Prognostic Signature of Immune Genes and Immune-Related LncRNAs in Neuroblastoma: A Study Based on GEO and TARGET Datasets

The prognostic value of immune-related genes and lncRNAs in neuroblastoma has not been elucidated, especially in subgroups with different outcomes. This study aimed to explore immune-related prognostic signatures. Immune-related prognostic genes and lncRNAs were identified by univariate Cox regressi...

Full description

Saved in:
Bibliographic Details
Published in:Frontiers in oncology 2021-03, Vol.11, p.631546-631546
Main Authors: Zhong, Xiaodan, Tao, Ying, Chang, Jian, Zhang, Yutong, Zhang, Hao, Wang, Linyu, Liu, Yuanning
Format: Article
Language:English
Subjects:
immune-related
lncRNAs
neuroblastoma
Oncology
prognosis
validation
Citations: Items that this one cites
Items that cite this one
Online Access:Get full text
Tags: Add Tag
No Tags, Be the first to tag this record!
cited_by cdi_FETCH-LOGICAL-c462t-f84da4c4317215a5a8c878e610d0412927ac4e1010675f0110307f86292f7e753
cites cdi_FETCH-LOGICAL-c462t-f84da4c4317215a5a8c878e610d0412927ac4e1010675f0110307f86292f7e753
container_end_page 631546
container_issue
container_start_page 631546
container_title Frontiers in oncology
container_volume 11
creator Zhong, Xiaodan
Tao, Ying
Chang, Jian
Zhang, Yutong
Zhang, Hao
Wang, Linyu
Liu, Yuanning
description The prognostic value of immune-related genes and lncRNAs in neuroblastoma has not been elucidated, especially in subgroups with different outcomes. This study aimed to explore immune-related prognostic signatures. Immune-related prognostic genes and lncRNAs were identified by univariate Cox regression analysis in the training set. The top 20 C-index genes and 17 immune-related lncRNAs were included in prognostic model construction, and random forest and the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithms were employed to select features. The risk score model was constructed and assessed using the Kaplan-Meier plot and the receiver operating characteristic curve. Functional enrichment analysis of the immune-related lncRNAs was conducted using the STRING database. In GSE49710, five immune genes (CDK4, PIK3R1, THRA, MAP2K2, and ULBP2) were included in the risk score five genes (RS5_G) signature, and eleven immune-related lncRNAs (LINC00260, FAM13A1OS, AGPAT4-IT1, DUBR, MIAT, TSC22D1-AS1, DANCR, MIR137HG, ERC2-IT1, LINC01184, LINC00667) were brought into risk score LncRNAs (RS_Lnc) signature. Patients were divided into high/low-risk score groups by the median. Overall survival and event/progression-free survival time were shortened in patients with high scores, both in training and validation cohorts. The same results were found in subgroups. In grouping ability assessment, the area under the curves (AUCs) in distinguishing different groups ranged from 0.737 to 0.94, better in discriminating MYCN status and high risk in training cohort (higher than 0.9). Multivariate Cox analysis demonstrated that RS5_G and RS_Lnc were the independent risk factors for overall and event/progression-free survival (all p-values
doi_str_mv 10.3389/fonc.2021.631546
format article
fullrecord <record><control><sourceid>proquest_doaj_</sourceid><recordid>TN_cdi_doaj_primary_oai_doaj_org_article_434cb30f79d54599ab06ff3ea53380c6</recordid><sourceformat>XML</sourceformat><sourcesystem>PC</sourcesystem><doaj_id>oai_doaj_org_article_434cb30f79d54599ab06ff3ea53380c6</doaj_id><sourcerecordid>2506285404</sourcerecordid><originalsourceid>FETCH-LOGICAL-c462t-f84da4c4317215a5a8c878e610d0412927ac4e1010675f0110307f86292f7e753</originalsourceid><addsrcrecordid>eNpVkk1vEzEQhlcIRKvSOyfkI5ek_vYuB6RQ0hApalEaJG7WxGuHrXbtYnuRyq_HaULV-mJr3plnPPZbVe8JnjJWNxcueDOlmJKpZERw-ao6pZTxScPZz9fPzifVeUp3uCwpMMHsbXXCmJKqaeRp9fd7DDsfUu4Muu12HvIYLQoOLYdh9BYtrLcJgW-Pgcna9pBti1berK9nCXUeXdsxhm0PKYcBPqEZus1j-4C-QCp5waPF_OaRsJmtF_MN-gq5KDm9q9446JM9P-5n1Y-r-eby22R1s1hezlYTwyXNE1fzFrjhjChKBAioTa1qKwluMSe0oQoMt6RMJpVwmJQJsXK1LIpTVgl2Vi0P3DbAnb6P3QDxQQfo9GMgxJ2GWObvreaMmy3DTjWt4KJpYIulc8yCKC-OjSyszwfW_bgdbGuszxH6F9CXiu9-6V34o1VTCypJAXw8AmL4PdqU9dAlY_sevA1j0lRgSWvBMS-p-JBqYkgpWvfUhmC9d4DeO0DvHaAPDiglH55f76ng_3-zfyzwqyc</addsrcrecordid><sourcetype>Open