A multiomic ferroptosis-associated prognostic signature incorporating epigenetic and transcriptional biomarkers for hepatocellular carcinoma
BackgroundFerroptosis was reported to have tremendous promise in the treatment and prognosis of hepatocellular carcinoma (HCC). Here, we identified a novel ferroptosis-related prognostic signature incorporating epigenetic and transcriptional biomarkers could help predicting survival of patients with...
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| Veröffentlicht in: | Translational cancer research 2022-07, Vol.11 (7), p.1889-1897 |
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| container_title | Translational cancer research |
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| creator | Chen, Jida Zhu, Xinli Chen, Danzhi Jin, Lidan Xu, Wenbo Yu, Wei Zhang, Liwen |
| description | BackgroundFerroptosis was reported to have tremendous promise in the treatment and prognosis of hepatocellular carcinoma (HCC). Here, we identified a novel ferroptosis-related prognostic signature incorporating epigenetic and transcriptional biomarkers could help predicting survival of patients with HCC. MethodsWe employed multi-omics and clinical data from The Cancer Genome Atlas (TCGA) database to identify the ferroptosis-associated methylation CpG sites associated with HCC survival using sure independence screening (SIS). Then we utilized Kaplan-Meier curves to evaluate the prognostic significance of gene expression and DNA methylation. Receiver operating characteristic (ROC) curve was used predicting the 3- and 5-year survival. Mediation analysis of ferroptosis-related methylation and transcriptional score was performed. ResultsWe firstly identified 114 significant CpG sites under the criteria of false discovery rate (FDR) |
| doi_str_mv | 10.21037/tcr-21-2882 |
| format | Article |
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Here, we identified a novel ferroptosis-related prognostic signature incorporating epigenetic and transcriptional biomarkers could help predicting survival of patients with HCC. MethodsWe employed multi-omics and clinical data from The Cancer Genome Atlas (TCGA) database to identify the ferroptosis-associated methylation CpG sites associated with HCC survival using sure independence screening (SIS). Then we utilized Kaplan-Meier curves to evaluate the prognostic significance of gene expression and DNA methylation. Receiver operating characteristic (ROC) curve was used predicting the 3- and 5-year survival. Mediation analysis of ferroptosis-related methylation and transcriptional score was performed. ResultsWe firstly identified 114 significant CpG sites under the criteria of false discovery rate (FDR) <0.05 in training set. Then we screened out 5 candidate CpG sites in validation set for multivariate screening and stepwise regression. We found that the high-risk group had significantly shorter survival time than the low-risk group in the prognostic signature combined with epigenetic and transcriptional scores (HR =2.72 95% CI: 2.01-3.68, P=8.75E-11). And the predictive model involving clinical information, gene expression, and methylation data performed best for 3-year survival prediction (AUC =0.672) and 5-year survival prediction (AUC =0.742). ConclusionsOur results suggested a signature combining clinical information, ferroptosis-related gene expression, and methylation presented a superior ability for prognostic prediction in HCC, which may bring us novel tool and targets in the treatment of HCC.</description><identifier>ISSN: 2218-676X</identifier><identifier>EISSN: 2219-6803</identifier><identifier>DOI: 10.21037/tcr-21-2882</identifier><identifier>PMID: 35966333</identifier><language>eng</language><publisher>AME Publishing Company</publisher><subject>Original</subject><ispartof>Translational cancer research, 2022-07, Vol.11 (7), p.1889-1897</ispartof><rights>2022 Translational Cancer Research. All rights reserved. 2022 Translational Cancer Research.</rights><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c361t-7902beec2e28f4ae96c7e85fdd6915b6ec7b7405adac3f81e8bc334a4b40c6d33</citedby></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372242/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC9372242/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,727,780,784,885,27923,27924,53790,53792</link.rule.ids></links><search><creatorcontrib>Chen, Jida</creatorcontrib><creatorcontrib>Zhu, Xinli</creatorcontrib><creatorcontrib>Chen, Danzhi</creatorcontrib><creatorcontrib>Jin, Lidan</creatorcontrib><creatorcontrib>Xu, Wenbo</creatorcontrib><creatorcontrib>Yu, Wei</creatorcontrib><creatorcontrib>Zhang, Liwen</creatorcontrib><title>A multiomic ferroptosis-associated prognostic signature incorporating epigenetic and transcriptional biomarkers for hepatocellular carcinoma</title><title>Translational cancer research</title><description>BackgroundFerroptosis was reported to have tremendous promise in the treatment and prognosis of hepatocellular carcinoma (HCC). Here, we identified a novel ferroptosis-related prognostic signature incorporating epigenetic and transcriptional biomarkers could help predicting survival of patients with HCC. MethodsWe employed multi-omics and clinical data from The Cancer Genome Atlas (TCGA) database to identify the ferroptosis-associated methylation CpG sites associated with HCC survival using sure independence screening (SIS). Then we utilized Kaplan-Meier curves to evaluate the prognostic significance of gene expression and DNA methylation. Receiver operating characteristic (ROC) curve was used predicting the 3- and 5-year survival. Mediation analysis of ferroptosis-related methylation and transcriptional score