应用生物信息学方法筛选结直肠癌关键基因
|
摘要
目的采用4个芯片数据集来挖掘结直肠癌差异基因,通过基因注释和蛋白相互作用网络构建找到关键基因。方法下载GEO芯片数据GSE4398、GSE21815、GSE32323、GSE44076,筛选结直肠癌和正常组织间差异表达的基因,采用R3.4.4软件进行数据处理和分析,通过取交集获得候选的差异基因,通过Funrich软件进行基因功能分析,通过String和Cytoscape软件进行基因编码蛋白的相互作用分析。结果通过差异基因分析并取4个GEO数据集的交集,一共获得430个差异表达基因,其中表达上调的基因277个,表达下调的基因153个。基因富集分析发现,表达上调的基因主要位于细胞核、细胞浆、微管、中心体和细胞外;主要参与纺锤体组装;主要参与调节趋化因子活性,在细胞周期、有丝分裂G1-G1/S期、M-M/G1期、G2/M期、DNA破坏关键节点及DNA复制等信号通路中富集。153个表达下调的基因主要富集在细胞外、参与代谢过程,发挥的分子功能主要是催化活性和配体依赖性核受体活性,下调基因没有富集在某条信号通路上。通过蛋白互作网络初步鉴定了CDK1、CCNB1、TOP2A、MAD2L1、TTK、BUB1B、AURKA、RRM2、UBE2C、ASPM等结直肠癌相关的关键基因。结论通过基因芯片结合生物信息学方法,发现了结直肠癌相关的关键基因,有助于明确结直肠癌发病的分子机制,这些关键基因也可作为结直肠癌的治疗靶点。
Objective To integrate four microarray sets to screen differentially expressed genes and to find key genes with gene annotation and protein-protein interaction network construction.Methods Datasets were download from GSE4398,GSE21815,GSE32323,GSE44076,data processing and analysis process were done with R3.4.4 software,the differentially expressed genes overlaps were outputted,gene function analysis were completed with Funrich software,further protein-protein interaction were done with String and Cytoscape software.Results A total of 430 differentially expressed genes were obtained by differential gene analysis with overlaps of four GEO datasets,of which 277 genes were up-regulated and 153 genes were down-regulated.Up-regulated genes were mainly enriched in the nucleus and cytoplasm,tubes,central body and cells;mainly involved in spindle assembly;mainly involved in regulating chemokine activity,cell cycle G1-G1/S phase and mitosis,M-M/G1 and G2/M phase,DNA damage checkpoint and DNA replication signaling pathway.The down-regulated genes were mainly concentrated in the extracellular and involved in the metabolic process,and their molecular functions were mainly catalytic activity and ligand-dependent nuclear receptor activity.The down-regulated genes were not concentrated in a certain signaling pathway.CDK1,CCNB1,TOP2 A,MAD2 L1,TTK,BUB1 B,AURKA,RRM2,UBE2 C,ASPM were identified as key genes related to colorectal cancer by protein interaction network.Conclusion The key genes of colorectal cancer can be obtained by the combination of genechip and bioinformatics analysis,which can help us determining the potential molecular mechanism of colorectal cancer,These candidate genes also can be used as therapeutic targets for colorectal cancer.
Objective To integrate four microarray sets to screen differentially expressed genes and to find key genes with gene annotation and protein-protein interaction network construction.Methods Datasets were download from GSE4398,GSE21815,GSE32323,GSE44076,data processing and analysis process were done with R3.4.4 software,the differentially expressed genes overlaps were outputted,gene function analysis were completed with Funrich software,further protein-protein interaction were done with String and Cytoscape software.Results A total of 430 differentially expressed genes were obtained by differential gene analysis with overlaps of four GEO datasets,of which 277 genes were up-regulated and 153 genes were down-regulated.Up-regulated genes were mainly enriched in the nucleus and cytoplasm,tubes,central body and cells;mainly involved in spindle assembly;mainly involved in regulating chemokine activity,cell cycle G1-G1/S phase and mitosis,M-M/G1 and G2/M phase,DNA damage checkpoint and DNA replication signaling pathway.The down-regulated genes were mainly concentrated in the extracellular and involved in the metabolic process,and their molecular functions were mainly catalytic activity and ligand-dependent nuclear receptor activity.The down-regulated genes were not concentrated in a certain signaling pathway.CDK1,CCNB1,TOP2 A,MAD2 L1,TTK,BUB1 B,AURKA,RRM2,UBE2 C,ASPM were identified as key genes related to colorectal cancer by protein interaction network.Conclusion The key genes of colorectal cancer can be obtained by the combination of genechip and bioinformatics analysis,which can help us determining the potential molecular mechanism of colorectal cancer,These candidate genes also can be used as therapeutic targets for colorectal cancer.
