Screening of differentially expressed genes related to ischemic stroke and functional analysis with DNA microarray

Abstract

Background: Prognostic blood biomarkers in the setting of acute ischemic stroke have become increasingly relevant for risk stratification, monitoring disease and response to therapies, developing targets for neuroprotective treatment and as surrogate end points for treatment trials.

Aim: We aim to find the feature genes which can accurately detect acute ischemic stroke and perform function analysis of these crucial genes in peripheral blood mononuclear cells.

Materials and methods: The gene expression profile GSE22255 was downloaded from Gene Expression Omnibus (GEO) database which includes 20 ischemic stroke patients and 20 controls. The differentially expressed genes between patients and controls samples were identified with packages in R language. The selected differentially expressed genes were further analyzed using bioinformatics methods. Software STRING (Search Tool for the Retrieval of Interacting Genes) was used to establish co-expression network. GOTM (General Ocean Turbulence Model) software was used to obtain differentially expressed gene enriched modules. The functions of genes in modules were analyzed by using software GeneCodis.

Results: A total of 37 genes were identified as differentially expressed genes by comparing peripheral blood mononuclear cells gene expression of ischemic stroke patients and 20 controls. A co-expression network was constructed within 30 differentially expressed genes, among which gene interleukin-8 (IL-8) and tumor necrosis factor (TNF) showed the highest node degree. Genes in the module containing IL-8 and TNF were significantly enriched in 6 biological functions, and the most significant function was respond to stimulation.

Conclusions: Our results highlight that genes IL-8 and TNF have close relationship with acute ischemic stroke, and the expression patterns of these genes may be valid targets for new medications able to modify the ischemic stroke process.