Functional analysis of hepatic long non‐coding ribonucleic acids during liver transplantation in humans

• Published in: The journal of gene medicine Vol. 25; no. 7; pp. e3502 - n/a
• Main Authors: Tu, Dan, Zhang, Yihan, Liu, Xiao, Xu, Yan, Chen, Huixin, Hei, Ziqing, Yi, Shuhong, Ge, Mian
• Format: Journal Article
• Language: English
• Published: England Wiley Periodicals Inc 01.07.2023
• Subjects: Apoptosis; bioinformatics; Chromatin; Core protein; Cytoplasm; Cytosol; Gene Expression Profiling; Gene set enrichment analysis; Gene therapy; Genes; heterogeneous‐nuclear ribonucleoprotein U; Humans; Hypoxia; Hypoxia - metabolism; Ischemia; Liver; Liver - metabolism; Liver transplantation; Liver Transplantation - adverse effects; Liver transplants; Localization; long non‐coding RNAs; Non-coding RNA; Reperfusion; reperfusion injury; Ribonucleic acid; RNA; RNA, Long Noncoding - genetics; RNA, Long Noncoding - metabolism; RNA-binding protein; Transcriptomes; Transplants & implants; whole transcriptome sequencing; whole transcriptome sequencing; reperfusion injury; heterogeneous-nuclear ribonucleoprotein U; long non-coding RNAs; liver transplantation; bioinformatics
• ISSN: 1099-498X; 1521-2254
• DOI: 10.1002/jgm.3502

Background The potential function of long non‐coding RNAs (lncRNAs) in human hepatic ischemia–reperfusion injury (HIRI) remains to be clarified. Methods Clinical samples of transplanted liver tissues from 26 patients undergoing liver transplantation (LT) and normal liver tissues from seven patients undergoing hepatic hemangiomactomy (Con) were collected. Typical samples were subjected to whole transcriptome sequencing (RNA‐seq). Differentially expressed genes between groups were identified by DEGseq and were analyzed by enrichment analysis including Gene Ontology, Kyoto Encyclopedia of Genes and Genomes, and gene set enrichment analysis. Transcription of five lncRNAs including NONHSAG039942, NONHSAG071405, NONHSAG027516, LXLOC_058190, and LXLOC_024376 that presented significant difference in RNA‐sequencing were validated by a quantitative real‐time PCR (qRT‐PCR), for which the subcellular localization and the binding ability to known human RNA‐binding proteins (RBPs) were respectively predicted by LncLocator and catRAPID genomics v2.1. Results We identified 2917 lncRNAs and 2811 mRNAs that were differentially expressed (p < 0.05 and log2 fold change > 1 or < −1) between groups (LT vs. Con). NONHSAG039942, NONHSAG071405, LXLOC_058190, and LXLOC_024376 were validated by qRT‐PCR to be significantly increased in the LT group, and were all predicted to be localized in cytoplasm or cytosol. NONHSAG039942, NONHSAG071405, and LXLOC_058190 held an RBP interaction propensity score of 98.07%, 76.95%, and 152.99%, respectively, with heterogeneous‐nuclear ribonucleoprotein U (HNRNPU). Pathways significantly activated in transplant livers that involved HNRNPU as a core enrichment gene included hypoxia, ACE2 expression, apoptosis, spliceosome formation, etc. Conclusions NONHSAG039942, NONHSAG071405, and LXLOC_058190 were significantly increased in transplant livers after reperfusion and their role in HIRI may be associated with HNRNPU, a core protein that participates in hypoxia and chromatin accessibility. Long non‐coding RNAs (lncRNAs) play an important role in liver ischemia–reperfusion injury, and heterogeneous‐nuclear ribonucleoprotein U (HNRNPU) may be a central regulatory protein in the transplanted liver that is highly related to the functions of screened lncRNAs.