中国组织工程研究 ›› 2024, Vol. 28 ›› Issue (35): 5656-5661.doi: 10.12307/2024.600

• 组织工程相关大数据分析 Big data analysis in tissue engineering • 上一篇    下一篇

铁死亡对压疮的调控机制:生物信息学分析及实验结果验证

唐路路1,潘晓佳1,赖英桃2,王  力3   

  1. 1广州中医药大学第一临床医学院,广东省广州市  510405;2广州中医药大学第一附属医院,广东省广州市  510405;3广州中医药大学基础医学院,广东省广州市  510006
  • 收稿日期:2023-11-17 接受日期:2023-12-21 出版日期:2024-12-18 发布日期:2024-03-15
  • 通讯作者: 赖英桃,主任护师,硕士生导师,广州中医药大学第一附属医院,广东省广州市 510405 王力,广州中医药大学在读博士,广州中医药大学基础医学院,广东省广州市 510006
  • 作者简介:唐路路,男,1997年生,江苏省南通市人,汉族,广州中医药大学在读硕士,主要从事中西医结合大数据分析研究。
  • 基金资助:
    广东省中医药局科研项目(20231128),项目负责人:赖英桃

Regulatory mechanism of ferroptosis on pressure ulcers: bioinformatics analysis and experimental validation

Tang Lulu1, Pan Xiaojia1, Lai Yingtao2, Wang Li3   

  1. 1The First College of Clinical Medicine, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong Province, China; 2The First Affiliated Hospital, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong Province, China; 3School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
  • Received:2023-11-17 Accepted:2023-12-21 Online:2024-12-18 Published:2024-03-15
  • Contact: Lai Yingtao, Chief nurse practitioner, Master’s supervisor, The First Affiliated Hospital of Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong Province, China Wang Li, PhD candidate, School of Basic Medical Science, Guangzhou University of Chinese Medicine, Guangzhou 510006, Guangdong Province, China
  • About author:Tang Lulu, Master candidate, First Clinical Medical College, Guangzhou University of Chinese Medicine, Guangzhou 510405, Guangdong Province, China
  • Supported by:
    Scientific Research Project of Guangdong Provincial Bureau of Traditional Chinese Medicine, No. 20231128 (to LYT)

摘要:


文题释义:

生物信息学:主要研究基因组、转录组及蛋白质组等高通量生物学数据的分析、挖掘和解释,运用各种算法和工具对生物大数据进行处理和分析,以发现生物体内基因表达、蛋白质结构、代谢途径及信号转导等方面的规律。
铁死亡:是一种铁依赖性的非细胞凋亡形式的细胞死亡,由铁依赖性活性氧堆积和脂质过氧化引起。


背景:铁死亡介导的缺血再灌注损伤对压疮的发生发展起重要作用,可能存在压疮相关的铁死亡生物标志物,但其机制尚未阐明。

目的:通过生物信息学手段探讨压疮的分子机制,寻找压疮过程中铁死亡相关差异基因,为其临床治疗提供新的视角。
方法:使用GEO数据库和FerrDb数据库下载数据集并进行预处理。对单细胞转录组测序数据进行聚类和占比分析、代谢活性和拟时序分析、细胞通讯分析、铁死亡基因集细胞识别和富集分析,确定铁死亡差异基因,并通过动物实验进一步验证。将20只 SD 大鼠随机分为正常组和模型组,每组10只。正常组大鼠不进行任何处理,模型组大鼠采用缺血再灌注循环周期模式制备压疮大鼠模型,采用荧光定量 PCR和免疫印迹检测压疮大鼠创面组织内差异表达基因和蛋白的变化。

