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CN103374630B - Methods to detect the risk of liver cancer - Google Patents

Methods to detect the risk of liver cancer Download PDF

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CN103374630B
CN103374630B CN201210581819.2A CN201210581819A CN103374630B CN 103374630 B CN103374630 B CN 103374630B CN 201210581819 A CN201210581819 A CN 201210581819A CN 103374630 B CN103374630 B CN 103374630B
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liver cancer
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CN103374630A (en
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吕长益
田孟崇
吴政道
温义辉
林凯元
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Industrial Technology Research Institute ITRI
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Abstract

本发明关于侦测个体罹患肝癌机率的方法,包括侦测来自该个体生物样本中微小RNA miR-129-2的甲基化程度或表现程度。当该生物样本中miR-129-2的甲基化程度高于对照样本中miR-129-2的甲基化程度,或者该生物样本中miR-129-2的表现程度低于对照样本中miR-129-2的表现程度时,表示该个体倾向罹患肝癌或已罹患肝癌。

The present invention relates to a method for detecting the probability of an individual suffering from liver cancer, comprising detecting the methylation level or expression level of microRNA miR-129-2 in a biological sample from the individual. When the methylation level of miR-129-2 in the biological sample is higher than the methylation level of miR-129-2 in a control sample, or the expression level of miR-129-2 in the biological sample is lower than the expression level of miR-129-2 in the control sample, it indicates that the individual is prone to or has suffered from liver cancer.

Description

侦测罹患肝癌机率的方法Methods to detect the risk of liver cancer

技术领域本发明关于人类肝癌的生物标记。FIELD OF THE INVENTION The present invention relates to biomarkers for human liver cancer.

背景技术Background technique

微小RNA(miRNA)为约22个核苷酸的短内源性RNA。藉由与目标mRNA的碱基配对,miRNA作用为基因表现的后转录调节物,导致目标mRNA崩解或者抑制目标mRNA的表现。MicroRNAs (miRNAs) are short endogenous RNAs of approximately 22 nucleotides. By base-pairing with target mRNAs, miRNAs act as post-transcriptional regulators of gene expression, leading to disintegration of target mRNAs or inhibition of target mRNA expression.

数个研究显示miRNA在癌细胞中有不正常表现。在数种癌细胞株中观察到miRNA的表现受到抑制。一般推测miRNA抑制肿瘤形成是透过抑制致癌基因和调控与细胞凋亡或分化相关的基因表现。这种miRNA作用如肿瘤抑制基因(tumor suppressor gene),因此亦称为「肿瘤抑制微小RNA」(tumorsuppressor miRNA)。已知有68%的慢性淋巴性白血病(CLL)的患者,其miR-15及miR-16有缺失或被抑制的现象。。另一方面,相对于直肠及肺的正常组织,在直肠癌及肺癌组织中miR-143与miR-145呈现较低的表现程度。此外,miRNA let-7在肺癌细胞中亦受到抑制,而且藉由miRNA let-7的向下调节可侦测肺癌的不良预后结果。Several studies have shown that miRNAs are abnormally expressed in cancer cells. Suppression of miRNA expression was observed in several cancer cell lines. It is generally speculated that miRNAs inhibit tumor formation by inhibiting oncogenes and regulating the expression of genes related to apoptosis or differentiation. This miRNA acts like a tumor suppressor gene (tumor suppressor gene), so it is also called "tumor suppressor microRNA" (tumorsuppressor miRNA). It is known that 68% of patients with chronic lymphocytic leukemia (CLL) have deletion or inhibition of miR-15 and miR-16. . On the other hand, compared with normal tissues of rectum and lung, miR-143 and miR-145 showed lower expression levels in rectal cancer and lung cancer tissues. In addition, miRNA let-7 is also inhibited in lung cancer cells, and the downregulation of miRNA let-7 can detect the poor prognosis of lung cancer.

研究亦显示DNA甲基化在肿瘤抑制微小RNA的调控中扮演重要角色。DNA甲基化系指藉由DNA甲基转移酶(DNA methyltransferase)使CpG二核苷酸的胞嘧啶(cytosine)转变为5-甲基胞嘧啶(5-methylcytosine)的现象。CpG二核苷酸(亦称为「CpG位」)多位于基因5’端的区域。研究显示约70%的人类基因中可在启动子区域发现CpG位。当启动子区域中的CpG位被高甲基化时,推测位于下游的编码基因的转录可能受到抑制,因此无法表现。一般推测某些甲基结合蛋白与组织胺去乙醯酶(HDAC)及共抑制物(co-repressor)可辨识高甲基化的CpG位,因此改变染色体结构及形成去活性的异质染色质(heterochromatin)。数个研究显示异常的DNA甲基化发生在癌症的早期阶段,可能造成肿瘤抑制基因无法表现。近来的研究显示,DNA甲基化不但抑制肿瘤抑制基因的表现,也降低肿瘤抑制微小RNA的表现。Studies have also shown that DNA methylation plays an important role in the regulation of tumor suppressor microRNAs. DNA methylation refers to the phenomenon that cytosine of CpG dinucleotide is converted into 5-methylcytosine by DNA methyltransferase (DNA methyltransferase). CpG dinucleotides (also known as "CpG sites") are mostly located at the 5' end of the gene. Studies have shown that CpG sites can be found in the promoter region of about 70% of human genes. When the CpG site in the promoter region is hypermethylated, it is presumed that the transcription of the coding gene located downstream may be repressed and thus cannot be expressed. It is generally speculated that certain methyl-binding proteins, histamine deacetylase (HDAC) and co-repressors can recognize hypermethylated CpG sites, thereby changing the chromosome structure and forming inactive heterochromatin (heterochromatin) ). Several studies have shown that aberrant DNA methylation occurs in the early stages of cancer and may result in the failure of tumor suppressor genes to be expressed. Recent studies have shown that DNA methylation not only suppresses the expression of tumor suppressor genes, but also reduces the expression of tumor suppressor microRNAs.