Website</sourcetype><iscdi>true</iscdi><recordtype>article</recordtype><pqid>2506285404</pqid></control><display><type>article</type><title>Prognostic Signature of Immune Genes and Immune-Related LncRNAs in Neuroblastoma: A Study Based on GEO and TARGET Datasets</title><source>PubMed Central</source><creator>Zhong, Xiaodan ; Tao, Ying ; Chang, Jian ; Zhang, Yutong ; Zhang, Hao ; Wang, Linyu ; Liu, Yuanning</creator><creatorcontrib>Zhong, Xiaodan ; Tao, Ying ; Chang, Jian ; Zhang, Yutong ; Zhang, Hao ; Wang, Linyu ; Liu, Yuanning</creatorcontrib><description>The prognostic value of immune-related genes and lncRNAs in neuroblastoma has not been elucidated, especially in subgroups with different outcomes. This study aimed to explore immune-related prognostic signatures. Immune-related prognostic genes and lncRNAs were identified by univariate Cox regression analysis in the training set. The top 20 C-index genes and 17 immune-related lncRNAs were included in prognostic model construction, and random forest and the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithms were employed to select features. The risk score model was constructed and assessed using the Kaplan-Meier plot and the receiver operating characteristic curve. Functional enrichment analysis of the immune-related lncRNAs was conducted using the STRING database. In GSE49710, five immune genes (CDK4, PIK3R1, THRA, MAP2K2, and ULBP2) were included in the risk score five genes (RS5_G) signature, and eleven immune-related lncRNAs (LINC00260, FAM13A1OS, AGPAT4-IT1, DUBR, MIAT, TSC22D1-AS1, DANCR, MIR137HG, ERC2-IT1, LINC01184, LINC00667) were brought into risk score LncRNAs (RS_Lnc) signature. Patients were divided into high/low-risk score groups by the median. Overall survival and event/progression-free survival time were shortened in patients with high scores, both in training and validation cohorts. The same results were found in subgroups. In grouping ability assessment, the area under the curves (AUCs) in distinguishing different groups ranged from 0.737 to 0.94, better in discriminating MYCN status and high risk in training cohort (higher than 0.9). Multivariate Cox analysis demonstrated that RS5_G and RS_Lnc were the independent risk factors for overall and event/progression-free survival (all p-values &lt;0.001). Correlation analysis showed that RS5_G and RS_Lnc were negatively associated with aDC, CD8+ T cells, but positively correlated with Th2 cells. Functional enrichment analyzes demonstrated that immune-related lncRNAs are mainly enriched in cancer-related pathways and immune-related pathways. We identified the immune-related prognostic signature RS5_G and RS_Lnc. The predicting and grouping ability is close to being even better than those reported in other studies, especially in subgroups. This study provided prognostic signatures that may help clinicians to choose optimal treatment strategies and showed a new insight for NB treatment. These results need further biological experiments and clinical validation.</description><identifier>ISSN: 2234-943X</identifier><identifier>EISSN: 2234-943X</identifier><identifier>DOI: 10.3389/fonc.2021.631546</identifier><identifier>PMID: 33767996</identifier><language>eng</language><publisher>Switzerland: Frontiers Media S.A</publisher><subject>immune-related ; lncRNAs ; neuroblastoma ; Oncology ; prognosis ; validation</subject><ispartof>Frontiers in oncology, 2021-03, Vol.11, p.631546-631546</ispartof><rights>Copyright © 2021 Zhong, Tao, Chang, Zhang, Zhang, Wang and Liu.