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Construction of long non-coding RNA- and microRNA-mediated competing endogenous RNA networks in alcohol-related esophageal cancer

The current study aimed to explore the lncRNA–miRNA–mRNA networks associated with alcohol-related esophageal cancer (EC). RNA-sequencing and clinical data were downloaded from The Cancer Genome Atlas and the differentially expressed genes (DEGs), long non-coding RNAs (lncRNAs, DELs), and miRNAs (DEM...

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Autores principales: Du, Quan, Xiao, Ren-Dong, Luo, Rong-Gang, Xie, Jin-Bao, Su, Zu-Dong, Wang, Yu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9200351/
https://www.ncbi.nlm.nih.gov/pubmed/35704638
http://dx.doi.org/10.1371/journal.pone.0269742
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author Du, Quan
Xiao, Ren-Dong
Luo, Rong-Gang
Xie, Jin-Bao
Su, Zu-Dong
Wang, Yu
author_facet Du, Quan
Xiao, Ren-Dong
Luo, Rong-Gang
Xie, Jin-Bao
Su, Zu-Dong
Wang, Yu
author_sort Du, Quan
collection PubMed
description The current study aimed to explore the lncRNA–miRNA–mRNA networks associated with alcohol-related esophageal cancer (EC). RNA-sequencing and clinical data were downloaded from The Cancer Genome Atlas and the differentially expressed genes (DEGs), long non-coding RNAs (lncRNAs, DELs), and miRNAs (DEMs) in patients with alcohol-related and non-alcohol-related EC were identified. Prognostic RNAs were identified by performing Kaplan–Meier survival analyses. Weighted gene co-expression network analysis was employed to build the gene modules. The lncRNA–miRNA–mRNA competing endogenous RNA (ceRNA) networks were constructed based on our in silico analyses using data from miRcode, starBase, and miRTarBase databases. Functional enrichment analysis was performed for the genes in the identified ceRNA networks. A total of 906 DEGs, 40 DELs, and 52 DEMs were identified. There were eight lncRNAs and miRNAs each, including ST7-AS2 and miR-1269, which were significantly associated with the survival rate of patients with EC. Of the seven gene modules, the blue and turquoise modules were closely related to disease progression; the genes in this module were selected to construct the ceRNA networks. SNHG12–miR-1–ST6GAL1, SNHG3–miR-1–ST6GAL1, SPAG5-AS1–miR-133a–ST6GAL1, and SNHG12–hsa-miR-33a–ST6GA interactions, associated with the N-glycan biosynthesis pathway, may have key roles in alcohol-related EC. Thus, the identified biomarkers provide a novel insight into the molecular mechanism of alcohol-related EC.
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spelling pubmed-92003512022-06-16 Construction of long non-coding RNA- and microRNA-mediated competing endogenous RNA networks in alcohol-related esophageal cancer Du, Quan Xiao, Ren-Dong Luo, Rong-Gang Xie, Jin-Bao Su, Zu-Dong Wang, Yu PLoS One Research Article The current study aimed to explore the lncRNA–miRNA–mRNA networks associated with alcohol-related esophageal cancer (EC). RNA-sequencing and clinical data were downloaded from The Cancer Genome Atlas and the differentially expressed genes (DEGs), long non-coding RNAs (lncRNAs, DELs), and miRNAs (DEMs) in patients with alcohol-related and non-alcohol-related EC were identified. Prognostic RNAs were identified by performing Kaplan–Meier survival analyses. Weighted gene co-expression network analysis was employed to build the gene modules. The lncRNA–miRNA–mRNA competing endogenous RNA (ceRNA) networks were constructed based on our in silico analyses using data from miRcode, starBase, and miRTarBase databases. Functional enrichment analysis was performed for the genes in the identified ceRNA networks. A total of 906 DEGs, 40 DELs, and 52 DEMs were identified. There were eight lncRNAs and miRNAs each, including ST7-AS2 and miR-1269, which were significantly associated with the survival rate of patients with EC. Of the seven gene modules, the blue and turquoise modules were closely related to disease progression; the genes in this module were selected to construct the ceRNA networks. SNHG12–miR-1–ST6GAL1, SNHG3–miR-1–ST6GAL1, SPAG5-AS1–miR-133a–ST6GAL1, and SNHG12–hsa-miR-33a–ST6GA interactions, associated with the N-glycan biosynthesis pathway, may have key roles in alcohol-related EC. Thus, the identified biomarkers provide a novel insight into the molecular mechanism of alcohol-related EC. Public Library of Science 2022-06-15 /pmc/articles/PMC9200351/ /pubmed/35704638 http://dx.doi.org/10.1371/journal.pone.0269742 Text en © 2022 Du et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Du, Quan
Xiao, Ren-Dong
Luo, Rong-Gang
Xie, Jin-Bao
Su, Zu-Dong
Wang, Yu
Construction of long non-coding RNA- and microRNA-mediated competing endogenous RNA networks in alcohol-related esophageal cancer
title Construction of long non-coding RNA- and microRNA-mediated competing endogenous RNA networks in alcohol-related esophageal cancer
title_full Construction of long non-coding RNA- and microRNA-mediated competing endogenous RNA networks in alcohol-related esophageal cancer
title_fullStr Construction of long non-coding RNA- and microRNA-mediated competing endogenous RNA networks in alcohol-related esophageal cancer
title_full_unstemmed Construction of long non-coding RNA- and microRNA-mediated competing endogenous RNA networks in alcohol-related esophageal cancer
title_short Construction of long non-coding RNA- and microRNA-mediated competing endogenous RNA networks in alcohol-related esophageal cancer
title_sort construction of long non-coding rna- and microrna-mediated competing endogenous rna networks in alcohol-related esophageal cancer
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9200351/
https://www.ncbi.nlm.nih.gov/pubmed/35704638
http://dx.doi.org/10.1371/journal.pone.0269742
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