发明内容Contents of the invention

本案一实施形态提供一种侦测个体罹患肝癌机率的方法,包括侦测来自该个体的生物样本中微小RNA miR-129-2的甲基化程度,其中,该甲基化程度系由下列所述之方法所侦测:重亚硫酸限制组合分析法(combined bisulflterestriction analysis;COBRA)、定量甲基化特异聚合酶链反应(quantitativemethylation-specific polymerase chain reaction;q-MSP)、重亚硫酸定序法(bisulfite sequencing)、焦磷酸定序法(pyrosequencing)、次世代定序(nextgeneration sequencing;NGS)、及DNA甲基化数组芯片分析法(DNAmethylation array analysis)等,其中,当该生物样本中miR-129-2的甲基化程度高于对照样本中miR-129-2的甲基化程度时,表示该个体倾向于罹患肝癌或已罹患肝癌。An embodiment of the present case provides a method for detecting the probability of an individual suffering from liver cancer, including detecting the degree of methylation of microRNA miR-129-2 in a biological sample from the individual, wherein the degree of methylation is determined by the following Detected by the method described: combined bisulfite restriction analysis (combined bisulfite restriction analysis; COBRA), quantitative methylation-specific polymerase chain reaction (quantitativemethylation-specific polymerase chain reaction; q-MSP), bisulfite sequencing method (bisulfite sequencing), pyrosequencing (pyrosequencing), next generation sequencing (nextgeneration sequencing; NGS), and DNA methylation array chip analysis (DNAmethylation array analysis), etc., wherein, when miR- When the methylation degree of 129-2 is higher than that of miR-129-2 in the control sample, it means that the individual tends to suffer from liver cancer or has suffered from liver cancer.

本案另一实施形态提供一种侦测个体罹患肝癌机率的方法,包括侦测来自该个体的生物样本中微小RNA miR-129-2的表现程度,其中,该表现程度系由定量反转录聚合酶链反应(quantitative real time PCR;qRT-PCR)或微小RNA数组芯片分析法(miRNA array analysis)等所侦测,其中,当该生物样本中miR-129-2的表现程度低于对照样本中miR-129-2的表现程度时,表示该个体倾向于罹患肝癌或已罹患肝癌。Another embodiment of the present case provides a method for detecting the probability of an individual suffering from liver cancer, including detecting the expression level of microRNA miR-129-2 in a biological sample from the individual, wherein the expression level is determined by quantitative reverse transcription polymerization Detected by enzyme chain reaction (quantitative real time PCR; qRT-PCR) or microRNA array chip analysis (miRNA array analysis), wherein, when the expression level of miR-129-2 in the biological sample is lower than that in the control sample When the expression level of miR-129-2 is low, it means that the individual tends to suffer from liver cancer or has suffered from liver cancer.

附图说明Description of drawings

图1为显示本案一实施例中以COBRA分析法侦测正常肝组织、正常肝细胞、及六种HCC细胞(HepG2、HuH7、J7、Hep3B、Mahlavu、SK-Hep1)中miR-129-2甲基化的电泳图。Figure 1 shows the detection of miR-129-2 A in normal liver tissue, normal liver cells, and six kinds of HCC cells (HepG2, HuH7, J7, Hep3B, Mahlavu, SK-Hep1) by COBRA analysis in an example of this case Kylated electropherogram.

图2A~2F为显示本案一实施例中以重亚硫酸定序法(bisulfite sequencing)侦测正常肝组织、正常肝细胞、及六种HCC细胞(HepG2、HuH7、J7、Hep3B、Mahlavu、SK-Hep1)中miR-129-2的甲基化情况及比例的图。Figures 2A-2F show the detection of normal liver tissue, normal liver cells, and six types of HCC cells (HepG2, HuH7, J7, Hep3B, Mahlavu, SK- The methylation status and ratio of miR-129-2 in Hep1).

图3A为显示本案一实施例中在正常肝细胞与HCC细胞中miR-129-2表现程度的柱状图。FIG. 3A is a bar graph showing the expression levels of miR-129-2 in normal hepatocytes and HCC cells in an embodiment of the present case.

图3B为显示本案一实施例中在正常肝组织与HCC组织中miR-129-2表现程度的柱状图。Fig. 3B is a histogram showing the expression degree of miR-129-2 in normal liver tissue and HCC tissue in one embodiment of the present case.

图3C为显示本案一实施例中在有无经过5-氮杂胞苷(5-aza-cytidine;5-AzaC)处理的HCC细胞中miR-129-2表现程度的柱状图。FIG. 3C is a histogram showing the degree of expression of miR-129-2 in HCC cells treated with or without 5-aza-cytidine (5-AzaC) in an embodiment of the present case.

图4A及4B为显示本案一实施例中在有无经过lenti-miR-129-2感染的HuH7与J7细胞中miR-129-2表现程度的柱状图。4A and 4B are bar graphs showing the degree of expression of miR-129-2 in HuH7 and J7 cells with or without lenti-miR-129-2 infection in an embodiment of the present case.

图4C为显示本案一实施例中有无lenti-miR-129-2感染的J7细胞的群落形成的柱状图。Figure 4C is a histogram showing the colony formation of J7 cells infected with lenti-miR-129-2 or not in an embodiment of the present case.

图4D为显示本案一实施例中有无lenti-miR-129-2感染的HuH7细胞的群落形成的柱状图。Figure 4D is a histogram showing the colony formation of HuH7 cells infected with or without lenti-miR-129-2 in an embodiment of the present case.

图5A为显示本案一实施例中以COBRA分析法侦测组织样本(42对HCC组织)中miR-129-2的甲基化情况的电泳图。5A is an electropherogram showing the methylation of miR-129-2 in tissue samples (42 pairs of HCC tissues) detected by COBRA analysis in an embodiment of the present case.

图5B为显示本案一实施例中以COBRA分析法侦测组织样本(42对HCC组织)中miR-129-2甲基化程度的柱状图。5B is a histogram showing the degree of methylation of miR-129-2 in tissue samples (42 pairs of HCC tissues) detected by COBRA analysis in an embodiment of the present case.

图5C为显示本案一实施例中以q-MSP反应侦测组织样本中miR-129-2甲基化程度的柱状图。5C is a bar graph showing the degree of methylation of miR-129-2 in tissue samples detected by q-MSP reaction in an embodiment of the present invention.

图5D为显示本案一实施例中HCC组织与相邻正常组织中甲基化程度的盒须图(box plot)。FIG. 5D is a box plot showing the degree of methylation in HCC tissues and adjacent normal tissues in one embodiment of the present case.

