WO2012097477A1 - 体外评价肿瘤转移或预后的方法及核苷酸 - Google Patents

体外评价肿瘤转移或预后的方法及核苷酸 Download PDF

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WO2012097477A1
WO2012097477A1 PCT/CN2011/000108 CN2011000108W WO2012097477A1 WO 2012097477 A1 WO2012097477 A1 WO 2012097477A1 CN 2011000108 W CN2011000108 W CN 2011000108W WO 2012097477 A1 WO2012097477 A1 WO 2012097477A1
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znf382
tumor
methylation
cpg island
gene
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PCT/CN2011/000108
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French (fr)
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邓大君
高艳红
张宝珍
刘兆君
周静
管振坡
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北京市肿瘤防治研究所
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Priority to PCT/CN2011/000108 priority Critical patent/WO2012097477A1/zh
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  • the present invention relates to a method for evaluating tumor metastatic ability or prognosis survival time in vitro and artificial nucleotides used.
  • BACKGROUND OF THE INVENTION The ability to metastasize a malignant tumor is an important factor in determining the prognosis of a patient.
  • the distant metastasis of the tumor is not only the main factor that causes the patient to lose the opportunity for surgical treatment, but also the basic cause of the treatment failure after the recurrence of the operation.
  • Establishing a method to predict the metastatic ability of malignant tumors is a long-term goal, and has important guiding value for the development of post-operative treatment programs for cancer patients.
  • the aberrant methylation of pl5, pl6, hMLH1 and other gene CpG islands is also found to cause epigenetic inactivation of these genes.
  • the total protein and total mRNA levels of the target gene often do not change significantly. Due to the sensitive detection method of CpG island methylation, the abnormal methylation of CpG islands in a few cells can be detected, which may play a special role in the molecular typing of tumors.
  • ZNF382 Zinc finger transcription factor ZNF382 plays a very important regulatory role in cell proliferation, differentiation and apoptosis, inhibiting multiple oncogenes by inhibiting NF- ⁇ and AP-1 signaling pathways (eg MYC) , MITF, HMGA2, CDK6, STAT3, STAT5B, ID1 and IKBKE) expression [Cancer Research 2010, 70 (16): 6516-6526], may be a proapoptotic tumor-associated gene, in a variety of human tumors For example, nasopharyngeal carcinoma, esophageal cancer, colon cancer, gastric cancer, and breast cancer are prone to methylation inactivation.
  • the object of the present invention is to provide a method for evaluating tumor metastasis ability or tumor prognosis survival time in vitro and artificial nucleotides used for accurately determining tumor metastasis ability in early stage, and providing assistance for tumor treatment.
  • the present invention provides a method for evaluating tumor metastasis ability or tumor prognosis survival time in vitro, characterized in that the method comprises the following steps:
  • step (c) Evaluate tumor metastasis or tumor prognosis survival time. Further, the method for evaluating the tumor metastasis ability or the prognosis survival time of the tumor patient in vitro is characterized in that the step (b) comprises: designing and synthesizing the human ZNF382 gene with chemical modification or methylation DNA enrichment technology The primers paired with the CpG island target sequence were used to amplify the human ZNF382 gene methylated CpG island by the primer PCR method.
  • step (c) comprises: when the ZNF382 gene methylated CpG island exists in the tumor tissue, the human body has strong ability to resist malignant tumor metastasis, prognosis The survival time is long, on the contrary, the human body has poor ability to resist malignant tumor metastasis, and the prognosis survival time is short.
  • the present invention also provides a pair of primers for measuring a methylated CpG island of the human ZNF382 gene, the base sequence of which is shown in SEQ ID NO. 1 and 2.
  • the unmethylated cytosine is chemically modified to a uracil region, and is used to amplify the region in the 5'-end CpG island of the ZNF382 gene.
  • Base state compatible with the CpG site at the 5'-end CpG island of the ZNF382 gene, the unmethylated cytosine is chemically modified to a uracil region, and is used to amplify the region in the 5'-end CpG island of the ZNF382 gene. Base state.
  • the present invention further provides a pair of primers for determining a methylated CpG island of the human ZNF382 gene, the base sequences of which are set forth in SEQ ID NOS. 3 and 4.
  • the unmethylated cytosine is chemically modified to the uracil region, and is used to amplify the region in the 5'-end CpG island of the ZNF382 gene.
  • Base state. The present invention further provides a primer set for determining a methylated CpG island of a human ZNF382 gene, comprising a pair of primers and probes, wherein a base sequence of a pair of primers is as shown in SEQ ID NO. 5 and 6; The base sequence is shown in SEQ ID NO.
  • the unmethylated cytosine is chemically modified to uracil, and is used to amplify the ZNF382 gene 5, the region in the CpG island.
  • Base state. The invention also provides a DNA molecule having the base sequence set forth in SEQ ID NO. 11, SEQ ID NO. 12, SEQ ID NO. 13 or SEQ ID NO.
  • SEQ ID NO. 11 is a positive sense strand methylation sequence of human ZNF382 gene CpG island sodium bisulfite modified
  • SEQ ID NO. 12 is a human ZNF382 gene CpG island sodium bisulfite modified positive sense strand unmethylated sequence SEQ ID NO.
