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Altered Long Non-Coding RNA Transcriptomic Profiles in Ischemic Stroke.
Hum Gene Ther. 2018 06; 29(6):719-732.HG

Abstract

A previous study described the important regulatory roles of microRNAs (miRNAs) in ischemic stroke. However, the functional significance of long non-coding RNA (lncRNAs) in ischemic stroke was largely unknown. This study aimed to identify lncRNA profiling and elucidate the regulatory mechanisms in the pathophysiology of stroke. RNA sequencing was performed on the blood of three ischemic stroke patients and three normal controls. Differential expression analysis was used to identify differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs). After further correlation and co-expression analysis, the corresponding co-expression networks and miRN-lncRNA-mRNA interaction network were then constructed. The expression of DElncRNAs and DEmRNAs was verified in Gene Expression Omnibus. RNA sequencing and subsequent bioinformatics analysis produced a total of 61 DElncRNAs (14 upregulated and 47 downregulated) and 673 DEmRNAs (432 upregulated and 241 downregulated). LOC105372881 and LOC101929707 were the most highly increased and decreased lncRNAs in ischemic stroke. LncRNA-mRNA co-expression networks were constructed according to 3,008 positively co-expressed and 607 negatively co-expressed lncRNA-mRNA pairs. The DElncRNAs may play roles in the pathways of glycolysis/gluconeogenesis, arrhythmogenic right ventricular cardiomyopathy, adherens junction, lysosome, and hematopoietic cell lineage by regulating their co-expressed mRNAs. Combined with previous data, a miRNA-lncRNA-mRNA interaction network for ischemic stroke was constructed. Based on GSE22255, the expression of six DElncRNAs (CEBPA-AS1, LINC00884, HCG27, MATN1-AS1, HCG26, and LINC01184) and 11 DEmRNAs (TREML4, AHSP, PI3, TESC, ANXA3, OAS1, OAS2, IFI6, ISG15, IFI44L, and LY6E) was similar to the current sequencing data. This study is the first to identify blood lncRNAs in human ischemic stroke using RNA sequencing. The findings may be the foundation for understanding the potential role of lncRNAs in ischemic stroke.

Authors+Show Affiliations

1 Department of Neurology, First Affiliated Hospital of Shantou University Medical College , Shantou, China .2 Department of Pharmacy, First Affiliated Hospital of Shantou University Medical College , Shantou, China .2 Department of Pharmacy, First Affiliated Hospital of Shantou University Medical College , Shantou, China .1 Department of Neurology, First Affiliated Hospital of Shantou University Medical College , Shantou, China .1 Department of Neurology, First Affiliated Hospital of Shantou University Medical College , Shantou, China .1 Department of Neurology, First Affiliated Hospital of Shantou University Medical College , Shantou, China .

Pub Type(s)

Journal Article

Language

eng

PubMed ID

29284304

Citation

He, Wenzhen, et al. "Altered Long Non-Coding RNA Transcriptomic Profiles in Ischemic Stroke." Human Gene Therapy, vol. 29, no. 6, 2018, pp. 719-732.
He W, Wei D, Cai , et al. Altered Long Non-Coding RNA Transcriptomic Profiles in Ischemic Stroke. Hum Gene Ther. 2018;29(6):719-732.
He, W., Wei, D., Cai, ., Chen, S., Li, S., & Chen, W. (2018). Altered Long Non-Coding RNA Transcriptomic Profiles in Ischemic Stroke. Human Gene Therapy, 29(6), 719-732. https://doi.org/10.1089/hum.2017.064
He W, et al. Altered Long Non-Coding RNA Transcriptomic Profiles in Ischemic Stroke. Hum Gene Ther. 2018;29(6):719-732. PubMed PMID: 29284304.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Altered Long Non-Coding RNA Transcriptomic Profiles in Ischemic Stroke. AU - He,Wenzhen, AU - Wei,Duncan, AU - Cai,De, AU - Chen,Siqia, AU - Li,Shunxian, AU - Chen,Wenjie, Y1 - 2018/04/05/ PY - 2017/12/30/pubmed PY - 2019/6/8/medline PY - 2017/12/30/entrez KW - co-expression KW - ischemic stroke KW - lncRNA profiling KW - mRNA profiling SP - 719 EP - 732 JF - Human gene therapy JO - Hum. Gene Ther. VL - 29 IS - 6 N2 - A previous study described the important regulatory roles of microRNAs (miRNAs) in ischemic stroke. However, the functional significance of long non-coding RNA (lncRNAs) in ischemic stroke was largely unknown. This study aimed to identify lncRNA profiling and elucidate the regulatory mechanisms in the pathophysiology of stroke. RNA sequencing was performed on the blood of three ischemic stroke patients and three normal controls. Differential expression analysis was used to identify differentially expressed lncRNAs (DElncRNAs) and mRNAs (DEmRNAs). After further correlation and co-expression analysis, the corresponding co-expression networks and miRN-lncRNA-mRNA interaction network were then constructed. The expression of DElncRNAs and DEmRNAs was verified in Gene Expression Omnibus. RNA sequencing and subsequent bioinformatics analysis produced a total of 61 DElncRNAs (14 upregulated and 47 downregulated) and 673 DEmRNAs (432 upregulated and 241 downregulated). LOC105372881 and LOC101929707 were the most highly increased and decreased lncRNAs in ischemic stroke. LncRNA-mRNA co-expression networks were constructed according to 3,008 positively co-expressed and 607 negatively co-expressed lncRNA-mRNA pairs. The DElncRNAs may play roles in the pathways of glycolysis/gluconeogenesis, arrhythmogenic right ventricular cardiomyopathy, adherens junction, lysosome, and hematopoietic cell lineage by regulating their co-expressed mRNAs. Combined with previous data, a miRNA-lncRNA-mRNA interaction network for ischemic stroke was constructed. Based on GSE22255, the expression of six DElncRNAs (CEBPA-AS1, LINC00884, HCG27, MATN1-AS1, HCG26, and LINC01184) and 11 DEmRNAs (TREML4, AHSP, PI3, TESC, ANXA3, OAS1, OAS2, IFI6, ISG15, IFI44L, and LY6E) was similar to the current sequencing data. This study is the first to identify blood lncRNAs in human ischemic stroke using RNA sequencing. The findings may be the foundation for understanding the potential role of lncRNAs in ischemic stroke. SN - 1557-7422 UR - https://www.unboundmedicine.com/medline/citation/29284304/Altered_Long_Non_Coding_RNA_Transcriptomic_Profiles_in_Ischemic_Stroke_ L2 - https://www.liebertpub.com/doi/full/10.1089/hum.2017.064?url_ver=Z39.88-2003&rfr_id=ori:rid:crossref.org&rfr_dat=cr_pub=pubmed DB - PRIME DP - Unbound Medicine ER -