图6A为显示本案一实施例中以qRT-PCR反应侦测HCC组织与相邻正常组织中miR-129-2表现程度的柱状图。6A is a histogram showing the degree of expression of miR-129-2 in HCC tissues and adjacent normal tissues detected by qRT-PCR in an embodiment of the present case.

图6B为显示本案一实施例中HCC组织与相邻正常组织中miR-129-2表现比例的比例图。Fig. 6B is a ratio diagram showing the expression ratio of miR-129-2 in HCC tissues and adjacent normal tissues in one embodiment of the present case.

图7A为显示本案一实施例中以q-MSP反应侦测HCC血浆、肝硬化血浆与正常血浆中miR-129-2甲基化程度的柱状图。7A is a bar graph showing the degree of methylation of miR-129-2 in HCC plasma, liver cirrhosis plasma and normal plasma detected by q-MSP reaction in an embodiment of the present invention.

图7B为显示本案一实施例中在HCC血浆、肝硬化血浆与正常血浆中miR-129-2的甲基化程度的盒须图(box plot)。FIG. 7B is a box plot showing the degree of methylation of miR-129-2 in HCC plasma, liver cirrhosis plasma and normal plasma in one embodiment of the present case.

图7C为显示本案一实施例中计算HCC血浆样本组织及由健康血浆与肝硬化血浆所构成的样本组织之间miR-129-2甲基化程度的灵敏性与特异性之ROC曲线图。7C is a ROC curve showing the sensitivity and specificity of calculating the degree of methylation of miR-129-2 between HCC plasma sample tissue and sample tissue composed of healthy plasma and liver cirrhosis plasma in an embodiment of the present case.

具体实施方式Detailed ways

本发明之具体实施详细说明如下,然而以下的实施例仅用于进一步揭露本发明之技术内容,不应藉以限制本案的发明范畴。The detailed implementation of the present invention is as follows. However, the following examples are only used to further disclose the technical content of the present invention, and should not be used to limit the scope of the present invention.

本案一实施形态提供一种新颖微小RNA(miRNA)作为侦测人类肝癌的生物标记(biomarker)。根据高通量CpG微数组平台(high-throughput CpGmicroarray platform)的结果,本案发明人等从肝癌(hepatocellular carcinoma;HCC)细胞中的甲基化miRNA中,筛选出具有潜力的miRNA,即miR-129-2,作为肝癌的侦测标记。An embodiment of the present invention provides a novel microRNA (miRNA) as a biomarker for detecting human liver cancer. According to the results of the high-throughput CpG microarray platform (high-throughput CpGmicroarray platform), the inventors of this case screened out a potential miRNA, namely miR-129, from the methylated miRNA in hepatocellular carcinoma (HCC) cells. -2, as a detection marker for liver cancer.

此述之微小RNA(miRNA)系指人类(Homo sapiens)的miRNA,可获得自公开的数据库,例如miRBases数据库(http://mirbase.org)或者NCBI数据库(http://www.ncbi.nlm.nih.gov/)等。微小RNA(miRNA)由具有茎环结构(stem-loop form)的前驱体(precursor)经过切割、加工而形成成熟体(mature)。成熟体若为位于原前驱体5’端的活性片段则称为「5p」;成熟体若为位于原前驱体3’端的活性片段则称为「3p」。根据本案,miR-129-2系序列识别号1所示之90bp直线序列之前驱体。在后述的实施例及图4A、4B中,「miR-129-2-5p」表示miR-129-2位于5’端的成熟体活性片段,「miR-129-2-3p」表示位于miR-129-23’端的成熟体活性片段。The microRNA (miRNA) mentioned here refers to the miRNA of human beings (Homo sapiens), which can be obtained from public databases, such as miRBases database (http://mirbase.org) or NCBI database (http://www.ncbi.nlm .nih.gov/), etc. MicroRNA (miRNA) forms a mature body (mature) after cleavage and processing from a precursor (precursor) with a stem-loop structure. If the mature body is the active fragment located at the 5' end of the original precursor, it is called "5p"; if the mature body is the active fragment located at the 3' end of the original precursor, it is called "3p". According to this case, miR-129-2 is the precursor of the 90bp linear sequence shown in sequence identification number 1. In the examples described later and in Figures 4A and 4B, "miR-129-2-5p" indicates the mature active fragment of miR-129-2 located at the 5' end, and "miR-129-2-3p" indicates the active fragment located at the miR- 129-23' mature active fragment.

倾向于罹患肝癌或已罹患肝癌的个体可根据来自该个体的生物样本中miR-129-2的甲基化程度高于对照样本中对应的miR-129-2的甲基化程度来判断。可侦测的生物样本可获自新鲜或冷冻的肝癌组织、细胞、血液、血清、血浆等,但是并不限于此。对照样本可来自于经过诊断确认为无疾病的健康个体的正常组织、细胞、血液、血清、血浆等,或者来自相邻于所检测的肿瘤的相同组织型态的正常组织或细胞等。An individual who is prone to liver cancer or has suffered from liver cancer can be judged according to that the degree of methylation of miR-129-2 in the biological sample from the individual is higher than that of the corresponding miR-129-2 in the control sample. Detectable biological samples can be obtained from fresh or frozen liver cancer tissues, cells, blood, serum, plasma, etc., but are not limited thereto. Control samples can be from normal tissues, cells, blood, serum, plasma, etc. of healthy individuals diagnosed as disease-free, or from normal tissues or cells of the same tissue type adjacent to the tumor being tested.