  • SEQ ID NO. 13 is the antisense strand methylation sequence of human ZNF382 gene CpG island sodium bisulfite modified; SEQ ID NO. 13 is the anti-sense strand unmethylated sequence of human ZNF382 gene CpG island modification. Based on these sequences, PCR amplification primers or restriction sites for determining the presence of the methylated CpG island sequence of the ZNF382 gene can be designed.
  • the technical solution of the present invention is proposed based on the following research results: The hypothesis proposes that the occurrence of tumor has multi-factor, multi-path, multi-stage characteristics. The epigenetic characteristics and biological characteristics of cancer cells changed by different molecular pathways are also different, and the prognosis of tumor patients may also be different.
  • microsatellite highly unstable (MSI-H, associated with inactivation of DNA mismatch repair gene MLH1) has a higher prognosis than stable ones; prognosis of MGMT methylation-inactivated glioma patients with DNA repair gene Stronger than not losing.
  • the ZNF382 gene is a tumor-associated gene whose promoter region contains a CpG island. The gene maintains a non-methylated expression state in normal tissues, and the expression of the gene is significantly down-regulated in tumor tissues. We have found that up-regulation of ZNF382 expression can promote clues to cancer cell movement/invasion.
  • the cells in the host target organ are inactivated by methylation of the ZNF382 gene, it may affect the metastasis of the tumor and the survival time of the tumor patient. Therefore, by detecting the inactivation level of ZNF382 gene methylation in cancer tissues, it is possible to predict the body's ability to resist tumor cell metastasis and help prognosis, and become a new therapeutic target.
  • ZNF382 CpG island remains unmethylated in the normal gastric epithelial cell line (GES-1), whereas in gastric cancer cell lines (MGC803, BGC823, SGC7901, MKN45, MKN74, Hypermethylation occurred in AGS), suggesting that ZNF382 CpG island methylation is associated with the development of gastric cancer; in four colon cancer cell lines (Colo205, HCT116, RKO, SW480), ZNF382 CpG islands are all methylated, and almost All CpG sites are simultaneously fully methylated; 2 liver cancer cell lines
  • ZNF382 CpG island is completely methylated in A549 cells; prostate cancer cell line PC3 and leukemia cell line HL-60 are also partially methylated, and embryonic kidney cell line 293T remains completely unmethylated.
  • the state suggests that ZNF382 CpG island methylation plays a role in different types of tumors.
  • ZHPLC382 was performed in 54 cases of metastatic gastric cancer and 54 cases of non-metastatic gastric cancer by DHPLC.
  • Tissue DNA extraction DNA from tumor, ZNF382 CpG methylation positive control cells and unmethylated negative control cells were extracted separately;
  • the present inventors have found for the first time in the world that the presence of the ZNF382 gene methylated CpG island in cancer tissues is a marker that can be used to evaluate the metastatic tumor metastasis ability and prognosis survival time; using simple chemical modification-PCR amplification The technology can quickly detect whether the ZNF382 gene methylated CpG island is contained in the cancer tissue sample. Early and accurate evaluation of tumor metastasis ability and prognosis survival time, to help the treatment of tumors. BRIEF DESCRIPTION OF THE DRAWINGS
  • Figure 1 A is the ZNF382 gene CpG island.
  • Figure 1B is the ratio of methylated ZNF382 in gastric cancer and surgical margin tissue.
  • Figure 1C is a DHPLC chromatogram of PCR amplification products of gastric cancer and surgical margin tissue methylated ZNF382 (odd number indicates margin; even number indicates cancer; MB indicates M.ssII methylation positive control).
  • Figure 2 shows the results of sodium bisulfite-cloning sequencing of the PCR products of the A and B segments of the ZNF382 CpG island (top panel; scattered black bars are transcription-related methylation regions, and black elongated bars indicate methylated CpG DHPLC analysis chromatogram of the site and B-stage PCR products (bottom panel).
  • HCT116 and Caski ZNF382 fully methylated
  • HL60 and PC3 ZNF382 partially methylated
  • H1299 and GES-1 ZNF382 unmethylated.
  • Figure 3 shows the relationship between ZNF382 methylation and its transcription. Above: 22 human cell lines; lower panel: gastric cancer tissue (u, completely unmethylated; m, fully methylated; part m, partially methylated).
  • Figure 4 is a transient transfection of ZNF382 to increase the invasion/mobility of BGC823 cells (TransweU assay).
  • Figure 6 is a comparison of total survival time (months) in 108 patients with gastric cancer ZNF382 methylation positive and negative gastric cancer.
  • A Analysis of the results of denaturing high performance liquid chromatography (DHPLC);
  • B Analysis of the results of methylation-specific fluorescence quantitative PCR (MethyLight).
  • Figure 7 is a comparison of postoperative survival time (months) in 54 patients with non-metastatic gastric cancer with ZNF382 methylation positive and negative gastric cancer.
  • Figure 8 is a comparison of the overall survival rates of patients with positive and negative ZNF382 methylation in liver cancer tissues.
