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Novel tumor necrosis factor-related long non-coding RNAs signature for risk stratification and prognosis in glioblastoma

BACKGROUND: Tumor necrosis factor (TNF) is an inflammatory cytokine that can coordinate tissue homeostasis by co-regulating the production of cytokines, cell survival, or death. It widely expresses in various tumor tissues and correlates with the malignant clinical features of patients. As an import...

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Autores principales: Long, Shengrong, Wu, Bingbing, Yang, Liu, Wang, Lesheng, Wang, Bo, Yan, Yu, Jiang, Jiazhi, Yang, Bin, Zhou, Qiangqiang, Shi, Min, Liang, Wu, Wei, Wei, Li, Xiang
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10156969/
https://www.ncbi.nlm.nih.gov/pubmed/37153654
http://dx.doi.org/10.3389/fneur.2023.1054686
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author Long, Shengrong
Wu, Bingbing
Yang, Liu
Wang, Lesheng
Wang, Bo
Yan, Yu
Jiang, Jiazhi
Yang, Bin
Zhou, Qiangqiang
Shi, Min
Liang, Wu
Wei, Wei
Li, Xiang
author_facet Long, Shengrong
Wu, Bingbing
Yang, Liu
Wang, Lesheng
Wang, Bo
Yan, Yu
Jiang, Jiazhi
Yang, Bin
Zhou, Qiangqiang
Shi, Min
Liang, Wu
Wei, Wei
Li, Xiang
author_sort Long, Shengrong
collection PubMed
description BACKGROUND: Tumor necrosis factor (TNF) is an inflammatory cytokine that can coordinate tissue homeostasis by co-regulating the production of cytokines, cell survival, or death. It widely expresses in various tumor tissues and correlates with the malignant clinical features of patients. As an important inflammatory factor, the role of TNFα is involved in all steps of tumorigenesis and development, including cell transformation, survival, proliferation, invasion and metastasis. Recent research has showed that long non-coding RNAs (lncRNAs), defined as RNA transcripts >200 nucleotides that do not encode a protein, influence numerous cellular processes. However, little is known about the genomic profile of TNF pathway related-lncRNAs in GBM. This study investigated the molecular mechanism of TNF related-lncRNAs and their immune characteristics in glioblastoma multiforme (GBM) patients. METHODS: To identify TNF associations in GBM patients, we performed bioinformatics analysis of public databases - The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). The ConsensusClusterPlus, CIBERSORT, Estimate, GSVA and TIDE and first-order bias correlation and so on approaches were conducted to comprehensively characterize and compare differences among TNF-related subtypes. RESULTS: Based on the comprehensive analysis of TNF-related lncRNAs expression profiles, we constructed six TNF-related lncRNAs (C1RL-AS1, LINC00968, MIR155HG, CPB2-AS1, LINC00906, and WDR11-AS1) risk signature to determine the role of TNF-related lncRNAs in GBM. This signature could divide GBM patients into subtypes with distinct clinical and immune characteristics and prognoses. We identified three molecular subtypes (C1, C2, and C3), with C2 showing the best prognosis; otherwise, C3 showing the worst prognosis. Moreover, we assessed the prognostic value, immune infiltration, immune checkpoints, chemokines cytokines and enrichment analysis of this signature in GBM. The TNF-related lncRNA signature was tightly associated with the regulation of tumor immune therapy and could serve as an independent prognostic biomarker in GBM. CONCLUSION: This analysis provides a comprehensive understanding of the role of TNF-related characters, which may improve the clinical outcome of GBM patients.