miRNA的甲基化情形可由重亚硫酸限制组合分析法(combined bisulfiterestriction analysis;COBRA)、定量甲基化特异聚合酶链反应(quantitativemethylation-specific polymerase chain reaction;q-MSP)、重亚硫酸定序法(bisulfite sequencing)、焦磷酸定序法(pyrosequencing)、次世代定序(nextgeneration sequencing;NGS)、或者DNA甲基化数组芯片分析法(DNAmethylation array analysis)等方法来确认。重亚硫酸限制组合分析法(COBRA)系指将侦测的DNA先经过重亚硫酸(bisulfite)的处理,之后进行由PCR扩增(amplification),再藉由限制酶的切割、分解,以得知DNA甲基化程度或甲基化情况的分析方法。本发明中,miR-129-2进行COBRA分析法所使用的引子对包括序列识别号4或5所示之核苷酸序列,但不限于此。详细的COBRA操作流程可参见DNA Methylation Protocols,Methods in Molecular BiologyTM,HUMANA Press,Totowa,New Jersey,vol.200,p.71-86之记载。The methylation status of miRNA can be determined by combined bisulfite restriction analysis (combined bisulfite restriction analysis; COBRA), quantitative methylation-specific polymerase chain reaction (q-MSP), bisulfite sequencing (bisulfite sequencing), pyrosequencing (pyrosequencing), next generation sequencing (next generation sequencing; NGS), or DNA methylation array chip analysis (DNAmethylation array analysis) and other methods to confirm. Bisulfite Restriction Combinatorial Analysis (COBRA) means that the detected DNA is first treated with bisulfite, then amplified by PCR, and then cleaved and decomposed by restriction enzymes to obtain Know the DNA methylation degree or the analysis method of the methylation situation. In the present invention, the primer pair used for COBRA analysis of miR-129-2 includes the nucleotide sequence shown in sequence identification number 4 or 5, but is not limited thereto. For detailed COBRA operation procedures, please refer to the records in DNA Methylation Protocols, Methods in Molecular BiologyTM, HUMANA Press, Totowa, New Jersey, vol.200, p.71-86.

miRNA的甲基化图谱(methylation profile)可由重亚硫酸定序法(bisulfitesequencing)与定量甲基化特异聚合酶链反应(q-MSP)分析。当以重亚硫酸钠(sodium bisulfite)处理DNA序列时,DNA序列上的胞嘧啶(cytosine;C)会转变为脲嘧啶(uracil;U),但对于5-甲基胞嘧啶(5-methylcytosines;mC)却没有影响。因此,重亚硫酸钠的处理会诱导DNA序列的特异性变化而显现出有关甲基化情况的信息。本案一实施例中,以q-MSP分析miR-129-2的甲基化情况可使用序列识别号8或9所示之引子对,但不限于此。详细的q-MSP操作流程可参见DNA Methylation Protocols,Methods in Molecular BiologyTM,HUMANAPress,Totowa,New Jersey,vol.200,p.71-86。The methylation profile of miRNA can be analyzed by bisulfite sequencing and quantitative methylation-specific polymerase chain reaction (q-MSP). When the DNA sequence is treated with sodium bisulfite, the cytosine (cytosine; C) on the DNA sequence will be converted into uracil (U), but for 5-methylcytosine (5-methylcytosines; mC) It has no effect. Thus, sodium bisulfite treatment induces specific changes in DNA sequence revealing information about methylation status. In one embodiment of the present case, the primer pair shown in SEQ ID No. 8 or 9 can be used to analyze the methylation status of miR-129-2 by q-MSP, but is not limited thereto. The detailed q-MSP operation procedure can be found in DNA Methylation Protocols, Methods in Molecular BiologyTM, HUMANAPress, Totowa, New Jersey, vol.200, p.71-86.

本案另一实施形态提供一种侦测个体罹患肝癌机率的方法,包括侦测来自该个体的生物样本中微小RNA miR-129-2的表现程度,当该生物样本中miR-129-2的表现程度低于对照样本中miR-129-2的表现程度时,表示该个体倾向于罹患肝癌或已罹患肝癌。Another embodiment of this case provides a method for detecting the probability of an individual suffering from liver cancer, including detecting the expression level of microRNA miR-129-2 in a biological sample from the individual, when the expression of miR-129-2 in the biological sample When the degree is lower than the expression degree of miR-129-2 in the control sample, it means that the individual tends to suffer from liver cancer or has suffered from liver cancer.

miRNA的表现程度(expression level)可由定量反转录聚合酶链反应(quantitative real time PCR;qRT-PCR)或微小RNA数组芯片分析法(miRNAarray analysis)所侦测。qRT-PCR为改良的PCR反应,其特征在于在PCR反应过程中可实时(real-time)侦测扩增(amplified)的DNA。qRT-PCR的指数期(exponential phase)中可侦测的荧光循环数称为循环阈值(cycle threshold;Ct)。Ct值或相对于参考基因的Ct值差(ΔCt),可用于目标DNA的定量。本案一实施例中,以qRT-PCR侦测miR-129-2的表现程度所使用的引子对可包括如序列识别号6或7所示之核苷酸序列,但不限于此。人类肝癌组织中miRNA向下调节(down-regulation)的表现程度与该miRNA的甲基化情况一致,表示该miRNA是可信赖的肝癌检测生物标记。The expression level of miRNA can be detected by quantitative reverse transcription polymerase chain reaction (quantitative real time PCR; qRT-PCR) or microRNA array chip analysis (miRNAarray analysis). qRT-PCR is an improved PCR reaction, which is characterized in that amplified DNA can be detected in real-time during the PCR reaction. The detectable fluorescence cycle number in the exponential phase of qRT-PCR is called cycle threshold (Ct). The Ct value, or the difference in Ct value relative to the reference gene (ΔCt), can be used for the quantification of target DNA. In an embodiment of the present case, the pair of primers used to detect the expression level of miR-129-2 by qRT-PCR may include the nucleotide sequence shown in SEQ ID No. 6 or 7, but is not limited thereto. The expression degree of miRNA down-regulation in human liver cancer tissues is consistent with the methylation status of the miRNA, indicating that the miRNA is a reliable biomarker for liver cancer detection.

miRNA在肝癌组织中的生物功能可进一步以细胞群落的形成(colonyformation)来确认。本案一实施例中,使miR-129-2插入病毒核酸中并经由感染途径进入肝癌(HCC)细胞。该miRNA在HCC细胞中可抑制该细胞的群落形成,显示该miRNA在人类肝癌组织中作用为肿瘤抑制基因。The biological function of miRNA in liver cancer tissue can be further confirmed by the formation of cell colony (colony formation). In one embodiment of the present case, miR-129-2 was inserted into viral nucleic acid and entered into liver cancer (HCC) cells through infection. The miRNA can inhibit the colony formation of the cell in HCC cells, showing that the miRNA acts as a tumor suppressor gene in human liver cancer tissue.

