中国组织工程研究2024，Vol.28Issue(27)：4293-4299,7.DOI:10.12307/2024.520
CA9作为激素性股骨头坏死中软骨铁死亡特征基因的生物信息学鉴定
Bioinformatics identification of CA9 as a signature gene for cartilage-associated ferroptosis in steroid-induced osteonecrosis of the femoral head
摘要
Abstract
BACKGROUND:Disturbances in bone metabolism have a significant association with ferroptosis in steroid-induced osteonecrosis of the femoral head(SONFH).Furthermore,the pathologic process of SONFH is characterized by the presence of cartilage damage and degeneration.However,the specific regulatory targets and the relationship between ferroptosis and cartilage concerning SONFH remain unclear. OBJECTIVE:To employ bioinformatics and machine learning techniques to identify specific genes associated with ferroptosis that target cartilage and to investigate the correlation between ferroptosis and cartilage,thereby providing novel ideas and methodologies for the study and treatment of SONFH. METHODS:Disease datasets pertinent to the study and ferroptosis-related genes were retrieved from the GEO and FerrDb databases.Subsequently,the disease datasets were normalized and differential analysis using the R language to identify ferroptosis-related differential genes(Fe-DEGs).We conducted Gene Ontology(GO)functional enrichment analysis and Kyoto Encyclopedia of Genes and Genomes(KEGG)signaling pathway enrichment analysis of Fe-DEGs.Furthermore,ferroptosis-related signature genes were filtered based on the protein-protein interaction network of Fe-DEGs and machine learning methods.Finally,the rabbits were divided into normal and model groups.The normal group was given the same dose of saline to simulate the modeling drug,and the animal model of SONFH in rabbits was constructed by injection of modified horse serum combined with methylprednisolone.After successful modeling,the expression of signature gene was verified between different groups,and the phenotype of ferroptosis in cartilage was analyzed. RESULTS AND CONCLUSION:Through the normalization and differential analysis of the dataset,a total of 1 315 differentially expressed genes were identified.Additionally,379 ferroptosis-related genes were obtained from the FerrDb database.After intersecting both gene sets,19 Fe-DEGs were obtained.The GO analysis revealed that Fe-DEGs were mainly involved in biological processes such as cell migration and cellular response to oxidative stress,cellular components such as kinase complexes,amino acid complexes,and cytoplasmic membranes,as well as molecular functions such as kinase activity,receptor activity,and protein binding.The KEGG analysis revealed that Fe-DEGs were mainly enriched in the FoxO signaling pathway,vascular endothelial growth factor signaling pathway,and FcγR-mediated phagocytosis.Constructing a protein-protein interaction network and using machine learning,we identified the ferroptosis-related signature gene,CA9.The gene set enrichment analysis of the signature gene CA9 revealed an upregulated expression in biological processes such as fatty acid metabolism and O-GlcNAc glycosylation modification,while being inhibited in terms of neural activity and ligand-receptor interactions.RT-PCR and western blot results showed that compared with the normal group,the expressions of ACSL4 and CA9 at mRNA and protein levels were significantly higher in the model group(P<0.05),while the expressions of SLC7A11 and GPX4 at mRNA and protein levels were significantly lower in the model group(P<0.05),coinciding with the expression levels of the signature genes in the dataset.These findings indicate that the cartilage of SONFH is closely related to ferroptosis,and targeting the signature gene may provide certain ideas and directions for the study and treatment of SONFH.关键词
激素性股骨头坏死/软骨/铁死亡/生物信息学/特征基因/生物标志物/CA9/ACSL4/SLC7A11/GPX4Key words
steroid-induced osteonecrosis of the femoral head/cartilage/ferroptosis/bioinformatics/signature gene/biomarker/CA9/ACSL4/SLC7A11/GPX4分类
医药卫生引用本文复制引用
余鹏,孟东方,李慧英,张向北..CA9作为激素性股骨头坏死中软骨铁死亡特征基因的生物信息学鉴定[J].中国组织工程研究,2024,28(27):4293-4299,7.基金项目
河南省中医药科学研究专项(2021JDZY009,2023ZY2029),项目负责人:李慧英 （2021JDZY009,2023ZY2029）
河南省中医药科学研究专项(2022JDZX123),项目负责人:孟东方 （2022JDZX123）
河南中医药大学2022年度研究生科研创新类项目(2022KYCX084),项目负责人:余鹏 Henan Province Chinese Medicine Scientific Research Special Projects,Nos.2021JDZY009(to LHY),2023ZY2029(to LHY),and 2022JDZX123(to MDF) （2022KYCX084）
2022 Graduate Student Scientific Research and Innovation Program of Henan University of Chinese Medicine,No.2022KYCX084(to YP) （to YP）