  • Figure 9 is a comparison of ZNF382 methylation levels in colon cancer, margins, and normal colon tissue (DHPLC method).
  • Figure 10 is a comparison of ZNF382 methylation copy number in colon cancer and margin tissue (MethyLight method).
  • BEST MODE FOR CARRYING OUT THE INVENTION Example 1 Measurement of gastric cancer tissue by DHPLC ZNF382 gene CpG island methylation sequence to evaluate tumor metastasis ability or prognosis survival time
  • Subjects 108 For frozen tissues of gastric cancer, 50% of patients have lymph node metastases and vascular tumor thrombus or distant metastases, and 50% of matched patients have no lymph node metastasis or vascular tumor thrombus. Distal metastases, complete clinical pathology data and follow-up data;
  • PCR primer design Design and synthesis of universal PCR primers without CpG site (SEQ ID NO. 11 and 12) according to human ZNF382 CpG island sodium bisulfite modified positive sense strand sequence (SEQ ID NO. 11 and 12)
  • PCR amplification hot-start PCR amplification of methylated and unmethylated ZNF382 CpG islands in the sample to be tested after modification;
  • the overall survival rate of ZNF382 methylation-positive patients with gastric cancer was significantly higher than that of methylation-negative patients.
  • the ZNF382 CpG island sequence is a marker that can be used to determine gastric cancer metastasis. Tumor metastasis ability or prognosis survival time can be evaluated. The results of SEQ ID NO. 1, 2 and SEQ ID NO. 3, 4 are the same.
  • Example 2 Determination of gastric cancer tissue by sodium bisulfite cloning and sequencing ZNF382 gene CpG island methylation to evaluate tumor metastasis ability or prognosis survival time
  • Example 3 Determination of gastric cancer tissue by MethyLight ZNF382 gene CpG island methylation to assess tumor metastatic ability or prognosis survival time
  • PCR primer design Design, synthesis of methylation-specific MethyLight primers (SEQ ID NOS. 5 and 6) and probes (SEQ ID NO. 13 and 14) according to human ZNF382 methylated CpG island modified sequence (SEQ ID NO. 13 and 14) ID NO. 7), quantitative determination of 96pb methylation fragment;
  • Subjects 37 non-metastatic or recurrent liver cancer tissues and 39 metastatic or recurrent liver cancer tissues;