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spelling pubmed-101569692023-05-05 Novel tumor necrosis factor-related long non-coding RNAs signature for risk stratification and prognosis in glioblastoma Long, Shengrong Wu, Bingbing Yang, Liu Wang, Lesheng Wang, Bo Yan, Yu Jiang, Jiazhi Yang, Bin Zhou, Qiangqiang Shi, Min Liang, Wu Wei, Wei Li, Xiang Front Neurol Neurology BACKGROUND: Tumor necrosis factor (TNF) is an inflammatory cytokine that can coordinate tissue homeostasis by co-regulating the production of cytokines, cell survival, or death. It widely expresses in various tumor tissues and correlates with the malignant clinical features of patients. As an important inflammatory factor, the role of TNFα is involved in all steps of tumorigenesis and development, including cell transformation, survival, proliferation, invasion and metastasis. Recent research has showed that long non-coding RNAs (lncRNAs), defined as RNA transcripts >200 nucleotides that do not encode a protein, influence numerous cellular processes. However, little is known about the genomic profile of TNF pathway related-lncRNAs in GBM. This study investigated the molecular mechanism of TNF related-lncRNAs and their immune characteristics in glioblastoma multiforme (GBM) patients. METHODS: To identify TNF associations in GBM patients, we performed bioinformatics analysis of public databases - The Cancer Genome Atlas (TCGA) and the Chinese Glioma Genome Atlas (CGGA). The ConsensusClusterPlus, CIBERSORT, Estimate, GSVA and TIDE and first-order bias correlation and so on approaches were conducted to comprehensively characterize and compare differences among TNF-related subtypes. RESULTS: Based on the comprehensive analysis of TNF-related lncRNAs expression profiles, we constructed six TNF-related lncRNAs (C1RL-AS1, LINC00968, MIR155HG, CPB2-AS1, LINC00906, and WDR11-AS1) risk signature to determine the role of TNF-related lncRNAs in GBM. This signature could divide GBM patients into subtypes with distinct clinical and immune characteristics and prognoses. We identified three molecular subtypes (C1, C2, and C3), with C2 showing the best prognosis; otherwise, C3 showing the worst prognosis. Moreover, we assessed the prognostic value, immune infiltration, immune checkpoints, chemokines cytokines and enrichment analysis of this signature in GBM. The TNF-related lncRNA signature was tightly associated with the regulation of tumor immune therapy and could serve as an independent prognostic biomarker in GBM. CONCLUSION: This analysis provides a comprehensive understanding of the role of TNF-related characters, which may improve the clinical outcome of GBM patients. Frontiers Media S.A. 2023-04-20 /pmc/articles/PMC10156969/ /pubmed/37153654 http://dx.doi.org/10.3389/fneur.2023.1054686 Text en Copyright © 2023 Long, Wu, Yang, Wang, Wang, Yan, Jiang, Yang, Zhou, Shi, Liang, Wei and Li. 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 Neurology
Long, Shengrong
Wu, Bingbing
Yang, Liu
Wang, Lesheng
Wang, Bo
Yan, Yu
Jiang, Jiazhi
Yang, Bin
Zhou, Qiangqiang
Shi, Min
Liang, Wu
Wei, Wei
Li, Xiang
Novel tumor necrosis factor-related long non-coding RNAs signature for risk stratification and prognosis in glioblastoma
title Novel tumor necrosis factor-related long non-coding RNAs signature for risk stratification and prognosis in glioblastoma
title_full Novel tumor necrosis factor-related long non-coding RNAs signature for risk stratification and prognosis in glioblastoma
title_fullStr Novel tumor necrosis factor-related long non-coding RNAs signature for risk stratification and prognosis in glioblastoma
title_full_unstemmed Novel tumor necrosis factor-related long non-coding RNAs signature for risk stratification and prognosis in glioblastoma
title_short Novel tumor necrosis factor-related long non-coding RNAs signature for risk stratification and prognosis in glioblastoma
title_sort novel tumor necrosis factor-related long non-coding rnas signature for risk stratification and prognosis in glioblastoma
topic Neurology
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10156969/
https://www.ncbi.nlm.nih.gov/pubmed/37153654
http://dx.doi.org/10.3389/fneur.2023.1054686
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