乳腺癌癌旁组织特异性表达基因分析
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摘要
癌症研究中常用癌旁组织(normal tissues adjacent to the tumour, NAT)作对照,而癌旁组织与无肿瘤的正常组织的基因表达谱是有差异的。癌旁组织特异性表达基因的存在通常会干扰传统的转录图谱研究,然而目前关于癌旁与无肿瘤组织的基因表达谱差异的研究相对较少。本研究对14例乳腺癌患者的癌组织、癌旁组织和对侧正常乳腺组织样本进行高深度RNA测序和分析,发现癌旁组织相比对侧正常乳腺组织有102个差异表达基因。基因富集和蛋白-蛋白互作分析揭示这些差异表达基因显著富集在肿瘤坏死因子(tumour necrosis factor,TNF)和上皮间质转化(epithelial-mesenchymal transition, EMT)等癌症相关的基因集中。通过比较癌旁组织与癌组织、癌旁组织与对侧正常乳腺组织的转录图谱,发现23个癌旁组织特异性高表达的基因,即癌旁特异性激活(tumour-adjacent specific activation, TASA)基因。这些基因显著富集在TNF基因集中,其中15个是新发现的基因。结果表明,TASA基因在乳腺癌癌旁组织中普遍存在,并且与免疫系统的TNF信号有关。癌旁中存在类肿瘤型表达模式的基因,这些基因可能与肿瘤形成有关,但是往往在肿瘤-癌旁成对研究中被遗漏。
Normal tissues adjacent to the tumour(NAT) are widely used as controls in comparative studies to search for cancer-associated genes. However, the gene expression profiles between NAT and non-tumour-bearing tissues are different. The presence of NAT-specific expressed genes often hinders traditional transcriptional profiles studies. Further,studies on the differences in gene expression profiles between NAT and tumour-free tissues are infrequently performed. In this study, we sequenced and analysed the transcriptomes of tumour tissues(T), matched NAT and contralateral breast normal tissues(CBN) of 14 breast cancer patients, and identified 102 differentially expressed genes(DEGs) between CBN and NAT. Gene enrichment and protein-protein interaction(PPI) analyses revealed that these DEGs are significantly enriched in TNF(tumour necrosis factor) signalling and EMT(epithelial-mesenchymal transition) gene sets closely associated with oncogenesis. Comparative analyses of the transcriptomic profiles between NAT and CBN, NAT and T identified 23 NAT-specific highly-expressed genes, namely tumour-adjacent specifically activated(TASA) genes. These genes were significantly enriched in TNF signalling gene set, and 15 of which have not been previously reported. The results indicate that TASA genes are common in adjacent tissues and are related to the TNF signalling in the immune system.The tumour-adjacent tissues harbour tumour-like expressed genes that could contribute to tumour initiation but are often missed in NAT-T pair-wise studies.
Normal tissues adjacent to the tumour(NAT) are widely used as controls in comparative studies to search for cancer-associated genes. However, the gene expression profiles between NAT and non-tumour-bearing tissues are different. The presence of NAT-specific expressed genes often hinders traditional transcriptional profiles studies. Further,studies on the differences in gene expression profiles between NAT and tumour-free tissues are infrequently performed. In this study, we sequenced and analysed the transcriptomes of tumour tissues(T), matched NAT and contralateral breast normal tissues(CBN) of 14 breast cancer patients, and identified 102 differentially expressed genes(DEGs) between CBN and NAT. Gene enrichment and protein-protein interaction(PPI) analyses revealed that these DEGs are significantly enriched in TNF(tumour necrosis factor) signalling and EMT(epithelial-mesenchymal transition) gene sets closely associated with oncogenesis. Comparative analyses of the transcriptomic profiles between NAT and CBN, NAT and T identified 23 NAT-specific highly-expressed genes, namely tumour-adjacent specifically activated(TASA) genes. These genes were significantly enriched in TNF signalling gene set, and 15 of which have not been previously reported. The results indicate that TASA genes are common in adjacent tissues and are related to the TNF signalling in the immune system.The tumour-adjacent tissues harbour tumour-like expressed genes that could contribute to tumour initiation but are often missed in NAT-T pair-wise studies.
