基于生物信息分析学方法筛选多发性骨髓瘤差异表达基因
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摘要
目的基于生物信息学筛选多发性骨髓瘤(MM)的差异表达基因,并分析差异表达基因的生物学功能及其调控通路。方法从GEO数据库中下载基因芯片数据GSE113295,应用GEO2R在线分析工具基于R语言的limma包分析基因的表达数据,以P <0. 05、|log FC|> 1. 5为条件筛选出MM样本中的差异表达基因(DEGs),运用DAVID数据库在线分析工具(https://david. ncifcrf. gov)对DEGs进行基因本体(GO)分析和基因功能百科全书(KEGG)通路富集分析,利用STRING在线分析工具(https://string-db. org/)和Cytoscape软件构建差异基因所调控的蛋白相互作用网络,基于cyto Hubba插件挖掘在生物学过程中发挥至关重要作用的关键基因。结果本研究共获得1 380个DEGs,其GO功能在生物学层面上主要介导免疫反应、细胞通讯、细胞黏附、信号转导过程;在细胞组分层面上主要参与细胞质膜组成、整合及胞外间隙的调控;在分子功能层面主要富集于G蛋白偶联受体活性、细胞黏附分子活性、结构因子活性、细胞因子活性。KEGG信号通路分析显示,差异表达基因主要调控神经活性配体—受体相互作用、细胞黏附分子(CAMs)、过氧化物酶体增殖物激活受体(PPAR)信号通路。在差异表达基因调控的复杂的蛋白互作网络(PPI)中筛选出7个关键基因BUB1B、PPARG、MAPK14、FYN、IL6、ITPKB、ZH2。结论 MM样本的差异表达基因有1 380个,其中BUB1B、PPARG、MAPK14、FYN、IL6、ITPKB、ZH2可能参与MM的发生发展,主要调控免疫反应、细胞黏附、细胞质膜组成和整合等生物学过程,可通过神经活性配体—受体相互作用、CAMs、PPAR信号通路进一步探索MM的发病机制,为进一步探索MM的治疗靶点和预后标志物提供理论依据。
Objective To screen out differentially expressed genes of multiple myeloma( MM) based on bioinformatics,and to analyze the biological function and regulatory pathway of differentially expressed genes. Methods The gene chip data GSE113295 were downloaded from the GEO database. GEO2R on-line analysis tool was used to analyze the gene expression data based on limma package in R language. The differentially expressed gene( DEGs) in MM samples was screened out under the condition of P < 0. 05 and | log FC | > 1. 5. The gene ontology( GO) analysis and gene function encyclopedia( KEGG) pathway enrichment analysis of DEGs were carried out by using DAVID database online analysis tool( https://david. ncifcrf. gov). We constructed the protein interaction network( PPI) regulated by differential genes by STRING online analysis tool( https://string-db. org/) and Cytoscape software,and excavated the key genes( hub gene)which played an important role in the biological process based on cyto Hubba plug-in mining. Results A total of 1 380 DEGs were obtained,and their GO function mainly mediated immune response,cell communication,cell adhesion and signal transduction at the biological level; at the cell component level,it was mainly involved in the composition,integration and regulation of extracellular space; at the molecular functional level,it was mainly enriched in G protein-coupled receptor activity,cell adhesion molecule activity,structural factor activity and cytokine activity. KEGG signal pathway analysis showed that the differentially expressed genes mainly regulated neuroactive ligand-receptor interaction and cell adhesion molecule( CAMs),and peroxisome proliferator-activated receptor( PPAR) signaling pathway. Finally,seven key genes BUB1 B,PPARG,MAPK14,FYN,IL6,ITPKB,and ZH2 were screened out from the complex protein interaction network( PPI) regulated by differentially expressed genes. Conclusions There are 1 380 differentially expressed genes in MM samples,in which,BUB1 B,PPARG,MAPK14,FYN,IL6,ITPKB,and ZH2 are more likely to be involved in the occurrence and development of MM,mainly regulating immune response,cell adhesion,plasma membrane composition and integration. We can further explore the pathogenesis of MM through the interaction of neuroactive ligand-receptor and CAMs and PPAR to provide the theoretical basis for further exploring the therapeutic targets and prognostic markers of MM.
