The Study Of The LncRNA/mRNA Expression Profile And Bio-informatics Analysis Of Dilated Cardiomyopathy

ObjectiveThis study aimed to identify aberrantly expressed long noncoding RNA(lncRNA)and messenger RNA(mRNA)expression profiles of dilated cardiomyopathy(DCM)by RNA-seq technique.We intended to detect the molecular mechanism of DCM by using the bioinformatics methods.RT-PCR verification for the differential expressed lncRNAs to test the RNA-seq detection results.MethodThe samples of peripheral blood mononuclear cells used in this study were acquired from 8 patients and paired healthy control.All of the 8 patients were diagnosed with DCM and underwent internal medical treatment at Liaocheng Hospital between July 2015 and May 2016.Blood specimens were collected from each study subject into sterile EDTA tubes.RNA libraries were constructed by TruSeq Stranded Total RNA Library Prep Kit according to the manufacturer's instructions.Paired-end reads were harvested from Illumina HiSeq 4000 sequencer.Cuffdiff software was used to get the gene level FPKM as the expression profiles of lncRNA and mRNA,differentially expressed lncRNA and mRNA were identi-fied by calculating the fold change and p-value based on FPKM.GO and KEGG analysis were used to explore the potential function of the differentially expressed genes.Then we build the lncRNA-mRNA co-expression network based on the Pearson's correlation co-efficient.5 differentially expressed lncRNAs were randomly selected and RT-PCR was test-ed in the expanded sample.Result8 pairs of samples were detected by NanoDrop ND-2000 instrument and denatured agarose gel electrophoresis.RNA-seq technology was applied to obtain the original data.After quality control,low expression removed and standardized treatment,the lncRNA/ mRNA expression profiles of DCM group and normal control group were obtained.In total,88768 lncRNAs and 20315 mRNAs were detected,of which 988 lncRNAs(661 upregulated;327 down-regulated)and 1418 mRNAs(800 up-regulated;618 down-regulated)showed significantly different expression between the two groups.Hierarchical Clustering revealed systematic variations between the two groups.The aberrantly expressed mRNAs were mainly enriched for GO terms related to positive regulation of muscle tissue development,positive regulation of striated muscle tissue development,positive regulation of muscle organ development involved in biological process.The aberrantly expressed mRNAs were mainly enriched for GO terms related to proton-transporting V-type ATPase,V0 domain,proton-transporting two-sector ATPase complex,proton-transporting domain,proton-transporting ATP synthase complex,coupling factor F(o)in cell component.The aberrantly expressed mRNAs were mainly enriched for GO terms related to MHC protein complex binding,MHC class II protein complex binding in molecular function.KEGG pathway enrichment analysis show that the differentially expressed mRNAs mainly enriched in 17 biological pathways.Wnt signaling pathway may relate to the pathogenesis of DCM by involved in cardiac ventricular remodeling,cardiac hypertrophy and heart failure process.The lncRNA-mRNA co-expression network was constructed by calculating the correlation coefficient.The results of PCR are basically consistent with RNA-seq in the expanded sample.ConclusionThe results of RNA-seq suggest that the expression of lncRNAs and mRNAs were significantly different from the two groups.GO analysis showed that biological functions were difference in the two groups by up-regulated or down-regulated gene expression.KEGG pathway analysis showed that the differentially expressed mRNAs were significantly enriched in 17 biological pathways,and the Wnt signaling pathway may relate to dilated cardiomyopathy.The lncRNA-mRNA co-expression network was constructed preliminary,and the high degree lncRNA nodes may be the potential target for gene therapy.RNA-seq technology is a high-throughput detection method with high accuracy,high repeatability,wide detection range and reliable analysis.