNA) network and weighted gene co-expression network analysis (WGCNA), and to investigate their biological functions in DFU.Methods Expression profile datasets of circRNAs, lncRNAs, miRNAs, and mRNAs related to DFU were obtained from the Gene Expression Omnibus (GEO) database. Differentially expressed RNAs were identified using the limma package, and a ceRNA regulatory network was constructed. WGCNA was subsequently performed to identify key modules and hub genes associated with DFU healing, followed by the establishment of a hub ceRNA subnetwork. Quantitative real-time PCR (qRT-PCR) was used to determine the expression levels of candidate miRNAs in DFU and control tissues. An in vitro high-glucose model was established using human umbilical vein endothelial cells (HUVECs). Following transfection with miRNA mimics or inhibitors, the effects of hsa-miR-155-5p on cell proliferation, migration, invasion, and angiogenesis were evaluated. Western blot analysis was performed to detect the expression of proteins involved in the PI3K/Akt signaling pathway.Results A total of 66 differentially expressed miRNAs were identified, and a DFU-related ceRNA regulatory network was constructed. WGCNA identified a key module significantly associated with DFU healing and six hub genes, namely PDE9A, PADI2, PRR15L, B3GALT5, TMPRSS2, and NWD1. Integration of the ceRNA network further identified hsa-miR-155-5p, hsa-miR-204-5p, and hsa-miR-302d-3p as candidate miRNAs. qRT-PCR validation demonstrated that hsa-miR-155-5p expression was significantly lower in DFU tissues than in control tissues (P<0.05). In vitro experiments showed that overexpression of hsa-miR-155-5p significantly enhanced the proliferation, migration, invasion, and tube formation abilities of HUVECs under high-glucose conditions, while simultaneously increasing the expression levels of phosphorylated PI3K and Akt proteins (both P<0.05).Conclusion Integrated analysis based on the ceRNA network and WGCNA identified hsa-miR-155-5p as a key miRNA associated with DFU healing. hsa-miR-155-5p may promote endothelial cell function and angiogenesis through activation of the PI3K/Akt signaling pathway, suggesting its potential as a therapeutic target for DFU.

    图1 差异表达RNA的获取 A:差异表达circRNA火山图;B:差异表达circRNA热图;C:差异表达lncRNA火山图;D:差异表达lncRNA热图;E:差异表达mRNA火山图;F:差异表达mRNA热图Fig.1 Identification of differentially expressed RNAs A: Volcano plot of differentially expressed circRNAs; B: Heatmap of differentially expressed circRNAs; C: Volcano plot of differentially expressed lncRNAs; D: Heatmap of differentially expressed lncRNAs; E: Volcano plot of differentially expressed mRNAs; F: Heatmap of differentially expressed mRNAs
    图2 差异表达基因潜在生物学功能鉴定 A:GO富集分析;B: KEGG富集分析Fig.2 Functional enrichment analysis of differentially expressed genes A: GO enrichment analysis; B: KEGG pathway enrichment analysis
    图3 circRNA-miRNA-mRNA型ceRNA网络 A:表达上调的circRNA介导的ceRNA网络;B:表达下调的circRNA介导的ceRNA网络Fig.3 Construction of the circRNA-miRNA-mRNA ceRNA Network A: Upregulated circRNA-mediated ceRNA network; B: Downregulated circRNA-mediated ceRNA network
    图4 lncRNA-miRNA-mRNA型ceRNA网络 A:表达上调的lncRNA介导的ceRNA网络;B:表达下调的lncRNA介导的ceRNA网络Fig.4 Construction of the lncRNA-miRNA-mRNA ceRNA Network A: Upregulated lncRNA-mediated ceRNA network; B: Downregulated lncRNA-mediated ceRNA network
    图5 mRNA-miRNA-mRNA型ceRNA网络和相关RNA的KEGG富集分析图 A:表达上调的mRNA介导的ceRNA网络;B:表达下调的mRNA介导的ceRNA网络;C:表达上调的mRNA的KEGG富集情况;D:表达下调的mRNA的KEGG富集情况Fig.5 Construction of the mRNA-miRNA-mRNA ceRNA network and KEGG enrichment analysis A: Upregulated mRNA-mediated ceRNA network; B: Downregulated mRNA-mediated ceRNA network; C: KEGG enrichment analysis of upregulated mRNAs; D: KEGG enrichment analysis of downregulated mRNAs
    图6 WGCNA分析图 A:确定最优软阈值;B:基于最优软阈值构建的共表达网络基因聚类树;C:不同DFU状态计算模块的相关性;D:WGCNA中各模块的GS;E:棕色模块与DFU愈合状态的相关性Fig.6 Identification of key modules by WGCNA A: Determination of the optimal soft-threshold power; B: Gene dendrogram of the co-expression network; C: Module-trait correlation analysis between different DFU states; D:GS across different modules; E: Correlation between the brown module and DFU healing status
    图7 枢纽基因鉴定及诊断效能分析 A-F:PDE9A、PADI2、PRR15L、B3GALT5、TMPRSS2和NWD1等6个枢纽基因的ROC曲线;G-L:6个枢纽基因在DFU愈合组与非愈合组的表达差异Fig.7 Identification and diagnostic performance of hub genes A-F: ROC curves of PDE9A, PADI2, PRR15L, B3GALT5, TMPRSS2 and NWD1; G-L: Expression levels of hub genes in healed and non-healed DFU tissues
    图8 hsa-miR-155-5p表达水平与功能的验证 A:构建包含3个枢纽ceRNA与6个枢纽基因的网络;B:通过qRT-PCR检测不同miRNA的表达水平;C:CCK-8法评估hsa-miR-155-5p上调组的细胞增殖能力;D:CCK-8法评估hsa-miR-155-5p下调组的细胞增殖能力;E:划痕实验检测hsa-miR-155-5p上调组的细胞迁移能力;F:划痕实验检测hsa-miR-155-5p下调组的细胞迁移能力;G:Transwell实验评估hsa-miR-155-5p上调组的细胞迁移情况;H:Transwell实验评估hsa-miR-155-5p下调组的细胞迁移情况;I:血管生成实验评估hsa-miR-155-5p上调组与下调组的血管生成能力;J:通过Western blot检测PI3K/Akt信号通路相关蛋白的表达水平Fig.8 Validation of hsa-miR-155-5p expression and biological functions A: Construction of the hub ceRNA network; B: qRT-PCR validation of candidate miRNAs; C: Cell proliferation after hsa-miR-155-5p overexpression; D: Cell proliferation after hsa-miR-155-5p inhibition; E: Scratch assay after hsa-miR-155-5p overexpression; F: Scratch assay after hsa-miR-155-5p inhibition; G: Transwell migration assay after hsa-miR-155-5p overexpression; H: Transwell migration assay after hsa-miR-155-5p inhibition; I: Tube formation assay; J: Expression of PI3K/Akt pathway-related proteins detected by Western blot
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黄靓,眭轩,冯婧怡,蔡华安.基于ceRNA网络的糖尿病足溃疡关键miRNA筛选及功能验证[J].中国普通外科杂志,2026,35(7):1376-1387.
DOI:10.7659/j. issn.1005-6947.250660

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  • 收稿日期:2025-11-25
  • 最后修改日期:2026-03-09
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  • 在线发布日期: 2026-08-31
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