Objective To screen out differentially expressed genes of multiple myeloma( MM) based on bioinformatics,and to analyze the biological function and regulatory pathway of differentially expressed genes. Methods The gene chip data GSE113295 were downloaded from the GEO database. GEO2R on-line analysis tool was used to analyze the gene expression data based on limma package in R language. The differentially expressed gene( DEGs) in MM samples was screened out under the condition of P < 0. 05 and | log FC | > 1. 5. The gene ontology( GO) analysis and gene function encyclopedia( KEGG) pathway enrichment analysis of DEGs were carried out by using DAVID database online analysis tool( https://david. ncifcrf. gov). We constructed the protein interaction network( PPI) regulated by differential genes by STRING online analysis tool( https://string-db. org/) and Cytoscape software,and excavated the key genes( hub gene)which played an important role in the biological process based on cyto Hubba plug-in mining. Results A total of 1 380 DEGs were obtained,and their GO function mainly mediated immune response,cell communication,cell adhesion and signal transduction at the biological level; at the cell component level,it was mainly involved in the composition,integration and regulation of extracellular space; at the molecular functional level,it was mainly enriched in G protein-coupled receptor activity,cell adhesion molecule activity,structural factor activity and cytokine activity. KEGG signal pathway analysis showed that the differentially expressed genes mainly regulated neuroactive ligand-receptor interaction and cell adhesion molecule( CAMs),and peroxisome proliferator-activated receptor( PPAR) signaling pathway. Finally,seven key genes BUB1 B,PPARG,MAPK14,FYN,IL6,ITPKB,and ZH2 were screened out from the complex protein interaction network( PPI) regulated by differentially expressed genes. Conclusions There are 1 380 differentially expressed genes in MM samples,in which,BUB1 B,PPARG,MAPK14,FYN,IL6,ITPKB,and ZH2 are more likely to be involved in the occurrence and development of MM,mainly regulating immune response,cell adhesion,plasma membrane composition and integration. We can further explore the pathogenesis of MM through the interaction of neuroactive ligand-receptor and CAMs and PPAR to provide the theoretical basis for further exploring the therapeutic targets and prognostic markers of MM.
引文
[1]中国医师协会血液科医师分会,中华医学会血液学分会,中国医师协会多发性骨髓瘤专业委员会.中国多发性骨髓瘤诊治指南(2017年修订)[J].中华内科杂志,2017,56(11):866-870.
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[6]Bhutani M,Zhang Q,Friend R,et al.Investigation of a gene signature to predict response to immunomodulatory derivatives for patients with multiple myeloma:an exploratory,retrospective study using microarray datasets from prospective clinical trials[J].Lancet Haematol,2017,4(9):e443-e451.
[7]Davis S,Meltzer PS.GEOquery:a bridge between the Gene Expression Omnibus(GEO)and BioConductor[J].Bioinformatics,2007,23(14):1846-1847.
[8]Ritchie ME,Phipson B,Wu D,et al.Limma powers differential expression analyses for RNA-sequencing and microarray studies[J].Nucleic Acids Res,2015,43(7):e47.
[9]范翩翩,罗夕茗,黄媛媛,等.双下肢水肿-反复骨折-M蛋白[J].中华骨质疏松和骨矿盐疾病杂志,2017,5(2):155-159.
[10]唐尚权,刘风琼,余涛,等.以骨折为首发表现的骨髓瘤门诊漏诊16例分析[J].中国误诊学杂志,2008,8(1):117-118.
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[12]Saltarella I,Morabito F,Giuliani N,et al.Prognostic or predictive value of circulating cytokines and angiogenic factors for initial treatment of multiple myeloma in the GIMEMA MM0305 randomized controlled trial[J].J Hematol Oncol,2019,12(1):4.
[13]Vermeulen R,Saberi Hosnijeh F,Bodinier B,et al.Pre-diagnostic blood immune markers,incidence and progression of B-cell lymphoma and multiple myeloma:univariate and functionally informed multivariate analyses[J].Int J Cancer,2018,143(6):1335-1347.