引文
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[5]Aran D,Camarda R,Odegaard J,Paik H,Oskotsky B,Krings G,Goga A,Sirota M,Butte AJ.Comprehensive analysis of normal adjacent to tumor transcriptomes.Nat Commun,2017,8(1):1077.
[6]Slaughter DP,Southwick HW,Smejkal W.Field cancerization in oral stratified squamous epithelium;clinical implications of multicentric origin.Cancer,1953,6(5):963-968.
[7]Qi YX,Liu YB,Rong WH.RNA-Seq and its applications:a new technology for transcriptomics.Hereditas(Beijing),2011,33(11):1191-1202.祁云霞,刘永斌,荣威恒.转录组研究新技术:RNA-Seq及其应用.遗传,2011,33(11):1191-1202.
[8]Langmead B,Salzberg SL.Fast gapped-read alignment with Bowtie 2.Nat Methods,2012,9(4):357-359.
[9]Li B,Dewey CN.RSEM:accurate transcript quantification from RNA-Seq data with or without a reference genome.BMC Bioinform,2011,12:323.
[10]Nikolayeva O,Robinson MD.EdgeR for differential RNA-seq and ChIP-seq analysis:an application to stem cell biology.Methods Mol Biol,2014,1150:45-79.
[11]Szklarczyk D,Franceschini A,Wyder S,Forslund K,Heller D,Huerta-Cepas J,Simonovic M,Roth A,Santos A,Tsafou KP,Kuhn M,Bork P,Jensen LJ,von Mering C.STRING v10:protein-protein interaction networks,integrated over the tree of life.Nucleic Acids Res,2014,43(Database issue):447-452.
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[13]Consortium GT.The Genotype-Tissue Expression(GTEx)project.Nat Genet,2013,45(6):580-585.
[14]van Antwerp DJ,Martin SJ,Kafri T,Green DR,Verma IM.Suppression of TNF-alpha-induced apoptosis by NF-kappaB.Science,1996,274(5288):787-789.
[15]Jia Y,Zhou J,Luo X,Chen M,Chen Y,Wang J,Xiong H,Ying X,Hu W,Zhao W,Deng W,Wang L.KLF4overcomes tamoxifen resistance by suppressing MAPKsignaling pathway and predicts good prognosis in breast cancer.Cell Signal,2018,42:165-175.
[16]Delire B,St?rkel P.The Ras/MAPK pathway and hepatocarcinoma:pathogenesis and therapeutic implications.Eur J Clin Invest,2015,45(6):609-623.
[17]Foster KW,Frost AR,Mckie-Bell P,Lin CY,Engler JA,Grizzle WE,Ruppert JM.Increase of GKLF messenger RNA and protein expression during progression of breast cancer.Cancer Res,2000,60(22):6488-6495.
[18]Wang B,Zhao MZ,Cui NP,Lin DD,Zhang AY,Qin Y,Liu CY,Yan WT,Shi JH,Chen BP.Kruppel-like factor 4induces apoptosis and inhibits tumorigenic progression in SK-BR-3 breast cancer cells.FEBS Open Bio,2015,5:147-154.
[19]Smith LM,Wise SC,Hendricks DT,Sabichi AL,Bos T,Reddy P,Brown PH,Birrer MJ.CJun overexpression in MCF-7 breast cancer cells produces a tumorigenic,invasive and hormone resistant phenotype.Oncogene,1999,18(44):6063-6070.
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[21]Ma K.Embryonic left-right separation mechanism allows confinement of mutation-induced phenotypes to one lateral body half of bilaterians.Am J Med Genet A,2013,161A(12):3095-3114.