</rights><rights>Copyright © 2021 Zhong, Tao, Chang, Zhang, Zhang, Wang and Liu 2021 Zhong, Tao, Chang, Zhang, Zhang, Wang and Liu</rights><lds50>peer_reviewed</lds50><oa>free_for_read</oa><woscitedreferencessubscribed>false</woscitedreferencessubscribed><citedby>FETCH-LOGICAL-c462t-f84da4c4317215a5a8c878e610d0412927ac4e1010675f0110307f86292f7e753</citedby><cites>FETCH-LOGICAL-c462t-f84da4c4317215a5a8c878e610d0412927ac4e1010675f0110307f86292f7e753</cites></display><links><openurl>$$Topenurl_article</openurl><openurlfulltext>$$Topenurlfull_article</openurlfulltext><thumbnail>$$Tsyndetics_thumb_exl</thumbnail><linktopdf>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7985261/pdf/$$EPDF$$P50$$Gpubmedcentral$$Hfree_for_read</linktopdf><linktohtml>$$Uhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7985261/$$EHTML$$P50$$Gpubmedcentral$$Hfree_for_read</linktohtml><link.rule.ids>230,314,723,776,780,881,27903,27904,53769,53771</link.rule.ids><backlink>$$Uhttps://www.ncbi.nlm.nih.gov/pubmed/33767996$$D View this record in MEDLINE/PubMed$$Hfree_for_read</backlink></links><search><creatorcontrib>Zhong, Xiaodan</creatorcontrib><creatorcontrib>Tao, Ying</creatorcontrib><creatorcontrib>Chang, Jian</creatorcontrib><creatorcontrib>Zhang, Yutong</creatorcontrib><creatorcontrib>Zhang, Hao</creatorcontrib><creatorcontrib>Wang, Linyu</creatorcontrib><creatorcontrib>Liu, Yuanning</creatorcontrib><title>Prognostic Signature of Immune Genes and Immune-Related LncRNAs in Neuroblastoma: A Study Based on GEO and TARGET Datasets</title><title>Frontiers in oncology</title><addtitle>Front Oncol</addtitle><description>The prognostic value of immune-related genes and lncRNAs in neuroblastoma has not been elucidated, especially in subgroups with different outcomes. This study aimed to explore immune-related prognostic signatures. Immune-related prognostic genes and lncRNAs were identified by univariate Cox regression analysis in the training set. The top 20 C-index genes and 17 immune-related lncRNAs were included in prognostic model construction, and random forest and the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithms were employed to select features. The risk score model was constructed and assessed using the Kaplan-Meier plot and the receiver operating characteristic curve. Functional enrichment analysis of the immune-related lncRNAs was conducted using the STRING database. In GSE49710, five immune genes (CDK4, PIK3R1, THRA, MAP2K2, and ULBP2) were included in the risk score five genes (RS5_G) signature, and eleven immune-related lncRNAs (LINC00260, FAM13A1OS, AGPAT4-IT1, DUBR, MIAT, TSC22D1-AS1, DANCR, MIR137HG, ERC2-IT1, LINC01184, LINC00667) were brought into risk score LncRNAs (RS_Lnc) signature. Patients were divided into high/low-risk score groups by the median. Overall survival and event/progression-free survival time were shortened in patients with high scores, both in training and validation cohorts. The same results were found in subgroups. In grouping ability assessment, the area under the curves (AUCs) in distinguishing different groups ranged from 0.737 to 0.94, better in discriminating MYCN status and high risk in training cohort (higher than 0.9). Multivariate Cox analysis demonstrated that RS5_G and RS_Lnc were the independent risk factors for overall and event/progression-free survival (all p-values &lt;0.001). Correlation analysis showed that RS5_G and RS_Lnc were negatively associated with aDC, CD8+ T cells, but positively correlated with Th2 cells. Functional enrichment analyzes demonstrated that immune-related lncRNAs are mainly enriched in cancer-related pathways and immune-related pathways. We identified the immune-related prognostic signature RS5_G and RS_Lnc. The predicting and grouping ability is close to being even better than those reported in other studies, especially in subgroups. This study provided prognostic signatures that may help clinicians to choose optimal treatment strategies and showed a new insight for NB treatment. These results need further biological experiments and clinical validation.