Ziliang Shi, Zi Sang, Junmeng Xiao, Jianbin Hou, Mingfei Geng
{"title":"基于缺氧和凋亡相关基因预测肺腺癌患者的生存状态、免疫治疗反应和用药情况","authors":"Ziliang Shi, Zi Sang, Junmeng Xiao, Jianbin Hou, Mingfei Geng","doi":"10.1055/a-2458-7088","DOIUrl":null,"url":null,"abstract":"<p><p>To predict patient survival prognosis, we aimed to establish a novel set of gene features associated with hypoxia and apoptosis. RNA-seq and clinical data of LUAD were sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, while hypoxia and apoptosis-related genes were obtained from the Molecular Signatures Database (MsigDB). A 13-gene-prognostic model incorporating hypoxia and apoptosis genes was developed using univariate/multivariate Cox regression, Nonnegative Matrix Factorization (NMF) clustering, and LASSO regression. Patients were divided into high-risk (HR) and low-risk (LR) groups according to the median risk score. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed distinct biological processes between HR and LR groups, including hormone regulation and lipid metabolism pathways. Single sample gene set enrichment analysis (ssGSEA) indicated elevated cell infiltration levels of Neutrophils and T_helper_cells in the LR group, while NK cells and Th1cells were higher in the HR group. Immunophenoscore (IPS) and tumor immune dysfunction and exclusion (TIDE) analyses suggested potential benefits of immunotherapy for LR group patients. In conclusion, this prognostic feature integrating hypoxia- and apoptosis-related genes offers insights into predicting survival, immune status, and treatment response in LUAD patients, paving the way for personalized treatment strategies.</p>","PeriodicalId":12999,"journal":{"name":"Hormone and Metabolic Research","volume":" ","pages":"55-66"},"PeriodicalIF":2.0000,"publicationDate":"2025-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":"{\"title\":\"Prediction of the Survival Status, Immunotherapy Response, and Medication of Lung Adenocarcinoma Patients Based on Hypoxia- and Apoptosis-Related Genes.\",\"authors\":\"Ziliang Shi, Zi Sang, Junmeng Xiao, Jianbin Hou, Mingfei Geng\",\"doi\":\"10.1055/a-2458-7088\",\"DOIUrl\":null,\"url\":null,\"abstract\":\"<p><p>To predict patient survival prognosis, we aimed to establish a novel set of gene features associated with hypoxia and apoptosis. RNA-seq and clinical data of LUAD were sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, while hypoxia and apoptosis-related genes were obtained from the Molecular Signatures Database (MsigDB). A 13-gene-prognostic model incorporating hypoxia and apoptosis genes was developed using univariate/multivariate Cox regression, Nonnegative Matrix Factorization (NMF) clustering, and LASSO regression. Patients were divided into high-risk (HR) and low-risk (LR) groups according to the median risk score. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed distinct biological processes between HR and LR groups, including hormone regulation and lipid metabolism pathways. Single sample gene set enrichment analysis (ssGSEA) indicated elevated cell infiltration levels of Neutrophils and T_helper_cells in the LR group, while NK cells and Th1cells were higher in the HR group. Immunophenoscore (IPS) and tumor immune dysfunction and exclusion (TIDE) analyses suggested potential benefits of immunotherapy for LR group patients. In conclusion, this prognostic feature integrating hypoxia- and apoptosis-related genes offers insights into predicting survival, immune status, and treatment response in LUAD patients, paving the way for personalized treatment strategies.