Bioinformatics analysis of gene expression profiling for identification of potential key genes among ischemic stroke

Zhai, Kaihua; Kong, Xiangli; Liu, Boyu; Lou, Jian-Shu

doi:10.1097/md.0000000000007564

Cited by 12 publications

(12 citation statements)

References 48 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Tian et al [12] first examined the effects of sex on RNA expression using whole-genome microarrays by the comparison of human blood from IS cases with healthy controls. Recently, several studies identified key genes between IS cases and controls in human blood [7, 13–15]. However, the exact mechanism underlying sex differences in IS remains poorly understood.…”

Section: Discussionmentioning

confidence: 99%

Bioinformatics Analysis of Gene Expression Profiles of Sex Differences in Ischemic Stroke

Zhu

Nan

Wang

et al. 2019

BioMed Research International

View full text Add to dashboard Cite

Ischemic stroke (IS) is a complex disease with sex differences in epidemiology, presentations, and outcomes. However, the sex-specific mechanism underlying IS remains unclear. The purpose of this study was to identify key genes contributing to biological differences between sexes. First, we downloaded the gene expression data of GSE22255 from Gene Expression Omnibus (GEO). Differentially expressed genes (DEGs) were identified using R software and related packages. Second, DEGs were separately analyzed by Gene Ontology enrichment and pathways analyses. Third, protein-protein interaction (PPI) network was constructed to further investigate the interactions of DEGs. A total of 123 DEGs were identified between sexes, including 8 upregulated and 115 downregulated genes. In the PPI network, ten key genes were identified, including IL1α, IL1β, IL6, IL8, CXCL1, CXCL2, CXCL20, CCL4, ICAM1, and PTGS2. Functional enrichment analysis revealed that these genes were mainly enriched in biological processes of immune response and apoptotic process, also in pathways of TNF and NOD-like receptor signaling. In conclusion, the above ten genes may have a protective effect on IS females through their direct or indirect involvement in biological processes of immune response and apoptotic process, as well as in TNF and NOD-like receptor signaling pathways. The results of this study may help to gain new insights into the sex-specific mechanisms underlying IS females and may suggest potential therapeutic targets for disease treatment.

show abstract

Section: Discussionmentioning

confidence: 99%

Bioinformatics Analysis of Gene Expression Profiles of Sex Differences in Ischemic Stroke

Zhu

Nan

Wang

et al. 2019

BioMed Research International

View full text Add to dashboard Cite

show abstract

“…Based on sequencing profiles, bioinformatics analysis has been widely applied to screen potential molecular targets for IS ( Zhai et al, 2017 ; Zhou et al, 2019 ; Xie et al, 2020 ; Chen et al, 2021 ; Liu C. et al, 2022 ). Chen et al (2021) have determined that MAP1LC3B, PTGS2, and TLR4 are ferroptosis-related biomarkers for IS.…”

Section: Introductionmentioning

confidence: 99%

Knockdown of ATF3 suppresses the progression of ischemic stroke through inhibiting ferroptosis

Zhang

et al. 2023

Front. Mol. Neurosci.

View full text Add to dashboard Cite

ObjectiveCurrent therapies towards ischemic stroke (IS) are still not satisfied, and alternative strategies targeting ferroptosis may be another choice. The purpose of this study is to screen potential ferroptosis-related genes involving in IS.MethodsA rat model of IS was established via middle cerebral artery occlusion. Differentially expressed genes (DEGs) were screened from the model rats through transcriptional sequencing. Among the isolated DEGs, the expression of several attractive DEGs relating with ischemic injury was confirmed by qRT-PCR. Then, ATF3 relating with both IS and ferroptosis was selected a candidate gene for functional assays. After knockdown of ATF3 in the model rats, the infarction, histopathology, apoptosis, and ferroptosis in brain tissues were evaluated.ResultsIS model was successfully established in rats, exhibiting the emergence of infarction area, histopathological injury, and enhanced cell apoptosis. Total 699 up-regulated DEGs and 461 down-regulated DEGs were screened from the model rats. qRT-PCR verified the up-regulation of Hspa1b, Tfpi2, Ptx3, and Atf3, and the down-regulation of Smyd1 and Tacr2 in the Model group compared with those in the Sham group. It is noteworthy that knockdown of ATF3 decreased the infarction area, relieved histopathological injury, weakened apoptosis, and inhibited ferroptosis in the model rats.ConclusionSeveral candidate genes in relation with IS were revealed. More importantly, knockdown of ATF3 may relieve IS through inhibiting ferroptosis.

show abstract

“…Compared to prior studies [ 46 ], a merge of datasets and integration scheme were two dominant advantages in this study. On the one hand, merging datasets allowed for a larger sample size to incorporate more DEFRGs, which was conducive to subsequent machine learning analysis.…”

Section: Discussionmentioning

confidence: 99%

Identification of a ferroptosis-related gene pair biomarker with immune infiltration landscapes in ischemic stroke: a bioinformatics-based comprehensive study

et al. 2022

View full text Add to dashboard Cite

Background Ischemic stroke (IS) is a principal contributor to long-term disability in adults. A new cell death mediated by iron is ferroptosis, characterized by lethal aggregation of lipid peroxidation. However, a paucity of ferroptosis-related biomarkers early identify IS until now. This study investigated potential ferroptosis-related gene pair biomarkers in IS and explored their roles in immune infiltration. Results In total, we identified 6 differentially expressed ferroptosis-related genes (DEFRGs) in the metadata cohort. Of these genes, 4 DEFRGs were incorporated into the competitive endogenous RNA (ceRNA) network, including 78 lncRNA-miRNA and 16 miRNA-mRNA interactions. Based on relative expression values of DEFRGs, we constructed gene pairs. An integrated scheme consisting of machine learning algorithms, ceRNA network, and gene pair was proposed to screen the key DEFRG biomarkers. The receiver operating characteristic (ROC) curve witnessed that the diagnostic performance of DEFRG pair CDKN1A/JUN was superior to that of single gene. Moreover, the CIBERSORT algorithm exhibited immune infiltration landscapes: plasma cells, resting NK cells, and resting mast cells infiltrated less in IS samples than controls. Spearman correlation analysis confirmed a significant correlation between plasma cells and CDKN1A/JUN (CDKN1A: r = − 0.503, P < 0.001, JUN: r = − 0.330, P = 0.025). Conclusions Our findings suggested that CDKN1A/JUN could be a robust and promising gene-pair diagnostic biomarker for IS, regulating ferroptosis during IS progression via C9orf106/C9orf139-miR-22-3p-CDKN1A and GAS5-miR-139-5p/miR-429-JUN axes. Meanwhile, plasma cells might exert a vital interplay in IS immune microenvironment, providing an innovative insight for IS therapeutic target.

show abstract

Bioinformatics analysis of gene expression profiling for identification of potential key genes among ischemic stroke

Cited by 12 publications

References 48 publications

Bioinformatics Analysis of Gene Expression Profiles of Sex Differences in Ischemic Stroke

Bioinformatics Analysis of Gene Expression Profiles of Sex Differences in Ischemic Stroke

Knockdown of ATF3 suppresses the progression of ischemic stroke through inhibiting ferroptosis

Identification of a ferroptosis-related gene pair biomarker with immune infiltration landscapes in ischemic stroke: a bioinformatics-based comprehensive study

Contact Info

Product

Resources

About