  • Example 5 Determination of ZNF382 CpG island methylation by colon cancer tissue by DHPLC to evaluate tumor metastatic ability or prognosis survival time
  • Subjects 22 pairs of colon cancer and adjacent margin tissue;
  • Example 6 Determination of colon cancer tissue by MethyLight ZNF382 CpG island methylation to evaluate tumor metastatic ability or prognosis survival time

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Description

体外评价肿瘤转移或预后的方法及核苷酸
技术领域
本发明涉及一种体外评测肿瘤转移能力或预后生存时间长短的方法及 所用人工核苷酸。 背景技术 恶性肿瘤的转移能力是决定患者预后的重要因素。 肿瘤的远处转移既是 使患者失去手术治疗机会的主要因素, 也是手术后复发导致治疗失败的基本 原因。 建立预测恶性肿瘤的转移能力的方法是人们长期追求的目标, 对制定 肿瘤患者手术后治疗方案有重要指导价值。 根据肿瘤的病理形态学变化很难对患者手术后的转移和复发情况做出判 断, 人们对是否可用分子生物学的手段来对恶性肿瘤进行分子分型寄予了厚 望, 在 MMP7等基因的蛋白和 mRNA水平改变方面做出了诸多的努力。 尽 管国内外研究众多, 至今仍然缺乏能够早期准确识别恶性肿瘤转移能力的方 法。 在分子生物学飞速发展的今天, 人们对细胞癌变机制已经有了更加全面 的认识。 除去 p53、 APC等肿瘤抑制基因结构变异导致基因失活之外, 人们 发现 pl5、 pl6、 hMLHl等基因 CpG岛的异常甲基化也将导致这些基因的表 观遗传(epigenetic)失活。组织中存在这种表观遗传失活的细胞数目较少时, 目的基因的总蛋白和总 mRNA水平往往不会有明显变化。 由于 CpG岛甲基 化检测方法及其灵敏, 可检测到少数细胞中存在的 CpG岛异常甲基化变化, 在肿瘤的分子分型上可能发挥特殊作用。 锌指转录因子 ZNF382 (zinc finger transcription factor ZNF382)在细胞的增 殖、 分化和凋亡过程中起非常重要的调节作用, 通过抑制 NF-κΒ和 AP-1信 号通路来抑制多种癌基因 (如 MYC, MITF, HMGA2, CDK6, STAT3, STAT5B, ID1和 IKBKE)的表达 [Cancer Research 2010, 70 (16): 6516-6526],可能是一种 促凋亡的肿瘤相关基因, 在人类多种肿瘤中, 如鼻咽癌、 食管癌、 结肠癌、 胃癌、 乳腺癌, 易出现甲基化失活, 但目前未见利用 ZNF382甲基化失活来 测定机体抵御恶性肿瘤转移能力的报道。 发明的公开 本发明的目的是提供一种体外评测肿瘤转移能力或肿瘤预后生存时间 长短的方法及所用人工核苷酸, 以早期准确测定肿瘤转移能力, 对肿瘤的治 疗提供帮助。
为了达到上述目的, 本发明提出了如下技术方案: 本发明提供了一种体外评测肿瘤转移能力或肿瘤预后生存时间长短的方 法, 其特征是该方法包括下列步骤:
(a) 从肿瘤组织中提取基因组 DNA;
(b) 测定人 ZNF382基因甲基化 CpG岛的存在;
(c) 评测肿瘤转移能力或肿瘤预后生存时间长短。 进一步, 本发明的体外评测肿瘤转移能力或肿瘤患者预后生存时间长短 的方法, 其特征是步骤 (b) 包括: 利用化学修饰或甲基化 DNA富集技术, 设计并合成能够与人 ZNF382基因甲基化 CpG岛靶序列配对的引物,用该引 物 PCR法扩增人 ZNF382基因甲基化 CpG岛。 进一步, 本发明的体外评测肿瘤转移能力或肿瘤预后生存时间长短的方 法, 其特征是步骤 (c)包括: 肿瘤组织存在 ZNF382基因甲基化 CpG岛时, 则人体抵御恶性肿瘤转移能力强, 预后生存时间长, 反之则人体抵御恶性肿 瘤转移能力差, 预后生存时间短。 本发明的体外评测肿瘤转移能力或肿瘤预后生存时间长短的方法, 其中 所述的肿瘤是胃癌、 肝癌、 结肠癌或甲状腺癌。 本发明还提供了一对测定人 ZNF382基因甲基化 CpG岛的引物,其碱基 序列如 SEQ ID NO. 1和 2所示。 能够与 ZNF382基因 5'端 CpG岛中的不含 CpG 位点, 未甲基化胞嘧啶被化学修饰成尿嘧啶的区域互补, 用于扩增 ZNF382基因 5'端 CpG岛中所在区域胞嘧啶甲基化状态。 本发明进一步提供了一对测定人 ZNF382基因甲基化 CpG岛的引物,其 碱基序列如 SEQ ID NO. 3和 4所示。 能够与 ZNF382基因 5,端 CpG岛中的 不含 CpG位点, 未甲基化胞嘧啶被化学修饰成尿嘧啶的区域互补, 用于扩增 ZNF382基因 5'端 CpG岛中所在区域胞嘧啶甲基化状态。 