引文
[1]ARNOLD M,SIERRA M S,LAVERSANNE M,et al.Global patterns and trends in colorectal cancer incidence and mortality[J].Gut,2017,66(4):683-691.
[2]SIEGEL R L,MILLER K D,JEMAL A.Cancer statistics,2018[J].CA Cancer J Clin,2018,68(1):7-30.
[3]TO K K,TONG C W,WU M,et al.MicroRNAs in the prognosis and therapy of colorectal cancer:From bench to bedside[J].World J Gastroenterol,2018,24(27):2949-2973.
[4]LIANG B,LI C,ZHAO J.Identification of key pathways and genes in colorectal cancer using bioinformatics analysis[J].Med Oncol,2016,33(10):111-126.
[5]HONG Y,DOWNEY T,EU K W,et al.A metastasisprone signature for early-stage mismatch-repair proficient sporadic colorectal cancer patients and its implications for possible therapeutics[J].Clin Exp Metastasis,2010,27(2):83-90.
[6]IWAYA T,YOKOBORI T,NISHIDA N,et al.Downregulation of miR-144is associated with colorectal cancer progression via activation of mTOR signaling pathway[J].Carcinogenesis,2012,33(12):2391-2397.
[7]KOGO R,SHIMAMURA T,MIMORI K,et al.Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers[J].Cancer Res,2011,71(20):6320-6326.
[8]KHAMAS A,ISHIKAWA T,SHIMOKAWA K,et al.Screening for epigenetically masked genes in colorectal cancer Using 5-Aza-2′-deoxycytidine,microarray and gene expression profile[J].Cancer Geno Prote,2012,9(2):67-75.
[9]CLOSA A,CORDERO D,SANZ-PAMPLONA R,et al.I-dentification of candidate susceptibility genes for colorectal cancer through eQTL analysis[J].Carcinogenesis,2014,35(9):2039-2046.
[10]CORDERO D,SOLE X,CROUS-BOU M,et al.Large differences in global transcriptional regulatory programs of normal and tumor colon cells[J].BMC Cancer,2014,14(1):708-719.
[11]SANZ-PAMPLONA R,BERENGUER A,CORDERO D,et al.Aberrant gene expression in mucosa adjacent to tumor reveals a molecular crosstalk in colon cancer[J].Mol Cancer,2014,13(1):46-64.
[12]SOLE X,CROUS-BOU M,CORDERO D,et al.Discovery and validation of new potential biomarkers for early detection of colon cancer[J].PLoS One,2014,9(9):e106748-e106758.
[13]DUFFY M J.Use of biomarkers in screening for cancer[J].Adv Exp Med Biol,2015,867(1):27-39.
[14]BROWN A,GEIGER H.Chromosome integrity checkpoints in stem and progenitor cells:transitions upon differentiation,pathogenesis,and aging[J].Cell Mol Life Sci,2018,4(6):211-224.
[15]POPOVIC A,JAFFEE E M,ZAIDI N.Emerging strategies for combination checkpoint modulators in cancer immunotherapy[J].J Clin Invest,2018,128(8):3209-3218.
[16]WANG C,LIU Z,XU Z,et al.The role of chemokine receptor 9/chemokine ligand 25 signaling:from immune cells to cancer cells[J].Oncol Lett,2018,16(2):2071-2077.
[17]王水良.核受体的研究进展[J].遗传学报,2004,4(31):420-429.
