Bioinformatics-based Analysis to Screen Key Genes for Ischemia and Hypoxia after Spinal Cord Injury and Analysis of Immune Infiltration Patterns
10.3969/j.issn.1671-7414.2024.05.022
- VernacularTitle:基于生物信息学分析筛选脊髓损伤后缺血缺氧关键基因和免疫浸润模式分析
- Author:
Lijuan ZHU
1
;
Xin LI
;
Yuezhang MA
;
Jing ZHU
;
Zhibo ZHU
;
Rui ZHAO
Author Information
1. 陕西省人民医院麻醉科,西安 710068
- Keywords:
spinal cord injury;
key gene for ischemia and hypoxia;
immune infiltration;
comprehensive bioinformatics
- From:
Journal of Modern Laboratory Medicine
2024;39(5):120-124,151
- CountryChina
- Language:Chinese
-
Abstract:
Objective To screen ischemia and hypoxiarelated genes(IAHRGs)after spinal cord injury(SCI)and analyze their immune infiltration patterns by bioinformatics methods.Methods The expression profiles of SCI-related GSE5296,GSE47681 and GSE217797 were downloaded from the Gene Expression Omnibus(GEO)database,where GSE5296,GSE47681 samples were used as the test set and GSE217797 samples as the validation set,and the differentially expressed genes(DEGs)between SCI and healthy samples were obtained.IAHRGs were screened in GeneCards and MSigDB databases.The intersection of DEGs and IAHRGs yielded ischemic and hypoxia related differentially expressed genes(IAHRDEGs).Based on the IAHRDEGs,the key genes were jointly screened by LASSO model and SVM analysis.The key genes were subjected to logistic regression analysis and a diagnostic model was constructed.The diagnostic ability of the diagnostic model was analyzed by Nomogram and the column line graph of Logistic predictive values was plotted.The diagnostic value of the diagnostic model and key genes for SCI was evaluated using the receiver operating characteristics(ROC).Immune cell infiltration patterns of the disease were analyzed using the CIBERSORT tool.Results A total of 388 IAHRGs were screened,313 differentially expressed genes were detected between SCI and healthy samples,among which 312 were up-regulated and 1 was down-regulated.A sum of 27 up-regulated IAHRDEGs genes were obtained.Five key genes related to ischemia and hypoxia after SCI(Abca1,Caspl,Lpl,Procr,Tnfrsf1a)were screened by LASSO model and SVM analysis based on IAHRDEGs.Nomogram analysis confirms the effect of logistics diagnosis model.ROC curve analysis showed that Casp1,Lpl and Tnfrsf1a had higher diagnostic efficacy(AUC＞0.9),followed by Abca1 and Procr(AUC:0.7～0.9),and the logistics linear predictors had the best diagnostic effect(AUC=0.964).CIBERSORT analysis showed that five key genes were associated with the infiltration of eight types of immune cells(neutrophil cells,B cells naive,plasma cells,M0 macrophage,T cells CD4 naive,T cells CD4 follicular,Th17 cells,and NK resting).Conclusion The five key genes of Abcal,Caspl,Lpl,Procr,and Tnfrsfla,may be closely related to ischemic-hypoxic pathogenesis after SCI,and can be used as candidate molecular markers for the diagnosis and treatment after SCI.
