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Construction and integrated analysis of a lncRNA-associated competing endogenous RNA network reveal functional lncRNAs in pancreatic cancer

BACKGROUND: Long noncoding RNAs (lncRNAs) can serve as a competing endogenous RNA (ceRNA) in regulating gene expression in multiple cancers by sponging miRNA. However, this mechanism is poorly studied in pancreatic cancer. This study aims to identify functional lncRNAs and their potential regulatory...

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Autores principales: Liu, Yuanbin, Huo, Zhen, Wang, Weishen, Zhai, Shuyu, Wang, Yue, Weng, Yuanchi, Deng, Xiaxing, Lu, Xiongxiong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: AME Publishing Company 2020
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8798265/
https://www.ncbi.nlm.nih.gov/pubmed/35117727
http://dx.doi.org/10.21037/tcr.2020.04.03
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author Liu, Yuanbin
Huo, Zhen
Wang, Weishen
Zhai, Shuyu
Wang, Yue
Weng, Yuanchi
Deng, Xiaxing
Lu, Xiongxiong
author_facet Liu, Yuanbin
Huo, Zhen
Wang, Weishen
Zhai, Shuyu
Wang, Yue
Weng, Yuanchi
Deng, Xiaxing
Lu, Xiongxiong
author_sort Liu, Yuanbin
collection PubMed
description BACKGROUND: Long noncoding RNAs (lncRNAs) can serve as a competing endogenous RNA (ceRNA) in regulating gene expression in multiple cancers by sponging miRNA. However, this mechanism is poorly studied in pancreatic cancer. This study aims to identify functional lncRNAs and their potential regulatory mechanisms in pancreatic cancer. METHODS: Differentially expressed lncRNA (DE-lncRNA), miRNA (DE-miRNA) and mRNA (DE-mRNA) were analyzed using data from three datasets (GSE89139, GSE24279 and GSE62452) from the Gene Expression Omnibus (GEO). The lncRNA-miRNA-mRNA interactions were predicted using miRcode and Targetscan. Gene ontology (GO) and pathway analysis of DE-mRNAs were performed using clusterProfiler. Survival analysis was conducted using data from The Cancer Genome Atlas (TCGA) database. RESULTS: Three hundred sixty-six DE-lncRNAs, 28 DE-miRNAs and 330 DE-mRNAs from pancreatic cancer and adjacent tissue were identified. A ceRNA network including 75 DE-lncRNAs, 18 DE-miRNAs and 85 DE-mRNAs was constructed, among which 16 DE-lncRNAs were associated with overall survival and 13 DE-lncRNAs were correlated with tumor progression. Three functional lncRNAs, GABPB1-AS1, ST7-AS1 and PSMG3-AS1, were identified as key functional lncRNAs, and their differential expression and potential ceRNA regulatory mechanism were validated by qPCR using pancreatic cancer cell lines and tissues. CONCLUSIONS: Our study identifies novel lncRNAs associated with progression and prognosis of pancreatic cancer and contributes to better understanding of lncRNA-associated ceRNA regulatory mechanisms in pancreatic cancer.
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spelling pubmed-87982652022-02-02 Construction and integrated analysis of a lncRNA-associated competing endogenous RNA network reveal functional lncRNAs in pancreatic cancer Liu, Yuanbin Huo, Zhen Wang, Weishen Zhai, Shuyu Wang, Yue Weng, Yuanchi Deng, Xiaxing Lu, Xiongxiong Transl Cancer Res Original Article BACKGROUND: Long noncoding RNAs (lncRNAs) can serve as a competing endogenous RNA (ceRNA) in regulating gene expression in multiple cancers by sponging miRNA. However, this mechanism is poorly studied in pancreatic cancer. This study aims to identify functional lncRNAs and their potential regulatory mechanisms in pancreatic cancer. METHODS: Differentially expressed lncRNA (DE-lncRNA), miRNA (DE-miRNA) and mRNA (DE-mRNA) were analyzed using data from three datasets (GSE89139, GSE24279 and GSE62452) from the Gene Expression Omnibus (GEO). The lncRNA-miRNA-mRNA interactions were predicted using miRcode and Targetscan. Gene ontology (GO) and pathway analysis of DE-mRNAs were performed using clusterProfiler. Survival analysis was conducted using data from The Cancer Genome Atlas (TCGA) database. RESULTS: Three hundred sixty-six DE-lncRNAs, 28 DE-miRNAs and 330 DE-mRNAs from pancreatic cancer and adjacent tissue were identified. A ceRNA network including 75 DE-lncRNAs, 18 DE-miRNAs and 85 DE-mRNAs was constructed, among which 16 DE-lncRNAs were associated with overall survival and 13 DE-lncRNAs were correlated with tumor progression. Three functional lncRNAs, GABPB1-AS1, ST7-AS1 and PSMG3-AS1, were identified as key functional lncRNAs, and their differential expression and potential ceRNA regulatory mechanism were validated by qPCR using pancreatic cancer cell lines and tissues. CONCLUSIONS: Our study identifies novel lncRNAs associated with progression and prognosis of pancreatic cancer and contributes to better understanding of lncRNA-associated ceRNA regulatory mechanisms in pancreatic cancer. AME Publishing Company 2020-05 /pmc/articles/PMC8798265/ /pubmed/35117727 http://dx.doi.org/10.21037/tcr.2020.04.03 Text en 2020 Translational Cancer Research. All rights reserved. https://creativecommons.org/licenses/by-nc-nd/4.0/Open Access Statement: This is an Open Access article distributed in accordance with the Creative Commons Attribution-NonCommercial-NoDerivs 4.0 International License (CC BY-NC-ND 4.0), which permits the non-commercial replication and distribution of the article with the strict proviso that no changes or edits are made and the original work is properly cited (including links to both the formal publication through the relevant DOI and the license). See: https://creativecommons.org/licenses/by-nc-nd/4.0/.
spellingShingle Original Article
Liu, Yuanbin
Huo, Zhen
Wang, Weishen
Zhai, Shuyu
Wang, Yue
Weng, Yuanchi
Deng, Xiaxing
Lu, Xiongxiong
Construction and integrated analysis of a lncRNA-associated competing endogenous RNA network reveal functional lncRNAs in pancreatic cancer
title Construction and integrated analysis of a lncRNA-associated competing endogenous RNA network reveal functional lncRNAs in pancreatic cancer
title_full Construction and integrated analysis of a lncRNA-associated competing endogenous RNA network reveal functional lncRNAs in pancreatic cancer
title_fullStr Construction and integrated analysis of a lncRNA-associated competing endogenous RNA network reveal functional lncRNAs in pancreatic cancer
title_full_unstemmed Construction and integrated analysis of a lncRNA-associated competing endogenous RNA network reveal functional lncRNAs in pancreatic cancer
title_short Construction and integrated analysis of a lncRNA-associated competing endogenous RNA network reveal functional lncRNAs in pancreatic cancer
title_sort construction and integrated analysis of a lncrna-associated competing endogenous rna network reveal functional lncrnas in pancreatic cancer
topic Original Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8798265/
https://www.ncbi.nlm.nih.gov/pubmed/35117727
http://dx.doi.org/10.21037/tcr.2020.04.03
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