实施例Example

材料与方法Materials and Methods

患者样本的取得、细胞培养条件及5-氮杂胞苷(5-aza-cytidine;5-AzaC)的处理Acquisition of patient samples, cell culture conditions and treatment of 5-aza-cytidine (5-AzaC)

肝癌(HCC)细胞HepG2、HuH7、J7、Hep3B、Mahlavu及SK-Hep1培养于37℃、5%CO2的DMEM(Dulbecco’s modified Eagle’s medium)培养基中。在进行后续处理前的24小时,将HuH7细胞(1×105cells/well)与其它肝癌细胞(3×105cells/well)分别接种于6孔盘(6-well plate)中。以5μM的5-azaC(Sigma)处理细胞3天。每24小时更换含有5-azaC的新鲜培养基。42对肝癌(HCC)临床样本,包括肿瘤组织与肿瘤相邻的正常组织;41个肝癌血浆样本、8个肝硬化血浆样本以及10个健康人血浆样本取得自台湾台南奇美医院。进行重亚硫酸定序法及甲基化特异聚合酶链反应(MSP)的正常成人的肝组织染色体DNA(对照)购买自美国生技公司(US Biological)。作为甲基化特异聚合酶链反应(MSP)的对照组甲基化DNA(CpGenome Universal Methylated DNA)购买自Chemicon。Hepatocellular carcinoma (HCC) cells HepG2, HuH7, J7, Hep3B, Mahlavu and SK-Hep1 were cultured in DMEM (Dulbecco’s modified Eagle’s medium) medium at 37°C and 5% CO2. 24 hours before subsequent treatment, HuH7 cells (1×105 cells/well) and other liver cancer cells (3×105 cells/well) were seeded in 6-well plates, respectively. Cells were treated with 5-azaC (Sigma) at 5 μM for 3 days. Fresh medium containing 5-azaC was replaced every 24 h. 42 pairs of clinical samples of liver cancer (HCC), including tumor tissue and normal tissue adjacent to the tumor; 41 plasma samples of liver cancer, 8 plasma samples of liver cirrhosis, and 10 plasma samples of healthy people were obtained from Chi Mei Hospital, Tainan, Taiwan. Normal adult liver tissue chromosomal DNA (control) subjected to bisulfite sequencing and methylation-specific polymerase chain reaction (MSP) was purchased from US Biological. Methylated DNA (CpGenome Universal Methylated DNA) as a control group of methylation-specific polymerase chain reaction (MSP) was purchased from Chemicon.

重亚硫酸限制组合分析法(COBRA)与重亚硫酸定序法Combinatorial Bisulfite Restriction Analysis (COBRA) and Bisulfite Sequencing

使用EZ DNA甲基化套组(Zymo Research)处理来自肝癌(HCC)临床样本、肝癌(HCC)细胞、及成人正常肝细胞的染色体DNA(1μg),进行重亚硫酸的处理以及PCR的扩增反应(amplification)。在重亚硫酸限制组合分析法(COBRA)中,以内切酶BstUI在60oC处理上述的PCR产物过夜使其分解。分解的DNA片段可目视于1.5%(w/v)溴化乙啶(EtBr)染色的洋菜胶上。另一方面,用于重亚硫酸定序法的PCR产物以CloneJET PCR选殖套组(Thermo FisherScientific)选殖于pJET1.2/blunt选殖载体。经转形于大肠杆菌(E.coli)后,以ABI定序系统(Applied Biosystems)选择约10个选殖株并进行定序。Use EZ DNA Methylation Kit (Zymo Research) to process chromosomal DNA (1 μg) from clinical samples of liver cancer (HCC), liver cancer (HCC) cells, and adult normal liver cells for bisulfite treatment and PCR amplification Reaction (amplification). In the combinatorial bisulfite restriction assay (COBRA), the above-mentioned PCR product was treated with endonuclease BstUI at 60oC overnight to decompose it. Resolved DNA fragments can be visualized on agarose gum stained with 1.5% (w/v) ethidium bromide (EtBr). On the other hand, the PCR products used for bisulfite sequencing were cloned in the pJET1.2/blunt clone vector with the CloneJET PCR clone kit (Thermo Fisher Scientific). After being transformed into Escherichia coli (E.coli), about 10 selected strains were selected and sequenced with the ABI sequencing system (Applied Biosystems).

实时定量甲基化分析Real-time quantitative methylation analysis

如前述以重亚硫酸处理的DNA,进行荧光SYBR green的实时甲基化特异性PCR(qMSP)的扩增(amplification)。每一反应添加1倍PCR缓冲液、0.25mM的dNTP、0.25μM的顺向引子(forward primer)与0.25μM的反向引子(reverse primer)、1.5U的FastStart Taq DNA聚合酶(Roche)及1μl的荧光SYBR green(Cambrex)于总体积20μl中稀释1000倍。扩增反应(amplification)在ABI Prism7000序列侦测系统中进行,根据下列的热循环条件:94°C、7分钟;之后94°C、30秒,62°C、30秒及72°C、30秒的40个循环。根据上述记载,以下列公式计算β-肌动蛋白(β-actin)与miR-129-2之间的Ct值差,获得甲基化程度:Amplification (amplification) of fluorescent SYBR green real-time methylation-specific PCR (qMSP) was performed on the DNA treated with bisulfite as described above. Add 1X PCR buffer, 0.25mM dNTP, 0.25μM forward primer and 0.25μM reverse primer, 1.5U FastStart Taq DNA polymerase (Roche) and 1μl Fluorescent SYBR green (Cambrex) was diluted 1000-fold in a total volume of 20 μl. The amplification reaction (amplification) was carried out in the ABI Prism7000 sequence detection system, according to the following thermocycling conditions: 94°C, 7 minutes; then 94°C, 30 seconds, 62°C, 30 seconds and 72°C, 30 seconds 40 cycles of seconds. According to the above-mentioned records, the Ct value difference between β-actin (β-actin) and miR-129-2 is calculated with the following formula to obtain the degree of methylation:

对于组织样本:2[Ct(β-actin)-Ct(miR-129-2)]×100;For tissue samples: 2 [Ct(β-actin)-Ct(miR-129-2)] × 100;

对于血浆样本:2[Ct(β-actin)-Ct(miR-129-2)]×1000。For plasma samples: 2 [Ct(β-actin)-Ct(miR-129-2)] × 1000.