</description><subject>immune-related</subject><subject>lncRNAs</subject><subject>neuroblastoma</subject><subject>Oncology</subject><subject>prognosis</subject><subject>validation</subject><issn>2234-943X</issn><issn>2234-943X</issn><fulltext>true</fulltext><rsrctype>article</rsrctype><creationdate>2021</creationdate><recordtype>article</recordtype><sourceid>DOA</sourceid><recordid>eNpVkk1vEzEQhlcIRKvSOyfkI5ek_vYuB6RQ0hApalEaJG7WxGuHrXbtYnuRyq_HaULV-mJr3plnPPZbVe8JnjJWNxcueDOlmJKpZERw-ao6pZTxScPZz9fPzifVeUp3uCwpMMHsbXXCmJKqaeRp9fd7DDsfUu4Muu12HvIYLQoOLYdh9BYtrLcJgW-Pgcna9pBti1berK9nCXUeXdsxhm0PKYcBPqEZus1j-4C-QCp5waPF_OaRsJmtF_MN-gq5KDm9q9446JM9P-5n1Y-r-eby22R1s1hezlYTwyXNE1fzFrjhjChKBAioTa1qKwluMSe0oQoMt6RMJpVwmJQJsXK1LIpTVgl2Vi0P3DbAnb6P3QDxQQfo9GMgxJ2GWObvreaMmy3DTjWt4KJpYIulc8yCKC-OjSyszwfW_bgdbGuszxH6F9CXiu9-6V34o1VTCypJAXw8AmL4PdqU9dAlY_sevA1j0lRgSWvBMS-p-JBqYkgpWvfUhmC9d4DeO0DvHaAPDiglH55f76ng_3-zfyzwqyc</recordid><startdate>20210309</startdate><enddate>20210309</enddate><creator>Zhong, Xiaodan</creator><creator>Tao, Ying</creator><creator>Chang, Jian</creator><creator>Zhang, Yutong</creator><creator>Zhang, Hao</creator><creator>Wang, Linyu</creator><creator>Liu, Yuanning</creator><general>Frontiers Media S.A</general><scope>NPM</scope><scope>AAYXX</scope><scope>CITATION</scope><scope>7X8</scope><scope>5PM</scope><scope>DOA</scope></search><sort><creationdate>20210309</creationdate><title>Prognostic Signature of Immune Genes and Immune-Related LncRNAs in Neuroblastoma: A Study Based on GEO and TARGET Datasets</title><author>Zhong, Xiaodan ; Tao, Ying ; Chang, Jian ; Zhang, Yutong ; Zhang, Hao ; Wang, Linyu ; Liu, Yuanning</author></sort><facets><frbrtype>5</frbrtype><frbrgroupid>cdi_FETCH-LOGICAL-c462t-f84da4c4317215a5a8c878e610d0412927ac4e1010675f0110307f86292f7e753</frbrgroupid><rsrctype>articles</rsrctype><prefilter>articles</prefilter><language>eng</language><creationdate>2021</creationdate><topic>immune-related</topic><topic>lncRNAs</topic><topic>neuroblastoma</topic><topic>Oncology</topic><topic>prognosis</topic><topic>validation</topic><toplevel>peer_reviewed</toplevel><toplevel>online_resources</toplevel><creatorcontrib>Zhong, Xiaodan</creatorcontrib><creatorcontrib>Tao, Ying</creatorcontrib><creatorcontrib>Chang, Jian</creatorcontrib><creatorcontrib>Zhang, Yutong</creatorcontrib><creatorcontrib>Zhang, Hao</creatorcontrib><creatorcontrib>Wang, Linyu</creatorcontrib><creatorcontrib>Liu, Yuanning</creatorcontrib><collection>PubMed</collection><collection>CrossRef</collection><collection>MEDLINE - Academic</collection><collection>PubMed Central (Full Participant titles)</collection><collection>Directory of Open Access Journals</collection><jtitle>Frontiers in oncology</jtitle></facets><delivery><delcategory>Remote Search Resource</delcategory><fulltext>fulltext</fulltext></delivery><addata><au>Zhong, Xiaodan</au><au>Tao, Ying</au><au>Chang, Jian</au><au>Zhang, Yutong</au><au>Zhang, Hao</au><au>Wang, Linyu</au><au>Liu, Yuanning</au><format>journal</format><genre>article</genre><ristype>JOUR</ristype><atitle>Prognostic Signature of Immune Genes and Immune-Related LncRNAs in Neuroblastoma: A Study Based on GEO and TARGET Datasets</atitle><jtitle>Frontiers in oncology</jtitle><addtitle>Front Oncol</addtitle><date>2021-03-09</date><risdate>2021</risdate><volume>11</volume><spage>631546</spage><epage>631546</epage><pages>631546-631546</pages><issn>2234-943X</issn><eissn>2234-943X</eissn><abstract>The prognostic value of immune-related genes and lncRNAs in neuroblastoma has not been elucidated, especially in subgroups with different outcomes. This study aimed to explore immune-related prognostic signatures. Immune-related prognostic genes and