</p>\",\"PeriodicalId\":12999,\"journal\":{\"name\":\"Hormone and Metabolic Research\",\"volume\":\" \",\"pages\":\"55-66\"},\"PeriodicalIF\":2.0000,\"publicationDate\":\"2025-01-01\",\"publicationTypes\":\"Journal Article\",\"fieldsOfStudy\":null,\"isOpenAccess\":false,\"openAccessPdf\":\"\",\"citationCount\":\"0\",\"resultStr\":null,\"platform\":\"Semanticscholar\",\"paperid\":null,\"PeriodicalName\":\"Hormone and Metabolic Research\",\"FirstCategoryId\":\"3\",\"ListUrlMain\":\"https://doi.org/10.1055/a-2458-7088\",\"RegionNum\":4,\"RegionCategory\":\"医学\",\"ArticlePicture\":[],\"TitleCN\":null,\"AbstractTextCN\":null,\"PMCID\":null,\"EPubDate\":\"2024/11/22 0:00:00\",\"PubModel\":\"Epub\",\"JCR\":\"Q3\",\"JCRName\":\"ENDOCRINOLOGY & METABOLISM\",\"Score\":null,\"Total\":0}","platform":"Semanticscholar","paperid":null,"PeriodicalName":"Hormone and Metabolic Research","FirstCategoryId":"3","ListUrlMain":"https://doi.org/10.1055/a-2458-7088","RegionNum":4,"RegionCategory":"医学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"2024/11/22 0:00:00","PubModel":"Epub","JCR":"Q3","JCRName":"ENDOCRINOLOGY & METABOLISM","Score":null,"Total":0}
引用次数: 0
摘要
为了预测患者的生存预后,我们旨在建立一套与缺氧和细胞凋亡相关的新基因特征。LUAD的RNA-seq和临床数据来自癌症基因组图谱(TCGA)和基因表达总库(GEO)数据库,缺氧和凋亡相关基因来自分子特征数据库(MsigDB)。利用单变量/多变量 Cox 回归、非负矩阵因子化(NMF)聚类和 LASSO 回归建立了一个包含缺氧和凋亡基因的 13 基因预后模型。根据中位风险评分将患者分为高风险(HR)组和低风险(LR)组。基因本体(GO)和京都基因与基因组百科全书(KEGG)富集分析表明,HR 组和 LR 组之间存在不同的生物过程,包括激素调节和脂质代谢途径。单样本基因组富集分析(ssGSEA)表明,LR 组的中性粒细胞和 T_helper_cells细胞浸润水平升高,而 HR 组的 NK 细胞和 Th1cells 细胞浸润水平较高。免疫表观评分(IPS)和肿瘤免疫功能障碍与排斥(TIDE)分析表明,LR 组患者可能从免疫疗法中获益。总之,这种整合了缺氧和凋亡相关基因的预后特征为预测LUAD患者的生存、免疫状态和治疗反应提供了见解,为个性化治疗策略铺平了道路。
Prediction of the Survival Status, Immunotherapy Response, and Medication of Lung Adenocarcinoma Patients Based on Hypoxia- and Apoptosis-Related Genes.
To predict patient survival prognosis, we aimed to establish a novel set of gene features associated with hypoxia and apoptosis. RNA-seq and clinical data of LUAD were sourced from The Cancer Genome Atlas (TCGA) and Gene Expression Omnibus (GEO) databases, while hypoxia and apoptosis-related genes were obtained from the Molecular Signatures Database (MsigDB). A 13-gene-prognostic model incorporating hypoxia and apoptosis genes was developed using univariate/multivariate Cox regression, Nonnegative Matrix Factorization (NMF) clustering, and LASSO regression. Patients were divided into high-risk (HR) and low-risk (LR) groups according to the median risk score. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses revealed distinct biological processes between HR and LR groups, including hormone regulation and lipid metabolism pathways. Single sample gene set enrichment analysis (ssGSEA) indicated elevated cell infiltration levels of Neutrophils and T_helper_cells in the LR group, while NK cells and Th1cells were higher in the HR group. Immunophenoscore (IPS) and tumor immune dysfunction and exclusion (TIDE) analyses suggested potential benefits of immunotherapy for LR group patients. In conclusion, this prognostic feature integrating hypoxia- and apoptosis-related genes offers insights into predicting survival, immune status, and treatment response in LUAD patients, paving the way for personalized treatment strategies.
期刊介绍:
Covering the fields of endocrinology and metabolism from both, a clinical and basic science perspective, this well regarded journal publishes original articles, and short communications on cutting edge topics.
Speedy publication time is given high priority, ensuring that endocrinologists worldwide get timely, fast-breaking information as it happens.
Hormone and Metabolic Research presents reviews, original papers, and short communications, and includes a section on Innovative Methods. With a preference for experimental over observational studies, this journal disseminates new and reliable experimental data from across the field of endocrinology and metabolism to researchers, scientists and doctors world-wide.