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 IL1
Worldwide, stroke is ranked as the second most common cause of death behind ischemic heart disease, with about 17 million new cases and 6 million deaths each year [
Recently, accumulating evidences highlight sex differences in the IS incidence. The incidence of IS is higher among men than among women in most age groups. The prognosis of IS has also been reported differed between sexes. For instance, Rutten-Jacobs et al. [
Microarrays based on high-throughput platforms for the profiling of genome-wide expression emerge as a promising and efficient tool to identify genomic variants that modulate the risk to develop IS. To identify key genes contributing to biological differences between sexes, we conducted a comprehensive bioinformatics analysis based on gene expression microarray dataset. This study may provide new insights into the sex-specific mechanism underlying IS and may suggest potential therapeutic targets for disease treatment.
The gene expression data for the present study was obtained from Gene Expression Omnibus (GEO) database (
R software and related R packages were used to normalize and analyze differentially expressed genes (DEGs). Firstly, the dataset was normalized by log2 transformation in R software. Then, DEGs between IS females and males were screened by Linear Models for Microarray Data (limma) package in R. Significant genes were selected with thresholds of
To further analyze biological processes of DEGs in IS females compared with IS males, functional enrichment analysis for DEGs was carried out through the Database for Annotation, Visualization and Integrated Discovery (DAVID version 6.8, https://david.ncifcrf.gov/) [
The Search Tool for the Retrieval of Interacting Genes (STRING, version 10.5, https://www.string-db.org/) [
According to the cut-off criteria
Top 8 up- and 10 downregulated differentially expressed genes of ischemic stroke in women versus men.
Gene ID | Gene symbol | Adj. | logFC | Up- or downregulation |
---|---|---|---|---|
224588_at | XIST | 9.54E-23 | 8.47 | Up |
206207_at | CLC | 2.54E-17 | 5.09 | Up |
231592_at | TSIX | 7.49E-06 | 2.18 | Up |
204069_at | MEIS1 | 2.26 E-03 | 1.77 | Up |
228195_at | C2orf88 | 6.96 E-03 | 1.68 | Up |
209930_s_at | NFE2 | 7.56 E-03 | 1.62 | Up |
1559477_s_at | MEIS1 | 1.40 E-03 | 1.60 | Up |
223377_x_at | CISH | 2.21 E-03 | 1.59 | Up |
201909_at | RPS4Y1 | 2.76E-23 | -7.46 | Down |
205000_at | DDX3Y | 1.45E-19 | -7.24 | Down |
204470_at | CXCL1 | 4.96E-21 | -5.84 | Down |
207850_at | CXCL4 | 8.97 E-03 | -5.15 | Down |
39402_at | IL1 | 7.11E-14 | -5.01 | Down |
210118_s_at | IL1 | 8.14 E-04 | -4.75 | Down |
205476_at | CCL20 | 1.536 E-03 | -4.64 | Down |
1569203_at | CXCL2 | 6.72E-13 | -4.53 | Down |
205207_at | IL6 | 3.60 E-03 | -4.26 | Down |
228492_at | USP9Y | 4.22E-21 | -4.08 | Down |
Gene expression value of ischemic stroke (IS) women and men.
GO enrichment analysis was performed to gain a further insight into the biological processes of the selected DEGs related to IS females. As shown in Figure
Gene Ontology (GO) enrichment analysis of differentially expressed genes (DEGs) of ischemic stroke (IS) women and men.
KEGG pathways analysis was used to gain a deeper insight into pathways of the screened DEGs in our study. As shown in Figure
Enriched pathways of differentially expressed genes (DEGs) in ischemic stroke (IS) women and men analyzed by the Kyoto Encyclopedia of Genes and Genomes (KEGG).
In order to better understand the interactions of DEGs, PPI network construction was conducted using the STRING database. As shown in Figure
Protein-protein interaction (PPI) network associated with sex differences in ischemic stroke (IS). The red ones represent hub genes with node degree greater than or equal to 10.
IS is a complex neurological disorder with substantial morbidity and mortality. It is characterized with sex differences in terms of etiology, risk factors, and outcomes. Sex hormones (oestrogen and androgen), sex chromosomes (XX compared with XY), and social and environmental factors all help explaining these sex differences, albeit partly. The past decade witnessed substantial breakthroughs in the genetics of many types of diseases, including IS. A large number of genetic analyses of IS between sexes has been performed in animal models. Unfortunately, few microarray analyses have been attempted in sex differences of human IS. Tian et al. [
In our study, we aimed to determine sex differences of gene expression in the human serums of IS females compared with IS males using whole-genome microarrays. 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 IL1
Altered gene expression affects proteins and pathways in numerous biological functions in IS. We found that these genes were mainly enriched in biological processes of immune response and apoptotic process, as well as in pathways of TNF and NOD-like receptor signaling. An increasing number of studies demonstrated that immune response was implicated in both the manifestation and evolution of brain ischemia [
In conclusion, the ten above genes we have identified 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 and may suggest potential therapeutic targets for disease treatment.
The data used to support the findings of this study are available from the corresponding author upon request.
The authors declare that they have no conflicts of interest.
The present study was supported by the National Natural Science Foundation of China (grant No. 81273701), TCM Science and Technology Development Project of Shandong Province (grant No. 2015-391), and Science and Technology Development Project of Zibo City (grant No. 2015kj010136; 2017kj010074).