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食管鳞状细胞癌差异DNA甲基化位点初筛及异常甲基化谱的构建

徐若冰, 薛恒川, 王建平, 吴亮, 王建明

徐若冰, 薛恒川, 王建平, 吴亮, 王建明. 食管鳞状细胞癌差异DNA甲基化位点初筛及异常甲基化谱的构建[J]. 肿瘤防治研究, 2015, 42(01): 28-31. DOI: 10.3971/j.issn.1000-8578.2015.01.007
引用本文: 徐若冰, 薛恒川, 王建平, 吴亮, 王建明. 食管鳞状细胞癌差异DNA甲基化位点初筛及异常甲基化谱的构建[J]. 肿瘤防治研究, 2015, 42(01): 28-31. DOI: 10.3971/j.issn.1000-8578.2015.01.007
XU Ruobing, XUE Hengchuan, WANG Jianping, WU Liang, WANG Jianming. Screening of Differential DNA Methylation Profile and Construction of Aberrant Methylation Panel in Esophageal Squamous Cell Carcinoma[J]. Cancer Research on Prevention and Treatment, 2015, 42(01): 28-31. DOI: 10.3971/j.issn.1000-8578.2015.01.007
Citation: XU Ruobing, XUE Hengchuan, WANG Jianping, WU Liang, WANG Jianming. Screening of Differential DNA Methylation Profile and Construction of Aberrant Methylation Panel in Esophageal Squamous Cell Carcinoma[J]. Cancer Research on Prevention and Treatment, 2015, 42(01): 28-31. DOI: 10.3971/j.issn.1000-8578.2015.01.007

食管鳞状细胞癌差异DNA甲基化位点初筛及异常甲基化谱的构建

基金项目: 国家自然科学基金资助项目(81172268);江苏省高校自然科学研究重大项目基金资助(12KJA330001);江苏省高校优势学科建设工程基金项目(PAAD)
详细信息
    作者简介:

    徐若冰(1988-),女,硕士,主要从事肿瘤流行病学的研究

    通讯作者:

    王建明,E-mail: jmwang@njmu.edu.cn

  • 中图分类号: R735.1

Screening of Differential DNA Methylation Profile and Construction of Aberrant Methylation Panel in Esophageal Squamous Cell Carcinoma

  • 摘要: 目的 采用基因芯片技术初筛食管鳞状细胞癌和正常组织间差异DNA甲基化位点,构建特异性食管癌抑癌基因甲基化谱。方法 用Illumina公司450K芯片对食管鳞状细胞癌、癌旁及正常食管黏膜组织行DNA甲基化检测并行对照分析,共分析485 577个位点,按甲基化β差值和差异分值结合Genecards、Intogen等数据库筛选异常高基化位点,对筛选出的差异甲基化基因进一步采用飞行质谱法验证。结果 食管鳞状细胞癌和正常食管黏膜组织间差异显著的位点共33 717个,其中高甲基化位点27 670个,主要分布于基因体和启动子5'非翻译区。结合数据库对基因生物学功能的描述以及文献报道,初步筛选出包含TMEFF2、CDH13、ING2、CASZ1、IQGAP2、ADAMTS9、AIM2、TRIT1、KLF6、EBF3等在内的差异甲基化基因。其中AIM2基因3个CG位点的甲基化频率在病例和对照中的差异均无统计学意义。芯片检测中发现的CASZ1_CpG_5及其周围的多个CG位点在食管鳞状细胞癌组织中均呈现高甲基化状态。 结论 基因芯片技术可用于食管鳞状细胞癌差异甲基化位点的初筛,但构建的抑癌基因异常甲基化谱在应用前尚需进行大样本、多阶段验证。

     

    Abstract: Objective To screen differential DNA methylation between esophageal squamous cell carcinoma (ESCC) tisssues and normal esophageal tissues using gene-chip technology, and to construct aberrant methylation panel of tumor suppressor genes in esophageal squamous cell carcinoma. Methods Illumina 450K bead-chip was applied to detect methylation status in ESCC tissues and adjacent tissues from esophageal cancer patients and normal mucosa samples from healthy controls. A total of 485 577 loci sites were analyzed and compared. Aberrant hyper-methylated sites were filtrated according to delta beta value and diffscore, together with functional analysis based on Genecards and Intogen database. Screened genes were validated using mass spectrometry technology. Results A total of 33 713 differential methylated loci were found by comparing ESCC tissues and normal mucosa tissues, including 27 670 hyper-methylated sites, which mainly located in genosome and promoter 5' untranslated region. Considering description and literature reports of biological functions, a panel of aberrant methylation biomarkers was screened out, including TMEFF2,CDH13,ING2,CASZ1,IQGAP2,ADAMTS9,AIM2,TRIT1,KLF6,EBF3, etc. There was no significant difference in the methylation rate of three CG sites in AIM2 gene between cancer tissues and normal controls. CASZ1_CpG_5 together with other four surrounding CG sites showed significant higher methylated frequency in ESCC tissues detected by chip inspection. Conclusion Gene-chip technology could be applied for preliminary screening of differential methylated genes. However, aberrant methylation panel of genes in esophageal cancer should be further validated before being applied as a clinical biomarker.