实时定量反转录聚合酶链反应(qRT-PCR)Quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR)

使用TRIzol试剂(Invitrogen)萃取肝细胞与肝癌临床样本的总RNA(totalRNA)。根据使用者手册使用Superscript III反转录酶(Invitrogen)进行cDNA的合成。实时定量聚合酶链反应使用荧光SYBR Green PCR master mix(AppliedBiosystems)在ABI Prism7000序列侦测系统进行。在微小RNA成熟体的表现分析上,使用TaqMan miRNA分析系统(Applied Biosystems)根据操作手册进行。相对表现程度以ΔCt方法分析,U6及RNU44为内在对照组(internalcontrol)。The total RNA (totalRNA) of hepatocytes and liver cancer clinical samples was extracted using TRIzol reagent (Invitrogen). Synthesis of cDNA was performed using Superscript III reverse transcriptase (Invitrogen) according to the user manual. Real-time quantitative polymerase chain reaction was performed on ABI Prism7000 sequence detection system using fluorescent SYBR Green PCR master mix (Applied Biosystems). The performance analysis of mature microRNAs was performed using TaqMan miRNA Analysis System (Applied Biosystems) according to the operation manual. The degree of relative expression was analyzed by ΔCt method, and U6 and RNU44 were internal controls.

细胞群落的形成cell colony formation

将HuH7与J7细胞以密度2×104cells/well接种于96孔盘(96-wellplate)。以带有miR-129-2前驱体的重组慢病毒(lentivirus)或对照的慢病毒根据操作手册感染细胞。经过24小时感染后,将细胞与0.7%顶层琼脂(top agar)混合,移至每孔(well)含有1%底层琼脂(bottom agar)的6孔盘(6-well plate)中。以5μg/ml的嘌呤霉素(puromycin)筛选转染体四星期。形成的细胞群落以PBS洗涤,以绝对甲醇固定,结晶紫溶液(0.5%crystal violet solution)染色1小时。HuH7 and J7 cells were seeded in 96-well plates at a density of 2×104 cells/well. Cells were infected with recombinant lentivirus carrying miR-129-2 precursor or control lentivirus according to the operation manual. After 24 hours of infection, cells were mixed with 0.7% top agar and transferred to a 6-well plate containing 1% bottom agar per well. Transfectants were selected for four weeks with 5 μg/ml puromycin. The formed cell colonies were washed with PBS, fixed with absolute methanol, and stained with crystal violet solution (0.5% crystal violet solution) for 1 hour.

[实施例1]确认由DNA甲基化调节的具潜力的微小RNA[Example 1] Confirmation of potential microRNAs regulated by DNA methylation

根据上述COBRA分析法确认正常肝组织、正常肝细胞与六种肝癌(HCC)细胞(HepG2,HuH7,J7,Hep3B,Mahlavu及SK-Hep1)的miR-129-2的甲基化情形。结果如图1所示,显示在六个HCC细胞中miR-129-2有甲基化现象,但是在正常肝组织及细胞中则呈现无甲基化现象。The methylation status of miR-129-2 in normal liver tissue, normal liver cells, and six types of hepatocellular carcinoma (HCC) cells (HepG2, HuH7, J7, Hep3B, Mahlavu, and SK-Hep1) was confirmed according to the above COBRA analysis method. The results are shown in Figure 1, showing that miR-129-2 was methylated in six HCC cells, but not in normal liver tissues and cells.

进一步使用重亚硫酸定序法检测在HCC细胞与正常肝细胞中miR-129-2的甲基化情况。整体来说,检查miR-129-2中的33个CpG位。在正常肝细胞及组织中观察到低甲基化现象(如图2A~2B)。在正常肝组织NL-1663与NL-4149以及正常肝细胞中,miR-129-2的甲基化比例分别为2.1%、3.3%及0.6%。相反地,在HepG2、HuH7、J7、Hep3B、Mahlavu及SK-Hep1的HCC细胞中,miR-129-2的甲基化比例分别为64.5%、58.8%、71.5%、79.7%、72.7%及94.5%(如图2C~2F)。这些结果显示,相较于正常肝细胞而言,miR-129-2在HCC细胞中的高甲基化情形为一普遍现象。The methylation of miR-129-2 in HCC cells and normal liver cells was further detected by bisulfite sequencing. Overall, 33 CpG sites in miR-129-2 were examined. Hypomethylation was observed in normal liver cells and tissues (Figure 2A~2B). In normal liver tissues NL-1663 and NL-4149 and normal liver cells, the methylation ratios of miR-129-2 were 2.1%, 3.3% and 0.6%, respectively. In contrast, in HepG2, HuH7, J7, Hep3B, Mahlavu and SK-Hep1 HCC cells, the methylation ratios of miR-129-2 were 64.5%, 58.8%, 71.5%, 79.7%, 72.7% and 94.5%, respectively. % (as shown in Figure 2C~2F). These results indicate that hypermethylation of miR-129-2 is a common phenomenon in HCC cells compared to normal hepatocytes.

[实施例2]DNA甲基化调节的miR-129-2在HCC细胞中的表现[Example 2] Expression of miR-129-2 regulated by DNA methylation in HCC cells

为了评估miR-129-2的表现是否受到DNA甲基化的调控,以定量反转录PCR(quantitative reverse transcription PCR)检查正常肝细胞与HCC细胞中miR-129-2的表现程度。相较于正常肝细胞,所有HCC细胞中的miR-129-2表现皆降低(如图3A)。相同地,HCC组织样本中miR-129-2的表现也低于正常肝组织约16倍(如图3B)。而且,在经过5-氮杂胞苷(5-aza-cytidine;5-AzaC)处理后,HuH7细胞与J7细胞中miR-129-2的表现程度明显地增加,分别是未经5-AzaC处理细胞的2.5倍及16倍(如图3C)。从这些结果推论,DNA甲基化调节miR-129-2的表现,造成HCC细胞中miR-129-2的表现降低。In order to assess whether the expression of miR-129-2 is regulated by DNA methylation, quantitative reverse transcription PCR (quantitative reverse transcription PCR) was used to examine the expression degree of miR-129-2 in normal liver cells and HCC cells. Compared with normal hepatocytes, miR-129-2 expression was decreased in all HCC cells (Fig. 3A). Similarly, the expression of miR-129-2 in HCC tissue samples was also about 16 times lower than that in normal liver tissues (as shown in Figure 3B). Moreover, after 5-aza-cytidine (5-aza-cytidine; 5-AzaC) treatment, the expression levels of miR-129-2 in HuH7 cells and J7 cells were significantly increased, respectively. 2.5 times and 16 times of cells (as shown in Figure 3C). It was deduced from these results that DNA methylation regulates the expression of miR-129-2, resulting in a decreased expression of miR-129-2 in HCC cells.

