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Establishment of a prognostic model based on m(6)A regulatory factors and stemness of hepatocellular carcinoma using RNA-seq data and scRNA-seq data
BACKGROUND: Hepatocellular carcinoma (HCC) with high incidence and mortality is one of the most common malignant cancers worldwide. Increasing evidence has reported that N6-methyladenosine (m(6)A) modification has been considered as a major contribution to the occurrence and development of tumors. M...
Autores principales: | , , , , , , , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Springer Berlin Heidelberg
2023
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10587019/ https://www.ncbi.nlm.nih.gov/pubmed/37466793 http://dx.doi.org/10.1007/s00432-023-05045-x |
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author | Liang, Yan Chen, Sen Xie, Jinghe Yan, Guanrong Guo, Tingting Li, Tianyang Liu, Shoupei Zeng, Weiping Zhang, Shuai Ma, Keqiang Chen, Honglin Ou, Yimeng Wang, Bailin Gu, Weili Duan, Yuyou |
author_facet | Liang, Yan Chen, Sen Xie, Jinghe Yan, Guanrong Guo, Tingting Li, Tianyang Liu, Shoupei Zeng, Weiping Zhang, Shuai Ma, Keqiang Chen, Honglin Ou, Yimeng Wang, Bailin Gu, Weili Duan, Yuyou |
author_sort | Liang, Yan |
collection | PubMed |
description | BACKGROUND: Hepatocellular carcinoma (HCC) with high incidence and mortality is one of the most common malignant cancers worldwide. Increasing evidence has reported that N6-methyladenosine (m(6)A) modification has been considered as a major contribution to the occurrence and development of tumors. METHOD: In our study, we comprehensively analyzed the connection between m(6)A regulatory factors and cancer stem cells (CSCs) of HCC to establish a clinical tool for predicting its outcome. First, we concluded that the expression level of m(6)A regulatory factors was related with the stemness of hepatocellular carcinoma. Subsequently, we gained a ten hub regulatory factors that were associated with prognosis of hepatocellular carcinoma by overall survival (OS) analysis using ICGC and TCGA datasets, and these regulatory factors included YTHDF1, IGF2BP1, METTL3, IGF2BP3, HNRNPA2B1, IGF2BP2, RBM15B, HNRNPC, RBMX, and LRPPR. Next, we found that these ten hub m(6)A regulatory factors were highly expressed in CSCs, and CSCs related pathways were also enriched by the gene set variation analysis (GSVA). Then, correlation, consensus clustering and PCA analysis were performed to reveal potential therapeutic benefits of HCC. Moreover, univariate Cox regression (UNICOX), LASSON and multivariate Cox regression (MULTICOX) analyses were adopted to establish HCC prognosis prediction signature. RESULTS: Four regulatory factors RBM15B, LRPPRC, IGF2BP1, and IGF2BP3 were picked as valuable prognostic indicators. CONCLUSION: In summary, these ten hub regulatory factors would be useful therapeutic targets for HCC treatment, and RBM15B/LRPPRC/IGF2BP1/IGF2BP3 prognostic indicators can be used to guide therapy for HCC patients. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00432-023-05045-x. |
format | Online Article Text |
id | pubmed-10587019 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2023 |
publisher | Springer Berlin Heidelberg |
record_format | MEDLINE/PubMed |
spelling | pubmed-105870192023-10-21 Establishment of a prognostic model based on m(6)A regulatory factors and stemness of hepatocellular carcinoma using RNA-seq data and scRNA-seq data Liang, Yan Chen, Sen Xie, Jinghe Yan, Guanrong Guo, Tingting Li, Tianyang Liu, Shoupei Zeng, Weiping Zhang, Shuai Ma, Keqiang Chen, Honglin Ou, Yimeng Wang, Bailin Gu, Weili Duan, Yuyou J Cancer Res Clin Oncol Research BACKGROUND: Hepatocellular carcinoma (HCC) with high incidence and mortality is one of the most common malignant cancers worldwide. Increasing evidence has reported that N6-methyladenosine (m(6)A) modification has been considered as a major contribution to the occurrence and development of tumors. METHOD: In our study, we comprehensively analyzed the connection between m(6)A regulatory factors and cancer stem cells (CSCs) of HCC to establish a clinical tool for predicting its outcome. First, we concluded that the expression level of m(6)A regulatory factors was related with the stemness of hepatocellular carcinoma. Subsequently, we gained a ten hub regulatory factors that were associated with prognosis of hepatocellular carcinoma by overall survival (OS) analysis using ICGC and TCGA datasets, and these regulatory factors included YTHDF1, IGF2BP1, METTL3, IGF2BP3, HNRNPA2B1, IGF2BP2, RBM15B, HNRNPC, RBMX, and LRPPR. Next, we found that these ten hub m(6)A regulatory factors were highly expressed in CSCs, and CSCs related pathways were also enriched by the gene set variation analysis (GSVA). Then, correlation, consensus clustering and PCA analysis were performed to reveal potential therapeutic benefits of HCC. Moreover, univariate Cox regression (UNICOX), LASSON and multivariate Cox regression (MULTICOX) analyses were adopted to establish HCC prognosis prediction signature. RESULTS: Four regulatory factors RBM15B, LRPPRC, IGF2BP1, and IGF2BP3 were picked as valuable prognostic indicators. CONCLUSION: In summary, these ten hub regulatory factors would be useful therapeutic targets for HCC treatment, and RBM15B/LRPPRC/IGF2BP1/IGF2BP3 prognostic indicators can be used to guide therapy for HCC patients. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00432-023-05045-x. Springer Berlin Heidelberg 2023-07-19 2023 /pmc/articles/PMC10587019/ /pubmed/37466793 http://dx.doi.org/10.1007/s00432-023-05045-x Text en © The Author(s) 2023 https://creativecommons.org/licenses/by/4.0/Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article's Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article's Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/ (https://creativecommons.org/licenses/by/4.0/) . |
spellingShingle | Research Liang, Yan Chen, Sen Xie, Jinghe Yan, Guanrong Guo, Tingting Li, Tianyang Liu, Shoupei Zeng, Weiping Zhang, Shuai Ma, Keqiang Chen, Honglin Ou, Yimeng Wang, Bailin Gu, Weili Duan, Yuyou Establishment of a prognostic model based on m(6)A regulatory factors and stemness of hepatocellular carcinoma using RNA-seq data and scRNA-seq data |
title | Establishment of a prognostic model based on m(6)A regulatory factors and stemness of hepatocellular carcinoma using RNA-seq data and scRNA-seq data |
title_full | Establishment of a prognostic model based on m(6)A regulatory factors and stemness of hepatocellular carcinoma using RNA-seq data and scRNA-seq data |
title_fullStr | Establishment of a prognostic model based on m(6)A regulatory factors and stemness of hepatocellular carcinoma using RNA-seq data and scRNA-seq data |
title_full_unstemmed | Establishment of a prognostic model based on m(6)A regulatory factors and stemness of hepatocellular carcinoma using RNA-seq data and scRNA-seq data |
title_short | Establishment of a prognostic model based on m(6)A regulatory factors and stemness of hepatocellular carcinoma using RNA-seq data and scRNA-seq data |
title_sort | establishment of a prognostic model based on m(6)a regulatory factors and stemness of hepatocellular carcinoma using rna-seq data and scrna-seq data |
topic | Research |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10587019/ https://www.ncbi.nlm.nih.gov/pubmed/37466793 http://dx.doi.org/10.1007/s00432-023-05045-x |
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