[18]SUNG W W,LIN Y M,WU P R,et al.High nuclear/cytoplasmic ratio of Cdk1expression predicts poor prognosis in colorectal cancer patients[J].BMC cancer,2014,14(1):951.
[19]XIAO Z,XUE J,GU W Z,et al.Cyclin B1is an efficacypredicting biomarker for Chk1inhibitors[J].Biomarkers,2008,13(6):579-596.
[20]LI Y,BAI W,ZHANG J.MiR-200c-5p suppresses proliferation and metastasis of human hepatocellular carcinoma(HCC)via suppressing MAD2L1[J].Biomed Pharm,2017,92(1):1038-1044.
[21]ZHANG R,XU J,ZHAO J,et al.Proliferation and invasion of colon cancer cells are suppressed by knockdown of TOP2A[J].J Cell Biochem,2018,1(8):1-8.
[22]LING Y,ZHANG X,BAI Y,et al.Overexpression of Mps1in colon cancer cells attenuates the spindle assembly checkpoint and increases aneuploidy[J].Biochem Biophysical Res,2014,450(4):1690-1695.
[23]ZHANG X,LING Y,GUO Y,et al.Mps1kinase regulates tumor cell viability via its novel role in mitochondria[J].Cell Death Dis,2016,7(7):2292-2303.
[24]HAHN M M,VREEDE L,BEMELMANS S A,et al.Prevalence of germline mutations in the spindle assembly checkpoint gene BUB1Bin individuals with early-onset colorectal cancer[J].Genes Chrom Cancer,2016,55(11):855-863.
[25]KOH H M,JANG B G,HYUN C L,et al.Aurora kinase a is a prognostic marker in colorectal adenocarcinoma[J].J Pathol Transl Med,2017,51(1):32-39.
[26]NANA A W,WU S Y,YANG Y S,et al.Nano-Diamino-Tetrac(NDAT)enhances resveratrol-induced antiproliferation by action on the RRM2pathway in colorectal cancers[J].Horm Cancer,2018,5(7):25-34.
[27]CACCIOLA N A,CALABRESE C,MALAPELLE U,et al.UbcH10expression can predict prognosis and sensitivity to the antineoplastic treatment for colorectal cancer patients[J].Mole Carci,2016,55(5):793-807.
[28]KATO T A,OKAYASU R,JEGGO P A,et al.ASPM influences DNA double-strand break repair and represents apotential target for radiotherapy[J].Int J Radiat Biol,2011,87(12):1189-1195.
[2]SIEGEL R L,MILLER K D,JEMAL A.Cancer statistics,2018[J].CA Cancer J Clin,2018,68(1):7-30.
[3]TO K K,TONG C W,WU M,et al.MicroRNAs in the prognosis and therapy of colorectal cancer:From bench to bedside[J].World J Gastroenterol,2018,24(27):2949-2973.
[4]LIANG B,LI C,ZHAO J.Identification of key pathways and genes in colorectal cancer using bioinformatics analysis[J].Med Oncol,2016,33(10):111-126.
[5]HONG Y,DOWNEY T,EU K W,et al.A metastasisprone signature for early-stage mismatch-repair proficient sporadic colorectal cancer patients and its implications for possible therapeutics[J].Clin Exp Metastasis,2010,27(2):83-90.
[6]IWAYA T,YOKOBORI T,NISHIDA N,et al.Downregulation of miR-144is associated with colorectal cancer progression via activation of mTOR signaling pathway[J].Carcinogenesis,2012,33(12):2391-2397.
[7]KOGO R,SHIMAMURA T,MIMORI K,et al.Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers[J].Cancer Res,2011,71(20):6320-6326.
[8]KHAMAS A,ISHIKAWA T,SHIMOKAWA K,et al.Screening for epigenetically masked genes in colorectal cancer Using 5-Aza-2′-deoxycytidine,microarray and gene expression profile[J].Cancer Geno Prote,2012,9(2):67-75.
[9]CLOSA A,CORDERO D,SANZ-PAMPLONA R,et al.I-dentification of candidate susceptibility genes for colorectal cancer through eQTL analysis[J].Carcinogenesis,2014,35(9):2039-2046.
