基于生物信息学筛选并验证肺结核铁死亡相关长链非编码RNA及与免疫浸润的相关性分析
Bioinformatics-based screening and validation of ferroptosis-associated long noncoding RNA in pulmonary tuberculosis and correlation analysis with immune infiltration
魏星 1龚大彩 1郑兰 1青措 2吴瑕2
作者信息
- 1. 成都医学院第三附属医院成都市郫都区人民医院检验科,四川成都 611730
- 2. 成都医学院第三附属医院成都市郫都区人民医院呼吸内科,四川成都 611730
- 折叠
摘要
目的 基于生物信息学探讨肺结核铁死亡相关长链非编码RNA(lncRNA),并分析其与免疫细胞浸润的相关性.方法 收集2022年11月至2023年3月于成都市郫都区人民医院呼吸内科收治的13例肺结核患者及同期13名健康志愿者全血样本,随机选取3例肺结核患者和3名健康志愿者全血样本进行全基因组测序.对测序数据进行分析,筛选差异lncRNA和差异mRNA,并绘制火山图和热图.通过维恩图筛选肺结核铁死亡相关基因,进行基因本体富集分析和京都基因与基因组百科全书富集分析.筛选肺结核铁死亡关键基因,分析肺结核患者血液样本免疫细胞浸润情况.采用Spearman相关分析筛选获得肺结核铁死亡相关lncRNA,并采用外部数据集GSE54992进行验证及实时荧光定量聚合酶链反应进行检测,验证筛选lncRNA的表达情况和诊断价值.结果 全基因组测序显示,共得到636个差异lncRNA和1 530个差异mRNA,与铁死亡基因取交集,得到133个共同基因.富集分析显示,肺结核铁死亡基因主要涉及细胞对化学压力的反应、应对氧化应激、铁死亡、自噬等信号通路.筛选出10个肺结核铁死亡关键基因,与之最相关的3个lncRNA分别是MIATNB、LINC00667和LINC01465.肺结核组和对照组在17种免疫细胞中有表达.MIATNB与记忆B细胞(r=0.42)、单核细胞(r=0.49)呈正相关(P＜0.05),LINC01465与记忆B细胞呈正相关(r=0.35,P＜0.05),LINC00667与幼稚B细胞呈负相关(r=-0.42,P＜0.05).验证集GSE54992中,肺结核组MIATNB相对表达量高于对照组(P＜0.05);受试者操作特征曲线分析显示,MIATNB在肺结核中有较好的诊断价值.试验组MIATNB相对表达量高于对照组(P＜0.01).结论 通过全基因组测序联合生物信息学筛选出肺结核铁死亡相关lncRNA MIATNB,该基因在肺结核患者中高表达,与细胞免疫浸润密切相关,可能是肺结核诊断和治疗的潜在分子生物标志物.
Abstract
Objective To explore ferroptosis-associated long noncoding RNA(lncRNA)in pulmonary tuberculosis based on bioinformatics,and analyze its correlation with immune cell infiltration.Methods Whole blood samples were collected from 13 tuberculosis patients and 13 healthy volunteers admitted to Department of Respiratory Medicine in Chengdu Pidu District People's Hospital from November 2022 to March 2023.Whole blood samples from three tuberculosis patients and three healthy volunteers were randomly selected for whole genome sequencing.Sequencing data was analyzed,differential lncRNA and differential mRNA were screened,and volcano and heat maps were plotted.The ferroptosis-associated genes in pulmonary tuberculosis were screened by using Venn diagram,and gene ontology enrichment analysis and Kyoto Encyclopedia of Genes and Genomes enrichment analysis were performed.The ferroptosis-associated key genes in pulmonary tuberculosis were screened,and immune cell infiltration in blood samples of pulmonary tuberculosis patients was analyzed.Spearman correlation analysis was used to screen and obtain ferroptosis-associated lncRNA in pulmonary tuberculosis.The external dataset GSE54992 was used for validation,and real time fluorescent quantitative polymerase chain reaction was used for detection.The expression status and diagnostic value of the screened lncRNA were verified.Results Whole genome sequencing showed a total of 636 differentially expressed lncRNAs and 1 530 differentially expressed mRNAs,which were intersected with ferroptosis-associated genes to obtain 133 common genes.Enrichment analysis showed that ferroptosis-associated genes in pulmonary tuberculosis mainly involved signaling pathways such as cellular response to chemical stress,response to oxidative stress,iron death and autophagy.Ten ferroptosis-associated key genes in pulmonary tuberculosis were screened,and the three most relevant lncRNAs were MIATNB,LINC00667,and LINC01465.The tuberculosis group and the control group showed expression in 17 types of immune cells.MIATNB was positively correlated with memory B cells(r=0.42)and monocytes(r=0.49)(P＜0.05),LINC01465 was positively correlated with memory B cells(r=0.35,P＜0.05),and LINC00667 was negatively correlated with immature B cells(r=-0.42,P＜0.05).In the validation set GSE54992,the relative expression level of MIATNB in the tuberculosis group was higher than that in the control group(P＜0.05).The analysis of receiver operator characteristic curve showed that MIATNB had good diagnostic value in pulmonary tuberculosis.The relative expression level of MIATNB in the experimental group was higher than that in the control group(P＜0.01).Conclusion Screening of ferroptosis-associated lncRNA MIATNB in pulmonary tuberculosis through whole genome sequencing combined with bioinformatics.This gene is highly expressed in pulmonary tuberculosis patients and closely related to cellular immune infiltration,which may be a potential molecular biomarker for the diagnosis and treatment of pulmonary tuberculosis.
关键词
肺结核/铁死亡/长链非编码RNA/生物信息学Key words
Pulmonary tuberculosis/Ferroptosis/Long noncoding RNA/Bioinformatics引用本文复制引用
基金项目
四川省医学(青年创新)科研课题(Q21094)
成都市医学科研课题(2021139)
成都医学院-成都市郫都区人民医院联合科研基金项目(2021LHPJ-11)
出版年
2024
NETL
NSTL
万方数据