     

  • [1] Laird PW. Cancer epigenetics[J]. Hum Mol Genet, 2005, 14 Spec No 1: R65-76.
    [2] Kim YH, Lee HC, Kim SY, et al. Epigenomic analysis of aberrantly methylated genes in colorectal cancer identifies genes commonly affected by epigenetic alterations[J]. Ann Surg Oncol, 20 11, 18(8): 2338-47.
    [3] Shah AK, Saunders NA, Barbour AP, et al. Early diagnostic biomarkers for esophageal adenocarcinoma--the current state of play[J]. Cancer Epidemiol Biomarkers Prev, 2013, 22(7): 11 85-209.
    [4] Jjingo D, Conley AB, Yi SV, et al. On the presence and role of human gene-body DNA methylation[J]. Oncotarget, 2012, 3(4): 46 2-74.
    [5] Doi A, Park IH, Wen B, et al. Differential methylation of tissueand cancer-specific CpG island shores distinguishes human induced pluripotent stem cells, embryonic stem cells and fibroblasts[J]. Nat Genet, 2009, 41(12): 1350-3.
    [6] Ji H, Ehrlich LI, Seita J, et al. Comprehensive methylome map of lineage commitment from haematopoietic progenitors[J]. Nature, 20 10, 467(7313): 338-42.
    [7] Okano T, Gemma A, Hosoya Y, et al. Alterations in novel candidate tumor suppressor genes, ING1 and ING2 in human lung cancer[J]. Oncol Rep, 2006, 15(3): 545-9.
    [8] Borkosky SS, Gunduz M, Nagatsuka H, et al. Frequent deletion of ING2 locus at 4q35.1 associates with advanced tumor stage in head and neck squamous cell carcinoma[J]. J Cancer Res Clin Oncol, 2009, 135(5): 703-13.
    [9] Lu F, Dai DL, Martinka M, et al. Nuclear ING2 expression is reduced in human cutaneous melanomas[J]. Br J Cancer, 2006, 95 (1): 80-6.
    [10] Chen IF, Ou-Yang F, Hung JY, et al. AIM2 suppresses human breast cancer cell proliferation in vitro and mammary tumor growth in a mouse model[J]. Mol Cancer Ther, 2006, 5(1): 1-7.
    [11] Jin Z, Cheng Y, Olaru A, et al. Promoter hypermethylation of CDH13 is a common, early event in human esophageal adenocarcinogenesis and correlates with clinical risk factors[J]. Int J Cancer, 2008, 123(10): 2331-6.
    [12] Cho YG, Kim CJ, Park CH, et al. Genetic alterations of the KLF6 gene in gastric cancer[J]. Oncogene, 2005, 24(28): 4588-90.
    [13] Narla G, Heath KE, Reeves HL, et al. KLF6, a candidate tumor suppressor gene mutated in prostate cancer[J]. Science, 2001, 29 4(5551): 2563-6.
    [14] Reeves HL, Narla G, Ogunbiyi O, et al. Kruppel-like factor 6 (KLF6) is a tumor-suppressor gene frequently inactivated in colorectal cancer[J]. Gastroenterology, 2004, 126(4): 1090-103.
    [15] Spinola M, Galvan A, Pignatiello C, et al. Identification and functional characterization of the candidate tumor suppressor gene TRIT1 in human lung cancer[J]. Oncogene, 2005, 24(35): 5502-9.
    [16] Lin K, Taylor JR Jr, Wu TD, et al. TMEFF2 is a PDGF-AA binding protein with methylation-associated gene silencing in multiple cancer types including glioma[J]. PLoS One, 2011, 6(4): e18608.
    [17] Tsunoda S, Smith E, De Young NJ, et al. Methylation of CLDN6, FBN2, RBP1, RBP4, TFPI2, and TMEFF2 in esophageal squamous cell carcinoma[J]. Oncol Rep, 2009, 21(4): 1067-73.
    [18] Liu Z, Yang X, Li Z, et al. CASZ1, a candidate tumor-suppressor gene, suppresses neuroblastoma tumor growth through reprogramming gene expression[J]. Cell Death Differ, 2011, 18 (7): 1174-83.
    [19] Lung HL, Lo PH, Xie D, et al. Characterization of a novel epigenetically-silenced, growth-suppressive gene, ADAMTS9, and its association with lymph node metastases in nasopharyngeal carcinoma[J]. Int J Cancer, 2008, 123(2): 401-8.
    [20] Zhang C, Shao Y, Zhang W, et al. High-resolution melting analysis of ADAMTS9 methylation levels in gastric, colorectal, and pancreatic cancers[J]. Cancer Genet Cytogenet, 2010, 196(1): 38 -44.
    [21] Lo PH, Lung HL, Cheung AK, et al. Extracellular protease ADAMTS9 suppresses esophageal and nasopharyngeal carcinoma tumor formation by inhibiting angiogenesis[J]. Cancer Res, 2010, 70 (13): 5567-76.
    [22] Zhao LY, Niu Y, Santiago A, et al. An EBF3-mediated transcriptional program that induces cell cycle arrest and apoptosis[J]. Cancer Res, 2006, 66(19): 9445-52.
    [23] Jin SH, Akiyama Y, Fukamachi H, et al. IQGAP2 inactivation through aberrant promoter methylation and promotion of invasion in gastric cancer cells[J]. Int J Cancer, 2008, 122(5): 1040-6.
    [24] White CD, Khurana H, Gnatenko DV, et al. IQGAP1 and IQGAP2 are reciprocally altered in hepatocellular carcinoma[J]. BMC Gastroenterol, 2010, 10: 125.
    [25] Xie Y, Yan J, Cutz JC, et al. IQGAP2, A candidate tumour suppressor of prostate tumorigenesis[J]. Biochim Biophys Acta, 20 12, 1822(6): 875-84.
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出版历程
  • 收稿日期:  2013-12-01
  • 修回日期:  2014-01-21
  • 刊出日期:  2015-01-24

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