[10]CORDERO D,SOLE X,CROUS-BOU M,et al.Large differences in global transcriptional regulatory programs of normal and tumor colon cells[J].BMC Cancer,2014,14(1):708-719.
[11]SANZ-PAMPLONA R,BERENGUER A,CORDERO D,et al.Aberrant gene expression in mucosa adjacent to tumor reveals a molecular crosstalk in colon cancer[J].Mol Cancer,2014,13(1):46-64.
[12]SOLE X,CROUS-BOU M,CORDERO D,et al.Discovery and validation of new potential biomarkers for early detection of colon cancer[J].PLoS One,2014,9(9):e106748-e106758.
[13]DUFFY M J.Use of biomarkers in screening for cancer[J].Adv Exp Med Biol,2015,867(1):27-39.
[14]BROWN A,GEIGER H.Chromosome integrity checkpoints in stem and progenitor cells:transitions upon differentiation,pathogenesis,and aging[J].Cell Mol Life Sci,2018,4(6):211-224.
[15]POPOVIC A,JAFFEE E M,ZAIDI N.Emerging strategies for combination checkpoint modulators in cancer immunotherapy[J].J Clin Invest,2018,128(8):3209-3218.
[16]WANG C,LIU Z,XU Z,et al.The role of chemokine receptor 9/chemokine ligand 25 signaling:from immune cells to cancer cells[J].Oncol Lett,2018,16(2):2071-2077.
[17]王水良.核受体的研究进展[J].遗传学报,2004,4(31):420-429.
[18]SUNG W W,LIN Y M,WU P R,et al.High nuclear/cytoplasmic ratio of Cdk1expression predicts poor prognosis in colorectal cancer patients[J].BMC cancer,2014,14(1):951.
[19]XIAO Z,XUE J,GU W Z,et al.Cyclin B1is an efficacypredicting biomarker for Chk1inhibitors[J].Biomarkers,2008,13(6):579-596.
[20]LI Y,BAI W,ZHANG J.MiR-200c-5p suppresses proliferation and metastasis of human hepatocellular carcinoma(HCC)via suppressing MAD2L1[J].Biomed Pharm,2017,92(1):1038-1044.
[21]ZHANG R,XU J,ZHAO J,et al.Proliferation and invasion of colon cancer cells are suppressed by knockdown of TOP2A[J].J Cell Biochem,2018,1(8):1-8.
[22]LING Y,ZHANG X,BAI Y,et al.Overexpression of Mps1in colon cancer cells attenuates the spindle assembly checkpoint and increases aneuploidy[J].Biochem Biophysical Res,2014,450(4):1690-1695.
[23]ZHANG X,LING Y,GUO Y,et al.Mps1kinase regulates tumor cell viability via its novel role in mitochondria[J].Cell Death Dis,2016,7(7):2292-2303.
[24]HAHN M M,VREEDE L,BEMELMANS S A,et al.Prevalence of germline mutations in the spindle assembly checkpoint gene BUB1Bin individuals with early-onset colorectal cancer[J].Genes Chrom Cancer,2016,55(11):855-863.
[25]KOH H M,JANG B G,HYUN C L,et al.Aurora kinase a is a prognostic marker in colorectal adenocarcinoma[J].J Pathol Transl Med,2017,51(1):32-39.
[26]NANA A W,WU S Y,YANG Y S,et al.Nano-Diamino-Tetrac(NDAT)enhances resveratrol-induced antiproliferation by action on the RRM2pathway in colorectal cancers[J].Horm Cancer,2018,5(7):25-34.
[27]CACCIOLA N A,CALABRESE C,MALAPELLE U,et al.UbcH10expression can predict prognosis and sensitivity to the antineoplastic treatment for colorectal cancer patients[J].Mole Carci,2016,55(5):793-807.
[28]KATO T A,OKAYASU R,JEGGO P A,et al.ASPM influences DNA double-strand break repair and represents apotential target for radiotherapy[J].Int J Radiat Biol,2011,87(12):1189-1195.