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生物信息学证实了潜在的枢纽基因的存在,这些基因可以激活自噬,从而参与股骨头坏死中的软骨退化。

Bioinformatics proved the existence of potential hub genes activating autophagy to participate in cartilage degeneration in osteonecrosis of the femoral head.

机构信息

Department of Orthopedics, The Second Affiliated Hospital of Xi' an Jiaotong University, Xi'an, 710004, China.

Department of Physiology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada.

出版信息

J Mol Histol. 2024 Aug;55(4):539-554. doi: 10.1007/s10735-024-10200-w. Epub 2024 May 17.


DOI:10.1007/s10735-024-10200-w
PMID:38758521
Abstract

The obvious degeneration of articular cartilage occurs in the late stage of osteonecrosis of the femoral head (ONFH), which aggravates the condition of ONFH. This study aimed to demonstrate aberrant activation of autophagy processes in ONFH chondrocytes through bioinformatics and to predict and identify relevant hub genes and pathways. Differentially expressed genes (DEGs) were identified using R software in the GSE74089 dataset from the GEO database. DEGs were crossed with the Human Autophagy Database (HADb) autophagy genes to screen out autophagy-related differential genes (AT-DEGs). GSEA, GSVA, GO, and KEGG pathway enrichment analyses of AT-DEGs were performed. The STRING database was used to analyze the protein-protein interaction (PPI) of the AT-DEGs network, and the MCODE and CytoHubba plugin in the Cytoscape software was used to analyze the key gene cluster module and screen the hub genes. The PPI network of hub genes was constructed using the GeneMANIA database, and functional enrichment and gene connectivity categories were analyzed. The expression levels of hub genes of related genes in the ONFH patients were verified in the dataset GSE123568, and the protein expression was verified by immunohistochemistry in tissues. The analysis of DEGs revealed abnormal autophagy in ONFH cartilage. AT-DEGs in ONFH have special enrichment in macroautophagy, autophagosome membrane, and phosphatidylinositol-3-phosphate binding. In the GSE123568 dataset, it was also found that ATG2B, ATG4B, and UVRAG were all significantly upregulated in ONFH patients. By immunohistochemistry, it was verified that ATG2B, ATG4B, and UVRAG were significantly overexpressed. These three genes regulate the occurrence and extension of autophagosomes through the PI3KC3C pathway. Finally, we determined that chondrocytes in ONFH undergo positive regulation of autophagy through the corresponding pathways involved in three genes: ATG2B, ATG4B, and UVRAG.

摘要

股骨头坏死(ONFH)晚期出现明显的关节软骨退变,加重了 ONFH 的病情。本研究旨在通过生物信息学方法证明 ONFH 软骨细胞中自噬过程的异常激活,并预测和鉴定相关的枢纽基因和途径。使用 R 软件在 GEO 数据库中的 GSE74089 数据集识别差异表达基因(DEGs)。将 DEGs 与人类自噬数据库(HADb)自噬基因交叉,筛选出自噬相关差异基因(AT-DEGs)。对 AT-DEGs 进行 GSEA、GSVA、GO 和 KEGG 通路富集分析。使用 STRING 数据库分析 AT-DEGs 网络的蛋白质-蛋白质相互作用(PPI),并使用 Cytoscape 软件中的 MCODE 和 CytoHubba 插件分析关键基因聚类模块并筛选枢纽基因。使用 GeneMANIA 数据库构建枢纽基因的 PPI 网络,并分析功能富集和基因连接类别。在数据集 GSE123568 中验证 ONFH 患者相关基因的枢纽基因表达水平,并通过免疫组织化学在组织中验证蛋白质表达。DEGs 的分析表明 ONFH 软骨中存在异常自噬。ONFH 中的 AT-DEGs 在巨自噬、自噬体膜和磷脂酰肌醇-3-磷酸结合中具有特殊的富集。在 GSE123568 数据集还发现,ATG2B、ATG4B 和 UVRAG 在 ONFH 患者中均显著上调。通过免疫组织化学验证了 ATG2B、ATG4B 和 UVRAG 的显著过表达。这三个基因通过 PI3KC3C 通路调节自噬体的发生和延伸。最后,我们确定通过涉及三个基因(ATG2B、ATG4B 和 UVRAG)的相应途径,ONFH 软骨细胞发生自噬的正调控。

相似文献

[1]
Bioinformatics proved the existence of potential hub genes activating autophagy to participate in cartilage degeneration in osteonecrosis of the femoral head.

J Mol Histol. 2024-8

[2]
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[3]
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[4]
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[5]
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[6]
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[7]
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[8]
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[10]
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本文引用的文献

[1]
UVRAG cooperates with cargo receptors to assemble the ER-phagy site.

EMBO J. 2023-12-1

[2]
Activation of the Nrf-2 pathway by pinocembrin safeguards vertebral endplate chondrocytes against apoptosis and degeneration caused by oxidative stress.

Life Sci. 2023-11-15

[3]
The role of autophagy in mitigating osteoarthritis progression via regulation of chondrocyte apoptosis: A review.

Joint Bone Spine. 2024-5

[4]
Targeting regulated chondrocyte death in osteoarthritis therapy.

Biochem Pharmacol. 2023-9

[5]
Identification and assessment of novel dynamic biomarkers for monitoring non-traumatic osteonecrosis of the femoral head staging.

Clin Transl Med. 2023-6

[6]
Subchondral Bone Plate Classification: A New and More Sensitive Approach for Predicting the Prognosis of Osteonecrosis of the Femoral Head.

Cartilage. 2023-9

[7]
Autophagy and autophagy-related pathways in cancer.

Nat Rev Mol Cell Biol. 2023-8

[8]
Ginsenoside Rg1 attenuates the NASH phenotype by regulating the miR-375-3p/ATG2B/PTEN-AKT axis to mediate autophagy and pyroptosis.

Lipids Health Dis. 2023-2-10

[9]
Involvement of acetylation of ATG4B in controlling autophagy induction.

Autophagy. 2023-3

[10]
Identification of potential autophagy-related genes in steroid-induced osteonecrosis of the femoral head via bioinformatics analysis and experimental verification.

J Orthop Surg Res. 2022-2-12

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