Competing endogenous RNA network analysis for screening inflammation‑related long non‑coding RNAs for acute ischemic stroke

Abstract

Long non‑coding RNAs (lncRNAs) represent potential biomarkers for the diagnosis and treatment of various diseases; however, the role of circulating acute ischemic stroke (AIS)‑related lncRNAs remains relatively unknown. The present study aimed to screen crucial lncRNAs for AIS based on the competing endogenous RNA (ceRNA) hypothesis. The expression profile datasets for one mRNA, accession no. GSE16561, and four microRNAs (miRNAs), accession nos. GSE95204, GSE86291, GSE55937 and GSE110993, were downloaded from the Gene Expression Omnibus database. Differentially expressed genes (DEGs), lncRNAs (DELs), and miRNAs (DEMs) were identified, and ClusterProfiler was used to interpret the function of the DEGs. Based on the protein‑protein interaction (PPI) network and module analyses, hub DEGs were identified. A ceRNA network was established based on miRNA‑mRNA or miRNA‑lncRNA interaction pairs. In total, 2,041 DEGs and 5 DELs were identified between the AIS and controls samples in GSE16561, and 10 DEMs between at least two of the four miRNA expression profiles. A PPI network was constructed with 1,235 DEGs, among which 20 genes were suggested to be hub genes. The hub genes paxillin (PXN), FYN‑proto‑oncogene, Src family tyrosine kinase (FYN), ras homolog family member A (RHOA), STAT1, and growth factor receptor‑bound protein 2 (GRB2), were amongst the most significantly enriched modules extracted from the PPI network. Functional analysis revealed that these hub genes were associated with inflammation‑related signaling pathways. An AIS‑related ceRNA network was constructed, in which 4 DELs were predicted to function as ceRNAs for 9 DEMs, to regulate the five identified hub genes; that is, minichromosome maintenance complex component 3 associated protein‑antisense RNA 1 (MCM3AP‑AS1)/long intergenic non‑protein coding RNA 1089 (LINC01089)/hsa‑miRNA (miR)‑125a/FYN, inositol‑tetrakisphosphate 1‑kinase‑antisense RNA 1 (ITPK1‑AS1)/hsa‑let‑7i/RHOA/GRB2/STAT1, and human leukocyte antigen complex group 27 (HCG27)/hsa‑-miR‑19a/PXN interaction axes. In conclusion, MCM3AP‑AS1, LINC01089, ITPK1‑AS1, and HCG27 may represent new biomarkers and underlying targets for the treatment of AIS.

Figure 1.

Hierarchical clustering heat map for the differentially expressed mRNAs in acute ischemic stroke. Data were obtained from datasets in the Gene Expression Omnibus database. On the horizontal axis, the white box indicates the control samples, and the black box represents the acute ischemic stroke samples. The vertical axis indicates the gene expression level. Red, high expression; blue, low expression.

Figure 2.

Venn diagram of the common DEMs. DEMs were identified in at least two expression profile datasets out of four for miRNAs in acute ischemic stroke (accession nos. GSE95204, GSE86291, GSE55937, and GSE110993), and were either (A) downregulated or (B) upregulated. DEM, differentially expressed microRNA.

Figure 3.

Functional enrichment analysis for the differentially expressed genes. (A) Top 30 significant GO terms. (B) Top 10 significant KEGG pathways. KEGG, Kyoto Encyclopedia of Genes and Genomes; GO, gene ontology.

Figure 4.

A significant module that includes hub genes identified in the protein and protein interaction network for the differentially expressed genes in acute ischemic stroke. Blue, downregulated; red, upregulated. PXN, paxillin; RAF1, Raf-1 proto-oncogene serine/threonine kinase; TLR2, toll-like receptor 2; RPS6KA5, ribosomal protein S6 kinase A5; ITGA2B, integrin subunit α 2b; PRKCQ, protein kinase C θ; IL-1B, interleukin 1β; CBL, Cbl proto-oncogene; ZAP70, ζ chain of T cell receptor-associated protein kinase 70; TPM1, tropomyosin 1; PAK1, p21 (RAC1) activated kinase 1; RHOC, ras homolog family member C; ITGB5, integrin subunit β5; PAK2, p21 (RAC1) activated kinase 2; GRB2, growth factor receptor bound protein 2; PIK3AP1, phosphoinositide-3-kinase adaptor protein 1; FYN, FYN Proto-oncogene tyrosine-protein kinase; TPM2, tropomyosin 2; STAT1, signal transducer and activator of transcription 1; PTGS2, prostaglandin-endoperoxide synthase 2; FGR, FGR proto-oncogene Src family tyrosine kinase; ITPR3, inositol 1,4,5-trisphosphate receptor type 3; SYK, spleen-associated tyrosine kinase; HCK, HCK proto-oncogene Src family tyrosine kinase; RPS6KA3, ribosomal protein S6 kinase A3; CD79B, CD79b molecule; MAP4K1, mitogen-activated protein kinase kinase kinase kinase 1; CREB1, cAMP responsive element binding protein 1; SLA, Src-like adaptor; ITK, IL2 inducible T cell kinase; RHOA, Ras homolog family member A.

Figure 5.

Competing endogenous RNAs interaction network of all potential acute ischemic stroke-related long noncoding RNA/miRNA/mRNA axes. Blue, long noncoding RNAs; green, mRNA; red, microRNA. Hub genes are presented in red boxes. miR/miRNA, microRNA; PXN, paxillin; GRB2, growth factor receptor bound protein 2; FYN, FYN Proto-oncogene tyrosine-protein kinase; STAT1, signal transducer and activator of transcription 1; RHOA, Ras homolog family member A.

Figure 6.

Competing endogenous RNA interaction network between five inflammatory differentially expressed hub genes, and their related long noncoding RNA/miRNA axes in AIS. Purple, hub genes; red, microRNAs; green, long non-coding RNAs. miR/miRNA, microRNA; PXN, paxillin; GRB2, growth factor receptor bound protein 2; FYN, FYN Proto-oncogene tyrosine-protein kinase; STAT1, signal transducer and activator of transcription 1; RHOA, Ras homolog family member A.