{"title":"TGF-β signaling-related signature for predicting prognosis and therapeutic response in lower-grade glioma.","authors":"Jian Yan, Xingwang Zhou, Hua Yang","doi":"10.21037/tcr-24-144","DOIUrl":null,"url":null,"abstract":"<p><strong>Background: </strong>Low-grade glioma (LGG) is a tumor that includes World Health Organization (WHO) grade II and III glioma, the treatment of which consistently results in relapse and drug resistance. Transforming growth factor-beta (TGF-β) is a multifunctional cytokine that regulates various cellular processes, which is found to be abnormal in tumors and promotes glioma development and progression. In this study, we aimed to systematically evaluate the importance of the genes associated with TGF-β in LGG and discover the role of these genes in the prognosis and treatment response of LGG.</p><p><strong>Methods: </strong>We used the \"Bioconductor Limma\" and \"consensusClusterplus\" R packages to screen differential and prognostic TGF-β-related genes. The R package \"GSVA\" was used to estimate the infiltration of immune cells and metabolism signature. The drug sensitivity for each TGF-β subtype was assessed by the R package \"pRRophetic\". The Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm was used to assess the copy number variation (CNV). The onco-print tool of the \"complexheatmap package\" was employed to visualize the somatic mutation and copy number alteration (CNA) among TGF clusters.</p><p><strong>Results: </strong>We reported three subtypes (A, B, and C) of LGG according to the classification of TGF-β-related genes, where subtype A showed the best prognosis. Subtype B was highly enriched in immune cells. Somatic variations were observed to be diverse in all of the three TGF-β subtypes. Furthermore, another three genes (<i>SHA</i>, <i>AC062021.1</i>, and <i>SNCG</i>) related to TGF-β were identified, which can be a superior predictor of prognosis with a risk score.</p><p><strong>Conclusions: </strong>LGG can be divided into three subtypes based on TGF-β signaling-related genes with distinct immune infiltration, metabolism, somatic variations, and prognosis.</p>","PeriodicalId":23216,"journal":{"name":"Translational cancer research","volume":"13 9","pages":"4985-5002"},"PeriodicalIF":1.5000,"publicationDate":"2024-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11483406/pdf/","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Translational cancer research","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.21037/tcr-24-144","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/9/9 0:00:00","PubModel":"Epub","JCR":"Q4","JCRName":"ONCOLOGY","Score":null,"Total":0}
引用次数: 0
Abstract
Background: Low-grade glioma (LGG) is a tumor that includes World Health Organization (WHO) grade II and III glioma, the treatment of which consistently results in relapse and drug resistance. Transforming growth factor-beta (TGF-β) is a multifunctional cytokine that regulates various cellular processes, which is found to be abnormal in tumors and promotes glioma development and progression. In this study, we aimed to systematically evaluate the importance of the genes associated with TGF-β in LGG and discover the role of these genes in the prognosis and treatment response of LGG.
Methods: We used the "Bioconductor Limma" and "consensusClusterplus" R packages to screen differential and prognostic TGF-β-related genes. The R package "GSVA" was used to estimate the infiltration of immune cells and metabolism signature. The drug sensitivity for each TGF-β subtype was assessed by the R package "pRRophetic". The Genomic Identification of Significant Targets in Cancer (GISTIC) algorithm was used to assess the copy number variation (CNV). The onco-print tool of the "complexheatmap package" was employed to visualize the somatic mutation and copy number alteration (CNA) among TGF clusters.
Results: We reported three subtypes (A, B, and C) of LGG according to the classification of TGF-β-related genes, where subtype A showed the best prognosis. Subtype B was highly enriched in immune cells. Somatic variations were observed to be diverse in all of the three TGF-β subtypes. Furthermore, another three genes (SHA, AC062021.1, and SNCG) related to TGF-β were identified, which can be a superior predictor of prognosis with a risk score.
Conclusions: LGG can be divided into three subtypes based on TGF-β signaling-related genes with distinct immune infiltration, metabolism, somatic variations, and prognosis.
期刊介绍：
Translational Cancer Research (Transl Cancer Res TCR; Print ISSN: 2218-676X; Online ISSN 2219-6803; http://tcr.amegroups.com/) is an Open Access, peer-reviewed journal, indexed in Science Citation Index Expanded (SCIE). TCR publishes laboratory studies of novel therapeutic interventions as well as clinical trials which evaluate new treatment paradigms for cancer; results of novel research investigations which bridge the laboratory and clinical settings including risk assessment, cellular and molecular characterization, prevention, detection, diagnosis and treatment of human cancers with the overall goal of improving the clinical care of cancer patients. The focus of TCR is original, peer-reviewed, science-based research that successfully advances clinical medicine toward the goal of improving patients'' quality of life. The editors and an international advisory group of scientists and clinician-scientists as well as other experts will hold TCR articles to the high-quality standards. We accept Original Articles as well as Review Articles, Editorials and Brief Articles.
求助内容：
应助结果提醒方式：
京公网安备 11010802042870号
