Identification of m6A/m5C-related lncRNA signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinoma

Abstract N6-methyladenosine (m6A) and 5-methylcytosine (m5C) RNA modifications have garnered significant attention in the field of epigenetic research due to their close association with human cancers. This study we focus on elucidating the expression patterns of m6A/m5C-related long non-coding RNAs...

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Main Authors: Jianlin Wang, Huiwen Ren, Chao Xu, Bo Yu, Yiling Cai, Jian Wang, Xinye Ni
Format: Article
Language:English
Published: Nature Portfolio 2024-04-01
Series:Scientific Reports
Subjects:
Online Access:https://doi.org/10.1038/s41598-024-58743-y
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author Jianlin Wang
Huiwen Ren
Chao Xu
Bo Yu
Yiling Cai
Jian Wang
Xinye Ni
author_facet Jianlin Wang
Huiwen Ren
Chao Xu
Bo Yu
Yiling Cai
Jian Wang
Xinye Ni
author_sort Jianlin Wang
collection DOAJ
description Abstract N6-methyladenosine (m6A) and 5-methylcytosine (m5C) RNA modifications have garnered significant attention in the field of epigenetic research due to their close association with human cancers. This study we focus on elucidating the expression patterns of m6A/m5C-related long non-coding RNAs (lncRNAs) in esophageal squamous cell carcinoma (ESCC) and assessing their prognostic significance and therapeutic potential. Transcriptomic profiles of ESCC were derived from public resources. m6A/m5C-related lncRNAs were obtained from TCGA using Spearman’s correlations analysis. The m6A/m5C-lncRNAs prognostic signature was selected to construct a RiskScore model for survival prediction, and their correlation with the immune microenvironment and immunotherapy response was analyzed. A total of 606 m6A/m5C-lncRNAs were screened, and ESCC cases in the TCGA cohort were stratified into three clusters, which showed significantly distinct in various clinical features and immune landscapes. A RiskScore model comprising ten m6A/m5C-lncRNAs prognostic signature were constructed and displayed good independent prediction ability in validation datasets. Patients in the low-RiskScore group had a better prognosis, a higher abundance of immune cells (CD4 + T cell, CD4 + naive T cell, class-switched memory B cell, and Treg), and enhanced expression of most immune checkpoint genes. Importantly, patients with low-RiskScore were more cline benefit from immune checkpoint inhibitor treatment (P < 0.05). Our findings underscore the potential of RiskScore system comprising ten m6A/m5C-related lncRNAs as effective biomarkers for predicting survival outcomes, characterizing the immune landscape, and assessing response to immunotherapy in ESCC.
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spelling doaj.art-0db08cbe8b5a457fbc86c2ed36d640752024-04-14T11:15:21ZengNature PortfolioScientific Reports2045-23222024-04-0114111610.1038/s41598-024-58743-yIdentification of m6A/m5C-related lncRNA signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinomaJianlin Wang0Huiwen Ren1Chao Xu2Bo Yu3Yiling Cai4Jian Wang5Xinye Ni6Department of Radiotherapy, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical UniversityDepartment of Radiotherapy, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical UniversityDepartment of Radiotherapy, Jiangyin People’s HospitalDepartment of Radiotherapy, Jiangyin People’s HospitalDepartment of Radiotherapy, Jiangyin People’s HospitalDepartment of Radiotherapy, Jiangyin People’s HospitalDepartment of Radiotherapy, The Affiliated Changzhou Second People’s Hospital of Nanjing Medical UniversityAbstract N6-methyladenosine (m6A) and 5-methylcytosine (m5C) RNA modifications have garnered significant attention in the field of epigenetic research due to their close association with human cancers. This study we focus on elucidating the expression patterns of m6A/m5C-related long non-coding RNAs (lncRNAs) in esophageal squamous cell carcinoma (ESCC) and assessing their prognostic significance and therapeutic potential. Transcriptomic profiles of ESCC were derived from public resources. m6A/m5C-related lncRNAs were obtained from TCGA using Spearman’s correlations analysis. The m6A/m5C-lncRNAs prognostic signature was selected to construct a RiskScore model for survival prediction, and their correlation with the immune microenvironment and immunotherapy response was analyzed. A total of 606 m6A/m5C-lncRNAs were screened, and ESCC cases in the TCGA cohort were stratified into three clusters, which showed significantly distinct in various clinical features and immune landscapes. A RiskScore model comprising ten m6A/m5C-lncRNAs prognostic signature were constructed and displayed good independent prediction ability in validation datasets. Patients in the low-RiskScore group had a better prognosis, a higher abundance of immune cells (CD4 + T cell, CD4 + naive T cell, class-switched memory B cell, and Treg), and enhanced expression of most immune checkpoint genes. Importantly, patients with low-RiskScore were more cline benefit from immune checkpoint inhibitor treatment (P < 0.05). Our findings underscore the potential of RiskScore system comprising ten m6A/m5C-related lncRNAs as effective biomarkers for predicting survival outcomes, characterizing the immune landscape, and assessing response to immunotherapy in ESCC.https://doi.org/10.1038/s41598-024-58743-yEsophageal squamous cell carcinomam6Am5CPrognosislncRNA
spellingShingle Jianlin Wang
Huiwen Ren
Chao Xu
Bo Yu
Yiling Cai
Jian Wang
Xinye Ni
Identification of m6A/m5C-related lncRNA signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinoma
Scientific Reports
Esophageal squamous cell carcinoma
m6A
m5C
Prognosis
lncRNA
title Identification of m6A/m5C-related lncRNA signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinoma
title_full Identification of m6A/m5C-related lncRNA signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinoma
title_fullStr Identification of m6A/m5C-related lncRNA signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinoma
title_full_unstemmed Identification of m6A/m5C-related lncRNA signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinoma
title_short Identification of m6A/m5C-related lncRNA signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinoma
title_sort identification of m6a m5c related lncrna signature for prediction of prognosis and immunotherapy efficacy in esophageal squamous cell carcinoma
topic Esophageal squamous cell carcinoma
m6A
m5C
Prognosis
lncRNA
url https://doi.org/10.1038/s41598-024-58743-y
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