本发明进一步提供了测定人 ZNF382基因甲基化 CpG岛的引物组,包括 一对引物及探针, 其中一对引物的碱基序列如 SEQ ID NO. 5和 6所示; 探牟 ·' 的碱基序列如 SEQ ID NO. 7所示。 能够与 ZNF382基因 5,端 CpG岛中的不 含 CpG 位点, 未甲基化胞嘧啶被化学修饰成尿嘧啶的区域互补, 用于扩增 ZNF382基因 5,端 CpG岛中所在区域胞嘧啶甲基化状态。 本发明也提供了一种 DNA分子,其碱基序列如 SEQ ID NO. 11、 SEQ ID NO. 12、 SEQ ID NO. 13或 SEQ ID NO. 14所示。 SEQ ID NO. 11是人 ZNF382 基因 CpG岛亚硫酸氢钠修饰后正意义链甲基化序列; SEQ ID NO. 12是人 ZNF382基因 CpG岛亚硫酸氢钠修饰后正意义链未甲基化序列; SEQ ID NO. 13是人 ZNF382基因 CpG岛亚硫酸氢钠修饰后反意义链甲基化序列; SEQ ID NO. 13是人 ZNF382基因 CpG岛修饰后反意义链未甲基化序列。根据这些序 列可设计出测定 ZNF382基因甲基化 CpG岛序列存在的 PCR扩增引物或者 酶切点。 为达上述目的, 本发明的技术方案是基于下述研究结果提出的: 假说提出: 肿瘤的发生具有多因素、 多途径、 多阶段的特征。 通过不同 分子路径改变癌变的细胞其表观遗传特征及其生物学特征也不同, 肿瘤患者 的预后也会存在差异。例如微卫星高度不稳定(MSI-H, 与 DNA错配修复基 因 MLH1失活有关)的结肠癌患者的预后比稳定者强; DNA修复基因 MGMT 甲基化失活的神经胶质瘤患者的预后比不失活者强。 ZNF382 基因是一种肿 瘤相关基因, 其启动子区包含 CpG岛, 在正常组织中该基因保持非甲基化的 表达状态,在肿瘤组织中该基因的则表达明显下调。我们已发现上调 ZNF382 表达能够促进癌细胞运动 /侵袭的线索。据此提出, 如果宿主靶器官中的细胞 发生 ZNF382基因甲基化失活, 则可能影响肿瘤的转移和肿瘤患者的生存时 间。 因此, 通过检测癌组织中 ZNF382基因甲基化失活水平, 可能预测出机 体抵御肿瘤细胞转移能力, 帮助预后判断, 成为新的治疗靶点。
验证: 本实验室的胃癌发生或转移相关 DNA 甲基化组数据提示, 胃癌 组织 ZNF382甲基化比值显著高于癌旁正常组织; 利用变性高效液相色谱技 术(DHPLC), 所得结果相同 (图 1 ); 克隆测序分析见甲基化 CpG位点位于 该基因 5'非翻译区(5'UTR) (图 2 )。 表达相关性研究发现, 组织中 ZNF382 基因 mRNA表达水平与甲基化 ZNF382含量呈负相关 (图 3 )。 Transwell侵 袭实验表明, 转染 ZNF382表达载体能够促进癌细胞 BGC823细胞的运动或 侵袭能力 (图 4 ), 提示 ZNF382 CpG岛甲基化失活能够抑制癌细胞的转移。
我们分别用 DHPLC和定量 PCR分析了 22种细胞系中 ZNF382 CpG岛 甲基化和 ZNF382的转录水平, 结果发现 Z F382 CpG岛甲基化与其转录呈 负相关(图 2, 3 )。 ZNF382 CpG岛在正常胃上皮细胞系 (GES-1 )保持非甲 基化状态,而在胃癌细胞系( MGC803、 BGC823、 SGC7901、 MKN45、 MKN74、 AGS ) 中则发生高甲基化, 提示 ZNF382 CpG岛甲基化与胃癌的发生发展相 关;在 4种结肠癌细胞系中(Colo205、 HCT116、 RKO、 SW480), ZNF382 CpG 岛全部甲基化, 而且几乎所有 CpG位点同时全部甲基化; 2 例肝癌细胞系
(HepG2、 MHCC97H)、 3例宫颈癌细胞系 (HeLa、 Caski、 siha) 以及 1例 乳腺癌细胞系 (MCF-7 ) 中 ZNF382 CpG岛均发生甲基化; 2例肺癌细胞系
(H1299、 A549) 中, ZNF382 CpG岛在 A549细胞完全甲基化; 前列腺癌细 胞系 PC3和白血病细胞系 HL-60也处于部分甲基化状态, 胚肾细胞系 293T 中保持完全非甲基化状态, 提示 ZNF382 CpG岛甲基化在不同类型的肿瘤中 均发挥作用。
用 DHPLC对 54例转移性胃癌和 54例非转移性胃癌组织进行 ZNF382
CpG岛甲基化分析,发现非转移性胃癌组织中有 43例(79.6%)存在 ZNF382 甲基化,而转移性胃癌组织中 33例(61.1%)存在 ZNF382甲基化(p=0.035 )。 其中, 10例非转移性贲门癌或近端胃癌组织中 8例(80.0%)存在 ZNF382 CpG 岛甲基化, 9例转移性贲门癌或近端胃癌组织中仅有 3例(33.3%)存在 ZNF382 CpG 岛甲基化(;7=0.040)。 又采用 MethyLight (甲基化特异性荧光 PCR)的 方法对上述 54对胃癌组织 ZNF382 CpG岛甲基化进行分析, 结果与 DHPLC 高度相关 (图 5 ), 说明 DHPLC和 MethyLight两种定量分析方法均可用于 ZNF382 CpG岛甲基化分析。对随访资料进一步分析发现, 胃癌组织 ZNF382 甲基化阳性者术后总生存时间明显高于甲基化阴性者: 3 年生存率分别为 47.4%和 28.1%, 在单因素和多因素分析中差异有统计学显著性 (/7=0.001和 0.029) (图 6A)。 尤其重要的是, 在 54例非转移性胃癌患者中, ZNF382甲 基化阳性者术后 3年生存率显著高于甲基化阴性者 (88.4%比 54.5%,p=0.028) (图 7)。这些结果表明,通过检测胃癌组织(尤其是早期胃癌组织)中 ZNF382 甲基化 CpG岛的存在与否,能够敏感地测定出恶性肿瘤的转移能力和预后住 存时间的长短, ZNF382 甲基化阳性者的预后好于阴性者, 具有成为测定 ¾ 性肿瘤转移能力生物学标志物的应用前景。
