Identification Of Ischemic Stroke Long Non-coding RNA And MRNA Expression Profile Based On Microarray

Objective: This study aims to identify the long non-coding RNA(lncRNA)and mRNA expression profile of ischemic stroke(IS)through the high throughput microarray chip,to enrich the lncRNA and mRNA expression profile dada of IS,to provide basis of functional mechanism of IS-related lncRNAs,which may promote early diagnosis,prevention and control of IS.Methods: A case-control study(10 IS cases and 10 healthy controls)was conducted for the detection of lncRNA and mRNA expression profile microarray chip.The microarray chip belongs to Human LncRNA Expression Microarray V4.0(8 * 60 k),which can simultaneously detect lncRNA and mRNA expression profile.GeneSpring GX v12.1 software was used to analyze microarray data.KEGG Pathway enrichment analysis and Gene ontology(GO)analysis were performed to analyze the IS-related signaling pathways and the biological processes,cellular components and molecular functions which may be involved in IS.In addition,qRT-PCR was for determining the relative expression oflncRNA SERPINB9P1 between 78 IS patients and 80 healthy controls.Statistical analysis was conducted by SPSS 18.0 software.Besides,GraphPad Prism 5 software was used to draw the plotting of relative expression of lncRNA.Results:1.A total of 5067 differentially expressed lncRNAs were screened out in the microarray chip between IS cases and controls(P-value<0.05,False Discovery Rate(FDR)< 0.05),including 2497 upregulated and2570 downregulated.Among them,3610 lncRNAs showed the Fold Change(FC)?1.5,including 1788 upregulated and 1822 downregulated;1403 lncRNAs showed the FC?2,including 630 upregulated and 773 downregulated.2.A total of 3302 differentially expressed mRNAs were screened out in the microarray chip between IS cases and controls(P-value < 0.05,FDR < 0.05),including 1568 upregulated and 1734 downregulated.Among them,2331 mRNAs showed the FC ? 1.5,including 1119 upregulated and 1212 downregulated;733 mRNAs showed the FC?2,including 249 upregulated and 484 downregulated.3.KEGG Pathway enrichment analysis indicated that 4 related signaling pathways were obtained from the enrichment of the 1568 upregulated mRNAs while 34 related signaling pathways were obtained from the 1734 downregulated mRNAs.4.GO analysis showed the highest enrichment score of the 1568 upregulated mRNAs in biological process,cellular component and molecular function was protein modification by small protein conjugation,membrane-bounded organelle and RNA binding.While the highest enrichment score among the 1734 downregulated mRNAs in biological process,cellular component and molecular function was multicellular organism development,nuclear lumen and tubulin binding.5.92 differentially expressed antisense lncRNAs and their corresponding mRNAs(P<0.05,FDR<0.05)were identified in the present study.The top 10(with the greatest FC)antisense lncRNAs(their corresponding mRNAs)were RP11-445F12.2(LHX1),HHIP-AS1(HHIP),JMJD1C-AS1(JMJD1C),ERICH6-AS1(FAM194A),LOC101928069(PELI3),CTB-187M2.2(RNF112),RP5-955M13.4(KCNG1),HOXB-AS3(HOXB5),SH3BP5-AS1(SH3BP5),G001868(MFSD2A),respectively.6.The validation result of qRT-PCR indicated that lncRNA SERPINB9P1 showed significant difference between 78 IS patients and80 healthy controls(Z=-5.410,P=6.31 × 10-8).Besides,the relative expression of SERPINB9P1 in IS patients was lower than that in controls.Conclusions:1.This study identified the lncRNA and mRNA expression profile of IS.2.the upregulated signaling pathways(Protein processing in endoplasmic reticulum pathway and Ubiquitin mediated proteolysis pathway)and the downregulated signaling pathways(PI3K-Akt signaling pathway,HIF-1 signaling pathway,TNF signaling pathway,ErbB signaling pathway,Neurotrophin pathway,Focal adhesion pathway,and Estrogen signaling pathway)may be related with IS development through pathway enrichment analysis.On the other hand,the result of Go analysis indicated that the protein modification may play a key role in the process of IS.3.The top 10(with the greatest FC)pairs of antisense lncRNAs and their corresponding mRNAs were identified in this study.Among them,LHX1,HHIP,PELI3,HOXB5,RNF112,MFSD2 A,SH3BP5 and KCNG1 may be involved in the pathophysiological processes of IS or other related diseases in central nervous system.4.LncRNA SERPINB9P1 may act as a novel biomarker of IS.