[14]Desantis V,Frassanito MA,Tamma R,et al.Rhu-Epo down-regulates pro-tumorigenic activity of cancer-associated fibroblasts in multiple myeloma[J].Ann Hematol,2018,97(7):1251-1258.
[15]Fan L,Hong J,Huang H,et al.High expression of phosphorylated extracellular signal-regulated kinase(ERK1/2)is associated with poor prognosis in newly diagnosed patients with multiple myeloma[J].Med Sci Monit,2017,23:2636-2643.
[16]Xiao W,Xu Z,Chang S,et al.Rafoxanide,an organohalogen drug,triggers apoptosis and cell cycle arrest in multiple myeloma by enhancing DNA damage responses and suppressing the p38MAPK pathway[J].Cancer Lett,2019,444:45-59.
[17]Zhang L,Xu Y,Wang L,et al.Role of RACK1 on cell proliferation,adhesion,and bortezomib-induced apoptosis in multiple myeloma[J].Int J Biol Macromol,2019,121:1077-1085.
[18]Yang Y,Gu C,Luo C,et al.BUB1B promotes multiple myeloma cell proliferation through CDC20/CCNB axis[J].Med Oncol,2015,32(3):81.
[19]Di Martino MT,Arbitrio M,Guzzi PH,et al.A peroxisome proliferator-activated receptor gamma(PPARG)polymorphism is associated with zoledronic acid-related osteonecrosis of the jaw in multiple myeloma patients:analysis by DMET microarray profiling[J].Br J Haematol,2011,154(4):529-533.
[20]Kastritis E,Melea P,Bagratuni T,et al.Genetic factors related with early onset of osteonecrosis of the jaw in patients with multiple myeloma under zoledronic acid therapy[J].Leuk Lymphoma,2017,58(10):2304-2309.
[21]Harmer D,Falank C,Reagan MR.Interleukin-6 interweaves the bone marrow microenvironment,bone loss,and multiple myeloma[J].Front Endocrinol(Lausanne),2018,9:788.
[22]Abdollahi P,Vandsemb EN,Hjort MA,et al.Src family kinases are regulated in multiple myeloma cells by phosphatase of regenerating Liver-3[J].Mol Cancer Res,2017,15(1):69-77.
[23]Li B,Shi C,Zhao J,et al.Long noncoding RNA CCAT1 functions as a ceRNA to antagonize the effect of miR-410 on the down-regulation of ITPKB in human HCT-116 and HCT-8 cells[J].Oncotarget,2017,8(54):92855-92863.
[24]Sun KK,Shen XJ,Yang D,et al.MicroRNA-31 triggers G2/Mcell cycle arrest,enhances the chemosensitivity and inhibits migration and invasion of human gastric cancer cells by downregulating the expression of zeste homolog 2(ZH2)[J].Arch Biochem Biophys,2019,663:269-275.
[2]Siegel RL,Miller KD,Jemal A.Cancer statistics,2018[J].CACancer J Clin,2018,68(1):7-30.
[3]Lakshman A,Painuly U,Rajkumar SV,et al.Natural history of multiple myeloma with de novo del(17p)[J].Blood Cancer J,2019,9(3):32.
[4]Zmorzynski S,Szudy-Szczyrek A,Popek-Marciniec S,et al.ACEinsertion/deletion polymorphism(rs4646994)is associated with the increased risk of multiple myeloma[J].Front Oncol,2019,9:44.
[5]Hu AX,Huang ZY,Liu P,et al.A new ten-gene risk fraction model serving as prognostic indicator for clinical outcome of multiple myeloma[J].Tumour Biol,2016,37(12):1-9.
[6]Bhutani M,Zhang Q,Friend R,et al.Investigation of a gene signature to predict response to immunomodulatory derivatives for patients with multiple myeloma:an exploratory,retrospective study using microarray datasets from prospective clinical trials[J].Lancet Haematol,2017,4(9):e443-e451.
[7]Davis S,Meltzer PS.GEOquery:a bridge between the Gene Expression Omnibus(GEO)and BioConductor[J].Bioinformatics,2007,23(14):1846-1847.