为了研究 ZNF382甲基化是否在其它肿瘤中也有类似作用, 我们进一^ 用 MethyLight方法分析了 39例转移或复发性肝癌组织和 37例无转移或复 ¾ 肝癌组织中 ZNF382的甲基化与复发或转移和预后生存率的关系, 发现在 3; 例无转移或复发的肝癌组织中有 26例 (70.3%) 存在 ZNF382甲基化, 而 5 发或转移性的肝癌组织中只有 17例 (43.6%) 存在 ZNF382甲基化, 两组: έ 间具有显著性差异(ρ=0.019)。 对随访资料进一步分析发现, 在这 76例肝痏 组织中 ZNF382 甲基化阳性者术后总生存率显著高于甲基化阴性者: 3年住 存率分别为 55.8%和 30.3%,单因素分析具有统计学显著性 (/?=0.044) (图 8), 这些结果表明, 通过检测肝癌组织中 ZNF382甲基化 CpG岛序列的存在, 乜 能够敏感地测定肝癌的转移或复发潜能和生存时间的长短, 具有很好的临床 应用价值。
我们还用 DHPLC方法检测了 22对结肠癌和癌旁切缘组织以及 20例正 常结肠组织的 ZNF382 甲基化含量, 分别有 22 例癌 (95.6%)、 22 例切缘 (95.6%)、 12例正常 (60%) 组织存在 ZNF382甲基化; ZNF382甲基化含 量在结肠癌组中明显高于癌旁切缘和正常结肠组织(中位数, 0.305、 0.0831、
0.085、 /?=0.001 , 图 9)。 MethyLight方法也得到了此结果 (图 10)。 我们还 用 DHPLC方法检测了四例新鲜冰冻甲状腺癌组织, 发现 2例存在 ZNF382 启动子区高甲基化。该结果显示 ZNF382在甲状腺癌组织中也存在高甲基化。 基本操作步骤
1、 组织 DNA提取: 分别提取来自肿瘤、 ZNF382 CpG甲基化阳性对照细胞 和未甲基化阴性对照细胞 DNA;
2、 甲基化 ZNF382 CpG岛序列测定: 利用化学修饰法等手段修饰未甲基化 胞嘧啶; 根据 ZNF382 CpG岛修饰后序列, 设计和合成不含 CpG位点、 可同时扩增甲基化和非甲基化序列的通用 PCR上游和下游引物或者其 3, 端可与该序列所含甲基化 CpG位点特异性互补的甲基化特异性 PCR上游 和下游引物;用这些引物对修饰后待测样品中的 ZNF382 CpG岛进行 PCR 扩增,利用 DHPLC、克隆测序等方法,显示甲基化和非甲基化 ZNF382 CpG 岛扩增产物的存在;或者用 ZNF382甲基化 CpG岛修饰后序列特异性 PCR 引物和探针, MethyLight法定量测定甲基化的 ZNF382 CpG岛拷贝数;
3、 宿主抵御肿瘤转移能力及预后生存时间长短的判断: 在肿瘤组织存在 ZNF382基因甲基化 CpG岛时, 则人体抵御恶性肿瘤转移能力强, 预后生 存时间长, 反之则人体抵御恶性肿瘤转移能力差, 预后生存时间短。 本发明人在国际上首次发现, 癌组织中 ZNF382基因甲基化 CpG岛的存 在是一种能够用来评测恶性肿瘤转移能力及预后生存时间长短的标志物; 利 用简便的化学修饰 -PCR 扩增技术, 能够快速检出癌组织样品中是否含有 ZNF382基因甲基化 CpG岛。以早期准确评测肿瘤转移能力及预后生存时间, 对肿瘤的治疗提供帮助。 附图的简要说明
图 1 A是 ZNF382基因 CpG岛。
图 1B是胃癌及手术切缘组织甲基化 ZNF382比率。 图 1C是胃癌及手术切缘组织甲基化 ZNF382的 PCR扩增产物的 DHPLC色 谱图 (奇数表示切缘; 偶数表示癌; MB表示 M.sssI酶甲基化阳性对照)。 图 2是 ZNF382 CpG岛 A段和 B段 PCR产物的亚硫酸氢钠-克隆测序结果(上 图; 散落的小黑条为转录相关的甲基化区域, 黑色长条形表示甲基化的 CpG 位点) 和 B-段 PCR产物的 DHPLC分析色谱图 (下图)。 HCT116和 Caski: ZNF382完全甲基化; HL60和 PC3 : ZNF382部分甲基化; H1299和 GES-1 : ZNF382未甲基化。
图 3是 ZNF382甲基化与其转录的关系。 上图: 22种人细胞系; 下图: 胃癌 组织 (u, 完全非甲基化; m, 完全甲基化; part m, 部分甲基化)。
图 4是瞬时转染 ZNF382增加 BGC823细胞侵袭 /运动能力(TransweU实验)。 图 5是 DHPLC和 MethyLight两种方法检测胃组织 ZNF382甲基化含量的相 关性分析 (r=0.6,p=0.000)。
