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Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers

SIMPLE SUMMARY: Competing endogenous RNAs (ceRNAs) have gained attention in cancer research owing to their involvement in microRNA-mediated gene regulation. Here, we identified a shared ceRNA network across five hormone-dependent (HD) cancers (prostate, breast, colon, rectal, and endometrial), that...

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Autores principales: Jayarathna, Dulari K., Rentería, Miguel E., Sauret, Emilie, Batra, Jyotsna, Gandhi, Neha S.
Formato: Online Artículo Texto
Lenguaje:English
Publicado: MDPI 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8533463/
https://www.ncbi.nlm.nih.gov/pubmed/34681112
http://dx.doi.org/10.3390/biology10101014
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author Jayarathna, Dulari K.
Rentería, Miguel E.
Sauret, Emilie
Batra, Jyotsna
Gandhi, Neha S.
author_facet Jayarathna, Dulari K.
Rentería, Miguel E.
Sauret, Emilie
Batra, Jyotsna
Gandhi, Neha S.
author_sort Jayarathna, Dulari K.
collection PubMed
description SIMPLE SUMMARY: Competing endogenous RNAs (ceRNAs) have gained attention in cancer research owing to their involvement in microRNA-mediated gene regulation. Here, we identified a shared ceRNA network across five hormone-dependent (HD) cancers (prostate, breast, colon, rectal, and endometrial), that contain two long non-coding RNAs, nine mRNAs, and seventy-four microRNAs. Among them, two mRNAs and forty-one microRNAs were associated with at least one HD cancer survival. A similar analytical approach can be applied to identify shared ceRNAs across a group of related cancers, which will significantly contribute to understanding their shared disease biology. ABSTRACT: The discovery of microRNAs (miRNAs) has fundamentally transformed our understanding of gene regulation. The competing endogenous RNA (ceRNA) hypothesis postulates that messenger RNAs and other RNA transcripts, such as long non-coding RNAs and pseudogenes, can act as natural miRNA sponges. These RNAs influence each other’s expression levels by competing for the same pool of miRNAs through miRNA response elements on their target transcripts, thereby modulating gene expression and protein activity. In recent years, these ceRNA regulatory networks have gained considerable attention in cancer research. Several studies have identified cancer-specific ceRNA networks. Nevertheless, prior bioinformatic analyses have focused on long-non-coding RNA-associated ceRNA networks. Here, we identify an extended ceRNA network (including both long non-coding RNAs and pseudogenes) shared across a group of five hormone-dependent (HD) cancers, i.e., prostate, breast, colon, rectal, and endometrial cancers, using data from The Cancer Genome Atlas (TCGA). We performed a functional enrichment analysis for differentially expressed genes in the shared ceRNA network of HD cancers, followed by a survival analysis to determine their prognostic ability. We identified two long non-coding RNAs, nine genes, and seventy-four miRNAs in the shared ceRNA network across five HD cancers. Among them, two genes and forty-one miRNAs were associated with at least one HD cancer survival. This study is the first to investigate pseudogene-associated ceRNAs across a group of related cancers and highlights the value of this approach to understanding the shared molecular pathogenesis in a group of related diseases.
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spelling pubmed-85334632021-10-23 Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers Jayarathna, Dulari K. Rentería, Miguel E. Sauret, Emilie Batra, Jyotsna Gandhi, Neha S. Biology (Basel) Article SIMPLE SUMMARY: Competing endogenous RNAs (ceRNAs) have gained attention in cancer research owing to their involvement in microRNA-mediated gene regulation. Here, we identified a shared ceRNA network across five hormone-dependent (HD) cancers (prostate, breast, colon, rectal, and endometrial), that contain two long non-coding RNAs, nine mRNAs, and seventy-four microRNAs. Among them, two mRNAs and forty-one microRNAs were associated with at least one HD cancer survival. A similar analytical approach can be applied to identify shared ceRNAs across a group of related cancers, which will significantly contribute to understanding their shared disease biology. ABSTRACT: The discovery of microRNAs (miRNAs) has fundamentally transformed our understanding of gene regulation. The competing endogenous RNA (ceRNA) hypothesis postulates that messenger RNAs and other RNA transcripts, such as long non-coding RNAs and pseudogenes, can act as natural miRNA sponges. These RNAs influence each other’s expression levels by competing for the same pool of miRNAs through miRNA response elements on their target transcripts, thereby modulating gene expression and protein activity. In recent years, these ceRNA regulatory networks have gained considerable attention in cancer research. Several studies have identified cancer-specific ceRNA networks. Nevertheless, prior bioinformatic analyses have focused on long-non-coding RNA-associated ceRNA networks. Here, we identify an extended ceRNA network (including both long non-coding RNAs and pseudogenes) shared across a group of five hormone-dependent (HD) cancers, i.e., prostate, breast, colon, rectal, and endometrial cancers, using data from The Cancer Genome Atlas (TCGA). We performed a functional enrichment analysis for differentially expressed genes in the shared ceRNA network of HD cancers, followed by a survival analysis to determine their prognostic ability. We identified two long non-coding RNAs, nine genes, and seventy-four miRNAs in the shared ceRNA network across five HD cancers. Among them, two genes and forty-one miRNAs were associated with at least one HD cancer survival. This study is the first to investigate pseudogene-associated ceRNAs across a group of related cancers and highlights the value of this approach to understanding the shared molecular pathogenesis in a group of related diseases. MDPI 2021-10-09 /pmc/articles/PMC8533463/ /pubmed/34681112 http://dx.doi.org/10.3390/biology10101014 Text en © 2021 by the authors. https://creativecommons.org/licenses/by/4.0/Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (https://creativecommons.org/licenses/by/4.0/).
spellingShingle Article
Jayarathna, Dulari K.
Rentería, Miguel E.
Sauret, Emilie
Batra, Jyotsna
Gandhi, Neha S.
Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers
title Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers
title_full Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers
title_fullStr Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers
title_full_unstemmed Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers
title_short Identifying Complex lncRNA/Pseudogene–miRNA–mRNA Crosstalk in Hormone-Dependent Cancers
title_sort identifying complex lncrna/pseudogene–mirna–mrna crosstalk in hormone-dependent cancers
topic Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8533463/
https://www.ncbi.nlm.nih.gov/pubmed/34681112
http://dx.doi.org/10.3390/biology10101014
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