原发性骨髓纤维化相关基因和信号通路的生物信息学分析及临床验证  

Bioinformatic analysis and clinical verification of related genes and signaling pathways in primary myelofibrosis

作　　者：许晶[1] 万雪莹 任方刚[2] 冯劲宜 王宏伟[2] Xu Jing;Wan Xueying;Ren Fanggang;Feng Jinyi;Wang Hongwei(Department of Medical Cell Biology and Genetics,Shanxi Medical University,Taiyuan 030001,China;Institute of Hematology,the Second Hospital of Shanxi Medical University,Taiyuan 030001,China)

机构地区：[1]山西医科大学医学细胞生物与遗传学教研室,太原030001 [2]山西医科大学第二医院血液病研究所,太原030001

出　　处：《白血病．淋巴瘤》2024年第10期610-616,共7页Journal of Leukemia & Lymphoma

基　　金：山西省自然科学基金自由探索类青年项目(202203021212374)。

摘　　要：目的探讨原发性骨髓纤维化(PMF)相关基因和信号通路及其可能临床意义。方法从基因表达综合(GEO)数据库下载3个PMF的mRNA表达数据集(GSE26049、GSE61629、GSE53482),包括55个PMF患者和58个对照者外周血样本数据,应用在线工具GEO2R鉴定PMF患者和对照者间差异表达基因(DEG),对3个数据集共同DEG进行基因本体(GO)注释和京都基因与基因组百科全书(KEGG)通路富集分析,并构建蛋白互作(PPI)网络,通过cytoHubba程序中MCC方法和Degree方法分别计算PPI网络中各共同DEG的关键节点,选取排名前10的核心(hub)基因,从中获得两种方法共同hub基因。回顾性收集2017年9月至2021年6月就诊于山西医科大学第二医院的25例PMF患者和10例对照者(造血干细胞移植正常供体或缺铁性贫血患者)的外周血样本,采用反转录-荧光定量聚合酶链反应(RT-qPCR)检测各样本中上述筛选的共同hub基因表达水平,对两组间各基因在转录水平上的表达进行比较。结果从3个数据集中筛选出PMF患者和对照者间239个共同DEG,包括153个下调DEG和86个上调DEG。GO富集分析显示,共同的下调DEG在转录、翻译和成纤维细胞增殖的负调控等生物过程显著富集,上调DEG主要富集在蛋白泛素化和泛素依赖的蛋白分解代谢等过程。KEGG通路分析显示,上调的共同DEG和下调的共同DEG富集在PI3K/Akt信号通路、癌症通路和癌症转录调控异常等方面。MCC方法和Degree方法排名前10的hub基因中有8个是两方法共有的,包括6个下调共同DEG(TP53、MYC、ATM、FYN、PTPRC、ATRX)和2个上调共同DEG(VEGFA、FOXO3)。这8个共同hub基因主要参与PI3K/Akt信号通路、细胞周期和癌症转录调控信号通路。对临床样本进行RT-qPCR检测显示,与对照组相比,PMF患者6个下调的共同DEG mRNA相对表达量低,但差异均无统计学意义(均P>0.05);PMF组2个上调的共同DEG mRNA相对表达量高,差异均有统计学意义(U值分别为33Objective To explore the genes related to primary myelofibrosis(PMF)and signaling pathways as well as the possible clinical significance.Methods A total of 3 mRNA expression datasets of PMF(GSE26049,GSE61629 and GSE53482)were downloaded from Gene Expression Omnibus(GEO)database,including the data of peripheral blood samples from 55 PMF patients and 58 controls.The differentially expressed genes(DEG)between PMF patients and the controls were identified by using online tool GEO2R.Gene ontology(GO)annotation,Kyoto Encyclopedia of Genes and Genomes(KEGG)pathway enrichment analysis were performed on the common DEG of the 3 datasets,and then protein interaction(PPI)network was constructed.The key nodes of the common DEG in PPI network were calculated by using MCC method and Degree method in cytoHubba program;finally the top 10 hub genes were selected and the hub genes shared by the 2 methods were obtained.Peripheral blood samples of 25 PMF patients and 10 controls(normal hematopoietic stem cell transplant donors or iron deficiency anemia patients)admitted to the Second Hospital of Shanxi Medical University from September 2017 to June 2021 were retrospectively collected.Reverse transcription-fluorescence quantitative polymerase chain reaction(RT-qPCR)was used to detect the expression levels of 10 screened common hub genes in each sample,and the expressions of all genes at transcriptional level of the two groups were compared.Results A total of 239 common DEG between PMF patients and the controls were screened out in the 3 datasets,including 153 downregulated DEG and 86 upregulated DEG.The GO enrichment analysis showed that the common downregulated DEG were significantly enriched in negative regulation of transcription,translation and fibroblast proliferation,while the upregulated DEG were mainly enriched in protein ubiquitination and ubiquitin-dependent protein catabolic process.The KEGG pathway analysis indicated that the upregulated common DEG and downregulated common DEG were both enriched in PI3K/Akt signaling pathw

关 键 词：原发性骨髓纤维化 分子生物学 计算生物学 

分 类 号：R551.3[医药卫生—血液循环系统疾病]