图 6是 108例胃癌组织 ZNF382甲基化阳性和阴性胃癌患者术后总生存时间 (月) 比较。 A: 变性高效液相色谱法 (DHPLC) 测定结果分析; B: 甲基 化特异性荧光定量 PCR法 (MethyLight) 测定结果分析。
图 7是 54例非转移性胃癌组织 ZNF382甲基化阳性和阴性胃癌患者术后生存 时间 (月) 比较。
图 8是肝癌组织中 ZNF382甲基化阳性和阴性患者总生存率比较。
图 9是结肠癌、 切缘以及正常结肠组织中 ZNF382甲基化含量比较(DHPLC 方法)。
图 10是结肠癌、切缘组织中 ZNF382甲基化拷贝数比较(MethyLight方法)。 实现本发明的最佳方式 实施例 1:通过 DHPLC测定胃癌组织 ZNF382基因 CpG岛甲基化序列来评 测肿瘤转移能力或预后生存时间长短
1.实验对象: 108 对胃癌冷冻组织, 其中 50%的患者存在淋巴结转移灶 和脉管癌栓或远处转移灶, 50%的配对患者胃癌组织既无淋巴结转移也未见 脉管癌栓或远处转移灶, 均有完整的临床病理资料和随访资料;
2.常规蛋白酶 K消化和乙醇沉淀法提取组织 DNA 1-10 μg;
3.使用 5M亚硫酸氢钠法修饰 DNA中未甲基化胞嘧啶;
1) 用无菌三蒸水 18 μΐ溶解上述 DNA样品 2 μg, 95°C水浴 20 min, 冰浴;
2) 各管加入 3 M NaOH 2 μΐ, 混匀, 42°C水浴 20 min, 以使 DNA变 性解链; 3) 新鲜配置 5.0 M NaHS03溶液 (4 ml): 加 1.9 g Na2S205到 2.5 ml无 菌三蒸水中, 加入 2 M NaOH 0.7 ml, 加入 1 M对苯二酚 0.5 ml, 50°C水浴, 反复倒置混匀直至完全溶解;
4) 各管 DNA样品加入 5.0 M NaHSO3 380 l, 混匀, 再加入 200 μΐ液 体石蜡阻止管内液体蒸发,置 50°C水浴中过夜修饰未甲基化胞嘧啶 为尿嘧啶;
5) 吸去顶层液体石蜡, 用 DNA纯化试剂盒(如 Promega Wizard DNA Clean-Up System, A7280), 按说明书所示提取修饰后 DNA:加入混 匀的树脂 1 ml, 混匀后静置 5 min; 将树脂 -DNA混合物转移至下 接微柱的注射管内, 抽真空法滤去液相, 并将 DNA等固相转移到 微柱滤膜上; 加入 80%异丙醇 2 ml, 抽真空; 弃注射管, 将微柱套 入 1.5 ml离心管上, 高速离心(10000g 20秒)去除柱内残留液体; 将微柱转移至新离心管上;
6) 向微柱内加入 80°C无菌三蒸水 50 μ1,静置 15min,高速离心( 10000g 20秒), 收集洗脱液; 再向微柱内加入 80°C无菌三蒸水 50 μΐ, 静 置 15min, 高速离心 (10000g 20秒), 合并洗脱液;
7) 向各管加入 3M NaOH 11 μ1, 混匀, 37°C温浴 15 min, 以终止修饰 反应;
8) 向各管加入 5M醋酸盐 166 μ1, 100%冰乙醇 750 μΐ, 混匀, -20°C 沉淀 4小时, 10000g 离心 30分钟,弃上清;向各管加入 200 μΐ 80% 冰乙醇, 混匀, 再离心, 弃上清;
9) 干燥后用 3〜6 μΐ 无菌三蒸水或 ΤΕ 缓冲液溶解修饰纯化后样品 DNA, -20°C保存备用;
4. PCR引物设计: 按人 ZNF382 CpG岛亚硫酸氢钠修饰后正意义链序列 (SEQ ID NO. 11和 12 )设计、合成不含 CpG位点的通用型 PCR引物(SEQ
ID NO. 1 , 2和 SEQ ID NO. 3、 4);
5. PCR扩增: 对修饰后待测样品中的甲基化和非甲基化 ZNF382 CpG岛 进行热启动 PCR扩增;
6.利用 DHPLC测定 437bp甲基化和非甲基化 ZNF382 CpG岛扩增产物 的存在;
7.结果: 54例转移性胃癌组织中只有 33例 (61.1%) 存在 ZNF382甲基 化, 而 54例非转移性胃癌组织中有 43例(79.6%)存在 ZNF382甲基化, 差 异存在统计学显著性 (p=0.035 )。
胃癌组织 ZNF382 甲基化阳性者手术后总生存率明显高于甲基化阴性 者, 3年生存率分别为 47.4%和 28.1%,在单因素和多因素分析中差异有统计 学显著性(p=0.001和 0.029; 图 6A。 在 54例非转移性胃癌患者中, ZNF382 甲基化阳性者术后 3 年生存率显著高于甲基化阴性者 (88.4%比 54.5%, /?=0.028; 图 7)。
8.结论: 胃癌组织中甲基化 ZNF382 CpG岛序列是一种能够用来测定胃 癌转移能力的标志物。 可以评测肿瘤转移能力或预后生存时间长短。 其中 SEQ ID NO. 1、 2和 SEQ ID NO. 3、 4的结果一样。 实施例 2:通过亚硫酸氢钠克隆测序法测定胃癌组织 ZNF382基因 CpG岛甲 基化来评测肿瘤转移能力或预后生存时间长短
1.同实施例 1步骤 1-5;
2.将 PCR产物连接到 AT-Clone试剂盒克隆载体中;
3.克隆测序 (图 2);
4.结果和结论: 同实施例 1。 实施例 3: 通过 MethyLight测定胃癌组织 ZNF382基因 CpG岛甲基化来评 测肿瘤转移能力或预后生存时间长短
1.同实施例 1步骤 1-3 ;