[实施例3]HCC细胞中miR-129-2作用为肿瘤抑制miRNA[Example 3] miR-129-2 acts as a tumor suppressor miRNA in HCC cells

为评估miR-129-2在HCC细胞中的生物功能,首先以带有miR-129-2前驱体的慢病毒(lenti-miR-129-2)感染,建立表现miR-129-2的HCC细胞(HuH7-miR、J7-miR)。之后使用Taqman分析法确认以lenti-miR-129-2感染的HCC细胞中miR-129-2成熟体的表现。HuH7细胞中lenti-miR-129-2的感染(HuH7-miR)使得成熟体miR-129-2-5p与miR-129-2-3p过度表现,其表现量较对照感染细胞(HuH7-Ctrl)分别提高约2000倍及1000倍(如图4A~4B)。同样地,lenti-miR-129-2感染的J7细胞(J7-miR),其miR-129-2-5p与miR-129-2-3p的表现量较对照感染细胞(J7-Ctrl)的表现量分别提高约500倍及1000倍。细胞群落实验证明,miR-129-2具有降低HCC细胞非贴附性生长(anchorage-independentgrowth)的能力。相较于对照的感染细胞(J7-Ctrl),表现miR-129-2的J7细胞(J7-miR)仅观察到1/3的细胞群落形成(如图4C)。相同地,以对照的慢病毒感染的HuH7(HuH7-miR)细胞中,每一培养皿(well)平均有47个群落形成(如图4D)。相反地,表现对照miRNA的HuH7细胞(HuH7-Ctrl)几乎没有群落形成。这些结果显示,miR-129-2在HCC细胞中作用如肿瘤抑制微小RNA(tumorsuppressor miRNA)。To evaluate the biological function of miR-129-2 in HCC cells, HCC cells expressing miR-129-2 were first infected with a lentivirus carrying miR-129-2 precursor (lenti-miR-129-2) (HuH7-miR, J7-miR). The expression of mature miR-129-2 in HCC cells infected with lenti-miR-129-2 was then confirmed using Taqman analysis. Infection of lenti-miR-129-2 in HuH7 cells (HuH7-miR) overexpressed mature miR-129-2-5p and miR-129-2-3p, and their expression levels were higher than those in control infected cells (HuH7-Ctrl) Respectively increased about 2000 times and 1000 times (as shown in Figure 4A~4B). Similarly, the expression of miR-129-2-5p and miR-129-2-3p in lenti-miR-129-2 infected J7 cells (J7-miR) was higher than that of control infected cells (J7-Ctrl). The amount is increased by about 500 times and 1000 times respectively. Cell colony experiments demonstrated that miR-129-2 has the ability to reduce the non-attachment growth of HCC cells (anchorage-independent growth). Compared with control infected cells (J7-Ctrl), only 1/3 of the cell colony formation was observed in J7 cells expressing miR-129-2 (J7-miR) (Fig. 4C). Similarly, in the HuH7 (HuH7-miR) cells infected with the control lentivirus, an average of 47 colonies were formed per well (as shown in FIG. 4D ). In contrast, HuH7 cells expressing the control miRNA (HuH7-Ctrl) had little colony formation. These results show that miR-129-2 functions as a tumor suppressor miRNA in HCC cells.

[实施例4]miR-129-2在HCC临床样本中的高甲基化与向下调节表现(down regulation)[Example 4] Hypermethylation and down regulation of miR-129-2 in HCC clinical samples (down regulation)

为了评估miR-129-2在临床样本中的甲基化情行,使用COBRA分析42对HCC肿瘤以及与该肿瘤相邻的正常组织(如图5A)。42对中有30对(~71%)的HCC组织显示miR-129-2具有高度甲基化(如图5B)。为了进一步定量甲基化程度,进行如上述的甲基化特异性PCR。除了3例例外(患者编号1111、2000及2756),相较于肿瘤相邻的正常组织,几乎所有的HCC临床样本都显示miR-129-2有较高的甲基化程度(如图5C~5D)。而且,使用q-MSP分析的结果与使用COBRA分析的结果有显著的相关性(correlation)。这些结果显示,miR-129-2在HCC临床样本中为高度甲基化,与前述HCC细胞的结果相符。To assess the methylation profile of miR-129-2 in clinical samples, 42 pairs of HCC tumors and normal tissues adjacent to the tumors were analyzed using COBRA (Fig. 5A). HCC tissues of 30 out of 42 pairs (~71%) showed hypermethylation of miR-129-2 (Fig. 5B). To further quantify the degree of methylation, methylation-specific PCR was performed as described above. Except for 3 cases (patient numbers 1111, 2000, and 2756), almost all HCC clinical samples showed a higher degree of methylation of miR-129-2 compared with normal tissues adjacent to the tumor (Fig. 5C~ 5D). Furthermore, there was a significant correlation between the results analyzed using q-MSP and the results analyzed using COBRA. These results show that miR-129-2 is highly methylated in HCC clinical samples, which is consistent with the aforementioned results in HCC cells.

又为了确认miR-129-2的表现是否因DNA的甲基化而向下调节(downregulation)其表现,因此进行qRT-PCR的分析。结果显示,相较于肿瘤相邻的正常组织,42个HCC临床样本中有29个(~69%)样本其miR-129-2的表现降低(如图6A~6B)。In order to confirm whether the expression of miR-129-2 is downregulated by DNA methylation (downregulation), qRT-PCR analysis was performed. The results showed that miR-129-2 expression was decreased in 29 out of 42 HCC clinical samples (~69%) compared with tumor-adjacent normal tissues (Fig. 6A~6B).