[8]Ritchie ME,Phipson B,Wu D,et al.Limma powers differential expression analyses for RNA-sequencing and microarray studies[J].Nucleic Acids Res,2015,43(7):e47.
[9]范翩翩,罗夕茗,黄媛媛,等.双下肢水肿-反复骨折-M蛋白[J].中华骨质疏松和骨矿盐疾病杂志,2017,5(2):155-159.
[10]唐尚权,刘风琼,余涛,等.以骨折为首发表现的骨髓瘤门诊漏诊16例分析[J].中国误诊学杂志,2008,8(1):117-118.
[11]徐静,瞿涛,王刚.多发性骨髓瘤致股骨干病理性骨折漏诊一例[J].中国医师进修杂志,2014(17):77-78.
[12]Saltarella I,Morabito F,Giuliani N,et al.Prognostic or predictive value of circulating cytokines and angiogenic factors for initial treatment of multiple myeloma in the GIMEMA MM0305 randomized controlled trial[J].J Hematol Oncol,2019,12(1):4.
[13]Vermeulen R,Saberi Hosnijeh F,Bodinier B,et al.Pre-diagnostic blood immune markers,incidence and progression of B-cell lymphoma and multiple myeloma:univariate and functionally informed multivariate analyses[J].Int J Cancer,2018,143(6):1335-1347.
[14]Desantis V,Frassanito MA,Tamma R,et al.Rhu-Epo down-regulates pro-tumorigenic activity of cancer-associated fibroblasts in multiple myeloma[J].Ann Hematol,2018,97(7):1251-1258.
[15]Fan L,Hong J,Huang H,et al.High expression of phosphorylated extracellular signal-regulated kinase(ERK1/2)is associated with poor prognosis in newly diagnosed patients with multiple myeloma[J].Med Sci Monit,2017,23:2636-2643.
[16]Xiao W,Xu Z,Chang S,et al.Rafoxanide,an organohalogen drug,triggers apoptosis and cell cycle arrest in multiple myeloma by enhancing DNA damage responses and suppressing the p38MAPK pathway[J].Cancer Lett,2019,444:45-59.
[17]Zhang L,Xu Y,Wang L,et al.Role of RACK1 on cell proliferation,adhesion,and bortezomib-induced apoptosis in multiple myeloma[J].Int J Biol Macromol,2019,121:1077-1085.
[18]Yang Y,Gu C,Luo C,et al.BUB1B promotes multiple myeloma cell proliferation through CDC20/CCNB axis[J].Med Oncol,2015,32(3):81.
[19]Di Martino MT,Arbitrio M,Guzzi PH,et al.A peroxisome proliferator-activated receptor gamma(PPARG)polymorphism is associated with zoledronic acid-related osteonecrosis of the jaw in multiple myeloma patients:analysis by DMET microarray profiling[J].Br J Haematol,2011,154(4):529-533.
[20]Kastritis E,Melea P,Bagratuni T,et al.Genetic factors related with early onset of osteonecrosis of the jaw in patients with multiple myeloma under zoledronic acid therapy[J].Leuk Lymphoma,2017,58(10):2304-2309.
[21]Harmer D,Falank C,Reagan MR.Interleukin-6 interweaves the bone marrow microenvironment,bone loss,and multiple myeloma[J].Front Endocrinol(Lausanne),2018,9:788.
[22]Abdollahi P,Vandsemb EN,Hjort MA,et al.Src family kinases are regulated in multiple myeloma cells by phosphatase of regenerating Liver-3[J].Mol Cancer Res,2017,15(1):69-77.
[23]Li B,Shi C,Zhao J,et al.Long noncoding RNA CCAT1 functions as a ceRNA to antagonize the effect of miR-410 on the down-regulation of ITPKB in human HCT-116 and HCT-8 cells[J].Oncotarget,2017,8(54):92855-92863.
[24]Sun KK,Shen XJ,Yang D,et al.MicroRNA-31 triggers G2/Mcell cycle arrest,enhances the chemosensitivity and inhibits migration and invasion of human gastric cancer cells by downregulating the expression of zeste homolog 2(ZH2)[J].Arch Biochem Biophys,2019,663:269-275.