was performed. ResultsWe firstly identified 114 significant CpG sites under the criteria of false discovery rate (FDR) <0.05 in training set. Then we screened out 5 candidate CpG sites in validation set for multivariate screening and stepwise regression. We found that the high-risk group had significantly shorter survival time than the low-risk group in the prognostic signature combined with epigenetic and transcriptional scores (HR =2.72 95% CI: 2.01-3.68, P=8.75E-11). And the predictive model involving clinical information, gene expression, and methylation data performed best for 3-year survival prediction (AUC =0.672) and 5-year survival prediction (AUC =0.742). ConclusionsOur results suggested a signature combining clinical information, ferroptosis-related gene expression, and methylation presented a superior ability for prognostic prediction in HCC, which may bring us novel tool and targets in the treatment of HCC.</description><subject>Original</subject><issn>2218-676X</issn><issn>2219-6803</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2022</creationdate><recordtype>article</recordtype><recordid>eNpVkU9rFjEQh4MotrS99QPk6MHV_NnNZi9CKVaFgheF3sJsdnYb3TdZJ1nB79APbd62CJ5mYB6emeHH2KUU75QUun9fPDVKNspa9YKdKiWHxlihXz72tjG9uTthFzn_EEIoKW0rzGt2orvBGK31KXu44od9LSEdguczEqWtpBxyAzknH6DgxDdKS0y5VCKHJULZCXmIPtGWCEqIC8ctLBjxiECceCGI2VPYqjjCysfqB_qJlPmciN_jBiV5XNd9BeIeyIdYiXP2aoY148VzPWPfbz5-u_7c3H799OX66rbx2sjS9INQI6JXqOzcAg7G92i7eZrMILvRoO_HvhUdTOD1bCXa0WvdQju2wptJ6zP24cm77eMBJ4-xHry6jUK98o9LENz_kxju3ZJ-u0H3SrWqCt48Cyj92jEXdwj5-A9ETHt2qheqtVp0pqJvn1BPKWfC-d8aKdxjhq5mWDt3zFD_BSoolTQ</recordid><startdate>202207</startdate><enddate>202207</enddate><creator>Chen, Jida</creator><creator>Zhu, Xinli</creator><creator>Chen, Danzhi</creator><creator>Jin, Lidan</creator><creator>Xu, Wenbo</creator><creator>Yu, Wei</creator><creator>Zhang, Liwen</creator><general>AME Publishing Company</general><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope></search><sort><creationdate>202207</creationdate><title>A multiomic ferroptosis-associated prognostic signature incorporating epigenetic and transcriptional biomarkers for hepatocellular carcinoma</title><author>Chen, Jida ; Zhu, Xinli ; Chen, Danzhi ; Jin, Lidan ; Xu, Wenbo ; Yu, Wei ; Zhang, Liwen</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c361t-7902beec2e28f4ae96c7e85fdd6915b6ec7b7405adac3f81e8bc334a4b40c6d33</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2022</creationdate><topic>Original</topic><toplevel>online_resources</toplevel><creatorcontrib>Chen, Jida</creatorcontrib><creatorcontrib>Zhu, Xinli</creatorcontrib><creatorcontrib>Chen, Danzhi</creatorcontrib><creatorcontrib>Jin, Lidan</creatorcontrib><creatorcontrib>Xu, Wenbo</creatorcontrib><creatorcontrib>Yu, Wei</creatorcontrib><creatorcontrib>Zhang, Liwen</creatorcontrib><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><jtitle>Translational cancer research</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Chen, Jida</au><au>Zhu, Xinli</au><au>Chen, Danzhi</au><au>Jin, Lidan</au><au>Xu, Wenbo</au><au>Yu, Wei</au><au>Zhang, Liwen</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>A multiomic ferroptosis-associated prognostic signature incorporating epigenetic and transcriptional biomarkers for hepatocellular carcinoma</atitle><jtitle>Translational cancer research</jtitle><date>2022-07</date><risdate>2022</risdate><volume>11</volume><issue>7</issue><spage>1889</spage><epage>1897</epage><pages>1889-1897</pages><issn>2218-676X</issn><eissn>2219-6803</eissn><abstract>BackgroundFerroptosis was reported to have tremendous promise in the treatment and prognosis of hepatocellular carcinoma (HCC). Here, we identified a novel ferroptosis-related prognostic signature incorporating epigenetic and transcriptional biomarkers could help predicting survival of patients with HCC. MethodsWe employed multi-omics and clinical data from The Cancer Genome Atlas (TCGA) database to identify the ferroptosis-associated methylation CpG sites associated with HCC survival using sure independence screening (SIS). Then we utilized Kaplan-Meier curves to evaluate the prognostic significance of gene expression and DNA methylation. Receiver operating characteristic (ROC) curve was used predicting the 3- and 5-year survival. Mediation analysis of ferroptosis-related methylation and transcriptional score was performed. ResultsWe firstly identified 114 significant CpG sites under the criteria of false discovery rate (FDR) <0.05 in training set. Then we screened out 5 candidate CpG sites in validation set for multivariate screening and stepwise regression. We found that the high-risk group had significantly shorter survival time than the low-risk group in the prognostic signature combined with epigenetic and transcriptional scores (HR =2.72 95% CI: 2.01-3.68, P=8.75E-11). And the predictive model involving clinical information, gene expression, and methylation data performed best for 3-year survival prediction (AUC =0.672) and 5-year survival prediction (AUC =0.742). ConclusionsOur results suggested a signature combining clinical information, ferroptosis-related gene expression, and methylation presented a superior ability for prognostic prediction in HCC, which may bring us novel tool and targets in the treatment of HCC.</abstract><pub>AME Publishing Company</pub><pmid>35966333</pmid><doi>10.21037/tcr-21-2882</doi><tpages>9</tpages><oa>free_for_read</oa></addata></record> |
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| title | A multiomic ferroptosis-associated prognostic signature incorporating epigenetic and transcriptional biomarkers for hepatocellular carcinoma |
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