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Machine learning-based transcriptome analysis of lipid metabolism biomarkers for the survival prediction in hepatocellular carcinoma
Hepatocellular carcinoma (HCC) is the most common primary malignancy of the liver with a very high fatality rate. Our goal in this study is to find a reliable lipid metabolism-related signature associated with prognostic significance for HCC. In this study, HCC lipid metabolism-related molecular sub...
Autores principales: | , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
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Frontiers Media S.A.
2022
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9554549/ https://www.ncbi.nlm.nih.gov/pubmed/36246607 http://dx.doi.org/10.3389/fgene.2022.1005271 |
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author | Xiong, Ronghong Wang, Hui Li, Ying Zheng, Jingpeng Cheng, Yating Liu, Shunfang Yang, Guohua |
author_facet | Xiong, Ronghong Wang, Hui Li, Ying Zheng, Jingpeng Cheng, Yating Liu, Shunfang Yang, Guohua |
author_sort | Xiong, Ronghong |
collection | PubMed |
description | Hepatocellular carcinoma (HCC) is the most common primary malignancy of the liver with a very high fatality rate. Our goal in this study is to find a reliable lipid metabolism-related signature associated with prognostic significance for HCC. In this study, HCC lipid metabolism-related molecular subtype analysis was conducted based on the 243 lipid metabolism genes collected from the Molecular Signatures Database. Several significant disparities in prognosis, clinicopathological characteristics, and immune and ferroptosis-related status were found across the three subtypes, especially between C1 and C3 subgroups. Differential expression analysis yielded 57 differentially expressed genes (DEGs) between C1 and C3 subtypes. GO and KEGG analysis was employed for functional annotation. Three of 21 prognostic DEGs (CXCL8, SLC10A1, and ADH4) were finally selected through machine-learning-based discovery and validation strategy. The risk score = (0.103) × expression value of CXCL8 + (−0.0333) × expression value of SLC10A1 + (−0.0812) × expression value of ADH4. We used these three to construct a HCC prognostic risk model, which stratified the patients of the validation cohort into two risk subtypes with significantly different overall survival. Our work provides possible significance of the lipid metabolism-associated model in stratifying patient prognosis and its feasibility to guide therapeutic selection. |
format | Online Article Text |
id | pubmed-9554549 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Frontiers Media S.A. |
record_format | MEDLINE/PubMed |
spelling | pubmed-95545492022-10-13 Machine learning-based transcriptome analysis of lipid metabolism biomarkers for the survival prediction in hepatocellular carcinoma Xiong, Ronghong Wang, Hui Li, Ying Zheng, Jingpeng Cheng, Yating Liu, Shunfang Yang, Guohua Front Genet Genetics Hepatocellular carcinoma (HCC) is the most common primary malignancy of the liver with a very high fatality rate. Our goal in this study is to find a reliable lipid metabolism-related signature associated with prognostic significance for HCC. In this study, HCC lipid metabolism-related molecular subtype analysis was conducted based on the 243 lipid metabolism genes collected from the Molecular Signatures Database. Several significant disparities in prognosis, clinicopathological characteristics, and immune and ferroptosis-related status were found across the three subtypes, especially between C1 and C3 subgroups. Differential expression analysis yielded 57 differentially expressed genes (DEGs) between C1 and C3 subtypes. GO and KEGG analysis was employed for functional annotation. Three of 21 prognostic DEGs (CXCL8, SLC10A1, and ADH4) were finally selected through machine-learning-based discovery and validation strategy. The risk score = (0.103) × expression value of CXCL8 + (−0.0333) × expression value of SLC10A1 + (−0.0812) × expression value of ADH4. We used these three to construct a HCC prognostic risk model, which stratified the patients of the validation cohort into two risk subtypes with significantly different overall survival. Our work provides possible significance of the lipid metabolism-associated model in stratifying patient prognosis and its feasibility to guide therapeutic selection. Frontiers Media S.A. 2022-09-28 /pmc/articles/PMC9554549/ /pubmed/36246607 http://dx.doi.org/10.3389/fgene.2022.1005271 Text en Copyright © 2022 Xiong, Wang, Li, Zheng, Cheng, Liu and Yang. 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 | Genetics Xiong, Ronghong Wang, Hui Li, Ying Zheng, Jingpeng Cheng, Yating Liu, Shunfang Yang, Guohua Machine learning-based transcriptome analysis of lipid metabolism biomarkers for the survival prediction in hepatocellular carcinoma |
title | Machine learning-based transcriptome analysis of lipid metabolism biomarkers for the survival prediction in hepatocellular carcinoma |
title_full | Machine learning-based transcriptome analysis of lipid metabolism biomarkers for the survival prediction in hepatocellular carcinoma |
title_fullStr | Machine learning-based transcriptome analysis of lipid metabolism biomarkers for the survival prediction in hepatocellular carcinoma |
title_full_unstemmed | Machine learning-based transcriptome analysis of lipid metabolism biomarkers for the survival prediction in hepatocellular carcinoma |
title_short | Machine learning-based transcriptome analysis of lipid metabolism biomarkers for the survival prediction in hepatocellular carcinoma |
title_sort | machine learning-based transcriptome analysis of lipid metabolism biomarkers for the survival prediction in hepatocellular carcinoma |
topic | Genetics |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC9554549/ https://www.ncbi.nlm.nih.gov/pubmed/36246607 http://dx.doi.org/10.3389/fgene.2022.1005271 |
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