结果与结论:①单细胞转录组测序数据聚类划分为6种细胞类型,压疮组2型和3型角质形成细胞占比较高。②不同细胞亚群之间具有明显的代谢异质性和演变轨迹。③2型和3型角质形成细胞在细胞通讯中作用最强,2型角质形成细胞配体-受体强度最佳。④2型角质形成细胞铁死亡得分较高,有显著上调或下调的差异基因,并得到27个GO富集条目、20个KEGG 富集条目和24个铁死亡相关差异基因,以谷胱甘肽过氧化物酶4(glutathione peroxidase 4,GPX4)和长链酯酰辅酶A合成酶4(acyl-CoA synthetase long chain family member 4,ACSL4)为主。⑤动物实验验证了与正常组相比,模型组大鼠铁死亡抑制蛋白GPX4表达下调,铁死亡促进蛋白ACSL4表达上调。上述结果证实,压疮组织中存在铁死亡,GPX4和ACSL4为调控压疮组织中铁死亡的重要基因。

https://orcid.org/0000-0003-0214-1491(唐路路);https://orcid.org/0000-0002-6186-836X(赖英桃);
https://orcid.org/0000-0002-2998-2875(王力)

中国组织工程研究杂志出版内容重点:组织构建;骨细胞;软骨细胞;细胞培养;成纤维细胞;血管内皮细胞;骨质疏松;组织工程

关键词: 生物信息学, 单细胞转录组测序, 压疮, 缺血再灌注, 组织损伤, 慢性创面, 铁死亡, 氧化应激, GPX4, ACSL4

Abstract: BACKGROUND: Ferroptosis-mediated ischemia-reperfusion injury plays a crucial role in the occurrence and progression in pressure ulcers, and there may be pressure ulcer-associated ferroptosis biomarkers, but the mechanism has not been elucidated.
OBJECTIVE: To investigate the molecular mechanisms underlying pressure ulcers using bioinformatic analysis, with a focus on identifying differentially expressed genes associated with ferroptosis during the process of pressure ulcer formation, thereby providing novel insights into the clinical treatment of pressure ulcers.
METHODS: The single-cell transcriptome sequencing dataset and ferroptosis-related genes were obtained and preprocessed from the Gene Expression Omnibus (GEO) and FerrDb databases. We performed clustering and proportion analyses, metabolic activity and pseudotime analysis, cell communication analysis, ferroptosis gene set cell population identification, and enrichment analysis to determine differentially expressed genes related to ferroptosis. Animal experiments were then conducted for further validation, with 20 Sprague-Dawley rats randomly assigned into a control group and a model group (n=10 per group). The control group received no treatment, while the model group underwent a cycle of ischemia-reperfusion to establish pressure ulcer models. Changes in differentially expressed genes and proteins in the wound tissues of pressure ulcer rats were detected using fluorescent quantitative PCR and western blot, respectively.
RESULTS AND CONCLUSION: The single-cell transcriptome sequencing data were clustered into six cell types, with a higher proportion of type 2 and type 3 keratinocytes observed in the pressure ulcer group. There was evident metabolic heterogeneity and evolutionary trajectory among cell populations. Type 2 and type 3 keratinocytes exhibited stronger cell communication, while type 2 keratinocytes demonstrating optimal ligand-receptor interactions. Type 2 keratinocytes demonstrated higher scores for ferroptosis, accompanied by significant upregulation or downregulation of specific genes. A total of 27 Gene Ontology enrichments, 20 Kyoto Encyclopedia of Genes and Genomes enrichments, and 24 ferroptosis-related differentially expressed genes, including glutathione peroxidase 4 (GPX4) and acyl-CoA synthetase long chain family member 4 (ACSL4), were identified. Animal experiments further confirmed the downregulation of GPX4, the ferroptosis-inhibiting protein, and the upregulation of ACSL4, the ferroptosis-promoting protein, in the model group. Overall, these findings indicate the presence of ferroptosis in pressure ulcer tissue. GPX4 and ACSL4 are important genes regulating ferroptosis in pressure ulcer tissues.

Key words: bioinformatics, single-cell transcriptome sequencing, pressure ulcer, ischemia-reperfusion, tissue injury, chronic wound, ferroptosis, oxidative stress, GPX4, ACSL4

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