2. PCR引物设计: 按人 ZNF382甲基化 CpG岛修饰后序列(SEQ ID NO. 13和 14 ) 设计、 合成甲基化特异性 MethyLight引物 (SEQ ID NO. 5和 6) 和探针 (SEQ ID NO. 7), 定量测定 96pb的甲基化片段;
3.以文献报道(Widschwendter et al. Cancer Res 2004, 64:3807-3813 )的不 含 CpG岛的 COL2A基因为参考基因 (但是不限于本基因), 用相应的寡核 苷酸引物 (SEQ ID NO. 8和 9) 和荧光标记探针 TaqMan (SEQ ID NO. 10; 6FAM-Col2aprobe-BHQ1 ) , 对经亚硫酸氢钠修饰的 DNA 模板含量进行定量 PCR扩增;
4.根据两者的 Ct值,利用公式 P^ZA^^^ ]计算甲基化 ZNF286含量;
5.结果: MethyLight的测定结果与 DHPLC高度相关(r=0.6; P=0.000) (图 5 ); ZNF382甲基化阳性患者的 3年生存率显著高于阴性患者 (44%比 32%; P=0.023 ; 图 6的 B图)。 实施例 4: 通过 MethyLight测定肝癌组织 ZNF382基因 CpG岛甲基化来评 测肿瘤转移能力或预后生存时间长短
1.实验对象: 37份无转移或复发肝癌组织和 39份转移或复发性肝癌组 织;
2.同实施例 3步骤 1-4; 3.结果: 无转移或复发的肝癌组织中有 26例 (70.3%) 存在 ZNF382甲 基化, 而复发或转移性的肝癌组织中只有 17例 (43.6% ) 存在 ZNF382甲基 化, 两组之间具有显著性差异 (p=0.019 )。 对随访资料进一步分析发现, ZNF382甲基化阳性者术后总生存率显著高于其甲基化阴性者: 3年生存率分 别为 55.8%和 30.3%, 单因素分析具有统计学显著性 (p=0.044 ) (图 8 )。 这 些结果表明, 通过检测肝癌组织中 ZNF382甲基化 CpG岛序列的存在, 也能 够敏感地测定肝癌的转移 /复发潜能和生存时间的长短,具有很好的临床应用 价值。 实施例 5: 通过 DHPLC测定结肠癌组织 ZNF382 CpG岛甲基化来评测肿瘤 转移能力或预后生存时间长短
1.实验对象: 22对结肠癌和癌旁切缘组织;
2.同实施例 1步骤 2-5 ;
3.结果: 22例癌 (95.6%)、 22例切缘 (95.6% ) 组织存在 ZNF382甲基 化; ZNF382甲基化含量在结肠癌组中明显高于癌旁切缘组织(中位数, 0.305、
0.0831 ; p=0.001 , 图 9)。 实施例 6: 通过 MethyLight测定结肠癌组织 ZNF382 CpG岛甲基化来评测 肿瘤转移能力或预后生存时间长短
1. 实验对象: 同实施例 5的 22对结肠癌和癌旁切缘组织;
2. 同实施例 1步骤 2-3 ;
3. .同实施例 3步骤 2-4;
4. 结果: 同实施例 5 (图 10)。

Claims

权利 要 求
1. 一种体外评测肿瘤转移能力或肿瘤预后生存时间长短的方法,其特征是该 方法包括下列步骤:
(a) 从肿瘤组织中提取基因组 DNA;
(b) 测定人 ZNF382基因甲基化 CpG岛的存在;
(c) 评测肿瘤转移能力或肿瘤预后生存时间长短。
2. 根据权利要求 1所述的体外评测肿瘤转移能力或肿瘤预后生存时间长短的 方法, 其特征是步骤 (b) 包括: 利用化学修饰或甲基化 DNA富集技术, 设 计并合成能够与人 ZNF382基因甲基化 CpG岛靶序列配对的引物,用该引物 PCR法扩增人 ZNF382基因甲基化 CpG岛。
3. 根据权利要求 2所述的体外评测肿瘤转移能力或肿瘤预后生存时间长短的 方法, 其特征是步骤 (c) 包括: 肿瘤组织存在 ZNF382基因甲基化 CpG岛 时, 则人体抵御恶性肿瘤转移能力强, 预后生存时间长, 反之则人体抵御恶 性肿瘤转移能力差, 预后生存时间短。
4.根据权利要求 1至 3任一权利要求所述的体外评测肿瘤转移能力或肿瘤预 后生存时间长短的方法, 其中所述的肿瘤是胃癌、肝癌、结肠癌或甲状腺癌。
5. 一对测定人 ZNF382基因甲基化 CpG岛的引物,其碱基序列如 SEQ ID NO. 1和 2所示。
6. 一对测定人 ZNF382基因甲基化 CpG岛的引物,其碱基序列如 SEQ ID NO. 3和 4所示。
7. 测定人 ZNF382基因甲基化 CpG岛的引物组, 包括一对引物及探针, 其 中一对引物的碱基序列如 SEQ ID NO. 5和 6所示;探针的碱基序列如 SEQ ID NO. 7所示。
8. —种 DNA分子, 其碱基序列如 SEQ ID NO. 11、 SEQ ID NO. 12、 SEQ ID NO. 13或 SEQ ID NO. 14所示。
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WO2007122369A2 (en) * 2006-04-13 2007-11-01 Oncomethylome Sciences Sa Novel tumour suppressor

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