lncRNAs were identified by univariate Cox regression analysis in the training set. The top 20 C-index genes and 17 immune-related lncRNAs were included in prognostic model construction, and random forest and the Least Absolute Shrinkage and Selection Operator (LASSO) regression algorithms were employed to select features. The risk score model was constructed and assessed using the Kaplan-Meier plot and the receiver operating characteristic curve. Functional enrichment analysis of the immune-related lncRNAs was conducted using the STRING database. In GSE49710, five immune genes (CDK4, PIK3R1, THRA, MAP2K2, and ULBP2) were included in the risk score five genes (RS5_G) signature, and eleven immune-related lncRNAs (LINC00260, FAM13A1OS, AGPAT4-IT1, DUBR, MIAT, TSC22D1-AS1, DANCR, MIR137HG, ERC2-IT1, LINC01184, LINC00667) were brought into risk score LncRNAs (RS_Lnc) signature. Patients were divided into high/low-risk score groups by the median. Overall survival and event/progression-free survival time were shortened in patients with high scores, both in training and validation cohorts. The same results were found in subgroups. In grouping ability assessment, the area under the curves (AUCs) in distinguishing different groups ranged from 0.737 to 0.94, better in discriminating MYCN status and high risk in training cohort (higher than 0.9). Multivariate Cox analysis demonstrated that RS5_G and RS_Lnc were the independent risk factors for overall and event/progression-free survival (all p-values &lt;0.001). Correlation analysis showed that RS5_G and RS_Lnc were negatively associated with aDC, CD8+ T cells, but positively correlated with Th2 cells. Functional enrichment analyzes demonstrated that immune-related lncRNAs are mainly enriched in cancer-related pathways and immune-related pathways. We identified the immune-related prognostic signature RS5_G and RS_Lnc. The predicting and grouping ability is close to being even better than those reported in other studies, especially in subgroups. This study provided prognostic signatures that may help clinicians to choose optimal treatment strategies and showed a new insight for NB treatment. These results need further biological experiments and clinical validation.</abstract><cop>Switzerland</cop><pub>Frontiers Media S.A</pub><pmid>33767996</pmid><doi>10.3389/fonc.2021.631546</doi><tpages>1</tpages><oa>free_for_read</oa></addata></record>
fulltext fulltext
identifier ISSN: 2234-943X
ispartof Frontiers in oncology, 2021-03, Vol.11, p.631546-631546
issn 2234-943X
2234-943X
language eng
recordid cdi_doaj_primary_oai_doaj_org_article_434cb30f79d54599ab06ff3ea53380c6
source PubMed Central
subjects immune-related
lncRNAs
neuroblastoma
Oncology
prognosis
validation
title Prognostic Signature of Immune Genes and Immune-Related LncRNAs in Neuroblastoma: A Study Based on GEO and TARGET Datasets
url http://sfxeu10.hosted.exlibrisgroup.com/loughborough?ctx_ver=Z39.88-2004&ctx_enc=info:ofi/enc:UTF-8&ctx_tim=2025-01-27T12%3A48%3A17IST&url_ver=Z39.88-2004&url_ctx_fmt=infofi/fmt:kev:mtx:ctx&rfr_id=info:sid/primo.exlibrisgroup.com:primo3-Article-proquest_doaj_&rft_val_fmt=info:ofi/fmt:kev:mtx:journal&rft.genre=article&rft.atitle=Prognostic%20Signature%20of%20Immune%20Genes%20and%20Immune-Related%20LncRNAs%20in%20Neuroblastoma:%20A%20Study%20Based%20on%20GEO%20and%20TARGET%20Datasets&rft.jtitle=Frontiers%20in%20oncology&rft.au=Zhong,%20Xiaodan&rft.date=2021-03-09&rft.volume=11&rft.spage=631546&rft.epage=631546&rft.pages=631546-631546&rft.issn=2234-943X&rft.eissn=2234-943X&rft_id=info:doi/10.3389/fonc.2021.631546&rft_dat=%3Cproquest_doaj_%3E2506285404%3C/proquest_doaj_%3E%3Cgrp_id%3Ecdi_FETCH-LOGICAL-c462t-f84da4c4317215a5a8c878e610d0412927ac4e1010675f0110307f86292f7e753%3C/grp_id%3E%3Coa%3E%3C/oa%3E%3Curl%3E%3C/url%3E&rft_id=info:oai/&rft_pqid=2506285404&rft_id=info:pmid/33767996&rfr_iscdi=true