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Comprehensive Analysis of Differentially Expressed Profiles of mRNA N6-Methyladenosine in Colorectal Cancer

Aim: To comprehensively profile the landscape of the mRNA N(6)-methyladenosine (m(6)A) modification in human colorectal cancer (CRC). Methods: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was explored to compare the difference in mRNA N(6)-methyladenosine (m(6)A) methylation between CRC...

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Autores principales: Li, Na, Guo, Qin, Zhang, Qiao, Chen, Bai-Jun, Li, Xiao-An, Zhou, Yan
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2022
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8787460/
https://www.ncbi.nlm.nih.gov/pubmed/35087827
http://dx.doi.org/10.3389/fcell.2021.760912
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author Li, Na
Guo, Qin
Zhang, Qiao
Chen, Bai-Jun
Li, Xiao-An
Zhou, Yan
author_facet Li, Na
Guo, Qin
Zhang, Qiao
Chen, Bai-Jun
Li, Xiao-An
Zhou, Yan
author_sort Li, Na
collection PubMed
description Aim: To comprehensively profile the landscape of the mRNA N(6)-methyladenosine (m(6)A) modification in human colorectal cancer (CRC). Methods: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was explored to compare the difference in mRNA N(6)-methyladenosine (m(6)A) methylation between CRC tissues and adjacent normal control (NC) tissue. RNA-sequencing (RNA-seq) was performed to transcribe differentially expressed mRNAs. Conjoint analysis of MeRIP-seq and RNA-seq data was conducted to predict RNA-binding proteins (RBPs). Results: MeRIP-seq identified 1110 differentially m(6)A methylated sites (DMMSs) and 980 differentially m(6)A methylated genes (DMMGs) in CRC, with 50.13% of all modified genes showing unique m(6)A-modified peaks in CRC. RNA-seq showed 915 upregulated genes and 1463 downregulated genes in CRC. QRT-PCR verified the RNA-seq results by detecting the expression of some mRNAs. Conjoint analysis of MeRIP-seq and RNA-seq identified 400 differentially m(6)A methylated and expressed genes (DEGs), and pathway analysis detected that DMMGs and DEGs were closely related to cancer. After analyzing these DMMGs and DEGs through the GEPIA database, we found that the expression of B3GNT6, DKC1, SRPK1, and RIMKLB were associated with prognosis, and the expression of B3GNT6 and RIMKLB were associated with clinical stage. 17 RBPs were identified based on the DMMGs and DEGs, among which FXR1, FXR2, FMR1, IGF2BP2, IGF2BP3, and SRSF1 were obviously highly expressed in CRC, and FMR1, IGF2BP2, and IGF2BP3 were closely related to methylation, and might be involved in the development of CRC. Conclusion: This study comprehensively profiled m(6)A modification of mRNAs in CRC, which revealed possible mechanisms of m(6)A-mediated gene expression regulation.
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spelling pubmed-87874602022-01-26 Comprehensive Analysis of Differentially Expressed Profiles of mRNA N6-Methyladenosine in Colorectal Cancer Li, Na Guo, Qin Zhang, Qiao Chen, Bai-Jun Li, Xiao-An Zhou, Yan Front Cell Dev Biol Cell and Developmental Biology Aim: To comprehensively profile the landscape of the mRNA N(6)-methyladenosine (m(6)A) modification in human colorectal cancer (CRC). Methods: Methylated RNA immunoprecipitation sequencing (MeRIP-seq) was explored to compare the difference in mRNA N(6)-methyladenosine (m(6)A) methylation between CRC tissues and adjacent normal control (NC) tissue. RNA-sequencing (RNA-seq) was performed to transcribe differentially expressed mRNAs. Conjoint analysis of MeRIP-seq and RNA-seq data was conducted to predict RNA-binding proteins (RBPs). Results: MeRIP-seq identified 1110 differentially m(6)A methylated sites (DMMSs) and 980 differentially m(6)A methylated genes (DMMGs) in CRC, with 50.13% of all modified genes showing unique m(6)A-modified peaks in CRC. RNA-seq showed 915 upregulated genes and 1463 downregulated genes in CRC. QRT-PCR verified the RNA-seq results by detecting the expression of some mRNAs. Conjoint analysis of MeRIP-seq and RNA-seq identified 400 differentially m(6)A methylated and expressed genes (DEGs), and pathway analysis detected that DMMGs and DEGs were closely related to cancer. After analyzing these DMMGs and DEGs through the GEPIA database, we found that the expression of B3GNT6, DKC1, SRPK1, and RIMKLB were associated with prognosis, and the expression of B3GNT6 and RIMKLB were associated with clinical stage. 17 RBPs were identified based on the DMMGs and DEGs, among which FXR1, FXR2, FMR1, IGF2BP2, IGF2BP3, and SRSF1 were obviously highly expressed in CRC, and FMR1, IGF2BP2, and IGF2BP3 were closely related to methylation, and might be involved in the development of CRC. Conclusion: This study comprehensively profiled m(6)A modification of mRNAs in CRC, which revealed possible mechanisms of m(6)A-mediated gene expression regulation. Frontiers Media S.A. 2022-01-07 /pmc/articles/PMC8787460/ /pubmed/35087827 http://dx.doi.org/10.3389/fcell.2021.760912 Text en Copyright © 2022 Li, Guo, Zhang, Chen, Li and Zhou. https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Cell and Developmental Biology
Li, Na
Guo, Qin
Zhang, Qiao
Chen, Bai-Jun
Li, Xiao-An
Zhou, Yan
Comprehensive Analysis of Differentially Expressed Profiles of mRNA N6-Methyladenosine in Colorectal Cancer
title Comprehensive Analysis of Differentially Expressed Profiles of mRNA N6-Methyladenosine in Colorectal Cancer
title_full Comprehensive Analysis of Differentially Expressed Profiles of mRNA N6-Methyladenosine in Colorectal Cancer
title_fullStr Comprehensive Analysis of Differentially Expressed Profiles of mRNA N6-Methyladenosine in Colorectal Cancer
title_full_unstemmed Comprehensive Analysis of Differentially Expressed Profiles of mRNA N6-Methyladenosine in Colorectal Cancer
title_short Comprehensive Analysis of Differentially Expressed Profiles of mRNA N6-Methyladenosine in Colorectal Cancer
title_sort comprehensive analysis of differentially expressed profiles of mrna n6-methyladenosine in colorectal cancer
topic Cell and Developmental Biology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8787460/
https://www.ncbi.nlm.nih.gov/pubmed/35087827
http://dx.doi.org/10.3389/fcell.2021.760912
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