这些结果显示,miR-129-2在HCC样本中为高度甲基化且向下调节其表现,但这些情形并未发生在肿瘤相邻的正常组织中。此表示miR-129-2在肝癌及正常组织中的差异表现及/或甲基化程度可作为HCC诊断的标记。These results show that miR-129-2 is hypermethylated and downregulates its expression in HCC samples, but not in tumor-adjacent normal tissues. This means that the differential expression and/or methylation degree of miR-129-2 in liver cancer and normal tissues can be used as a marker for HCC diagnosis.

[实施例5]HCC血浆样本中miR-129-2的甲基化程度[Example 5] Methylation degree of miR-129-2 in HCC plasma samples

将奇美医院获得的41个HCC血浆样本、8个肝硬化血浆样本以及10个健康血浆样本分别进行q-MSP,以确认miR-129-2的甲基化程度。在41个HCC血浆样本中,有37个样本(90%)其miR-129-2的甲基化程度超过0.1(如图7A)。反之,没有一位健康捐赠者的血浆样本中miR-129-2的甲基化程度超过0.05,而肝硬化血浆样本中且仅有2例其miR-129-2甲基化程度超过0.1(如图7A所示)。为了进一步统计分析,将上述所得甲基化程度转换成log2数值。统计分析显示,HCC血浆中miR-129-2的甲基化程度显著高于健康者或肝硬化的血浆(P<0.01)(如图7B)。以接收者操作特征曲线(ROC)分析确认miR-129-2在肝癌诊断的灵敏性、特异性以及曲线下面积(AUC)及截取值(cutoff value)。在截取值(cut-off value)为-2.36时,可区别HCC与健康者及肝硬化,灵敏性为88%及特异性为100%(AUC=0.92,SE=0.039,95%CI=0.843-0.997,P<0.001)(如图7C)。ROC曲线分析显示使用miR-129-2在HCC诊断上的高准确性。41 HCC plasma samples, 8 cirrhotic plasma samples and 10 healthy plasma samples obtained from Chimei Hospital were subjected to q-MSP to confirm the degree of methylation of miR-129-2. Among the 41 HCC plasma samples, 37 samples (90%) had the degree of methylation of miR-129-2 exceeding 0.1 (as shown in Figure 7A). In contrast, none of the plasma samples from healthy donors had a methylation level of miR-129-2 exceeding 0.05, and only 2 samples from cirrhotic plasma samples had miR-129-2 methylation levels exceeding 0.1 (eg Figure 7A). For further statistical analysis, the degree of methylation obtained above was converted into a log2 value. Statistical analysis showed that the degree of methylation of miR-129-2 in HCC plasma was significantly higher than that in plasma of healthy subjects or liver cirrhosis (P<0.01) (Figure 7B). Receiver operating characteristic curve (ROC) analysis was used to confirm the sensitivity, specificity, area under the curve (AUC) and cutoff value of miR-129-2 in the diagnosis of liver cancer. When the cut-off value (cut-off value) is -2.36, HCC can be distinguished from healthy people and liver cirrhosis, with a sensitivity of 88% and a specificity of 100% (AUC=0.92, SE=0.039, 95%CI=0.843- 0.997, P<0.001) (as shown in Figure 7C). ROC curve analysis showed high accuracy in HCC diagnosis using miR-129-2.

虽然本发明已以较佳实施例揭露如上,然其并非用以限定本发明,任何熟悉此项技艺者,在不脱离本发明之精神和范围内,当可做些许更动与润饰,因此本发明之保护范围当视后附之申请专利范围所界定者为准。Although the present invention has been disclosed as above with preferred embodiments, it is not intended to limit the present invention. Anyone familiar with this art can make some changes and modifications without departing from the spirit and scope of the present invention. Therefore, this The scope of protection of an invention shall be defined in the scope of the appended patent application.

Claims (15)

1. detect individuality and suffer from a test kit for liver cancer probability, comprise for detecting the oligonucleotide from this individual biological specimen Microrna miR-129-2 methylation, wherein this miR-129-2 is the nucleotide sequence shown in recognition sequence number 1.
2. the individuality of the detecting described in claim 1 is suffered from the test kit of liver cancer probability, the methylation of wherein working as miR-129-2 in detected biological specimen during higher than the methylation of miR-129-2 in check sample, represents that this individuality tends to suffer from liver cancer or suffered from liver cancer.
3. the individuality of the detecting described in claim 1 is suffered from the test kit of liver cancer probability, and wherein this methylates and occurs in one or the above CpG position of this miR-129-2.
4. the individuality of the detecting described in claim 1 is suffered from the test kit of liver cancer probability, and wherein this methylation is detected by the method being selected from the following group forming: heavy sulfurous acid restriction combined analytical method (COBRA), quantitative Methylation specific PCR (q-MSP), heavy sulfurous acid sequencing method, tetra-sodium sequencing method, inferior generation sequencing (NGS) and DNA methylation array chip analysis method.
5. the individual test kit of suffering from liver cancer probability of the detecting described in claim 1, wherein, this oligonucleotide is the introduction pair shown in recognition sequence numbers 4 or 5.
6. the individuality of the detecting described in claim 5 is suffered from the test kit of liver cancer probability, and wherein this oligonucleotide is for the methylation with heavy sulfurous acid restriction combined analytical method (COBRA) detecting miR-129-2.
7. the individual test kit of suffering from liver cancer probability of the detecting described in claim 1, wherein this oligonucleotide is the introduction pair shown in recognition sequence numbers 8 or 9.
8. the individuality of the detecting described in claim 7 is suffered from the test kit of liver cancer probability, and wherein this oligonucleotide is for the methylation with quantitative Methylation specific PCR (q-MSP) detecting miR-129-2.
9. the individuality of the detecting described in claim 1 is suffered from the test kit of liver cancer probability, and wherein this biological specimen comprises hepatic tissue, blood, serum or blood plasma.
10. detect individuality and suffer from a test kit for liver cancer probability, comprise for detecting the oligonucleotide from this individual biological specimen Microrna miR-129-2 performance degree, wherein this miR-129-2 is the nucleotide sequence shown in recognition sequence number 1.
The individual test kit of suffering from liver cancer probability of detecting described in 11. claims 10, the performance degree of wherein working as miR-129-2 in detected biological specimen during lower than the performance degree of check sample miR-129-2, represents that this individuality tends to suffer from liver cancer or suffered from liver cancer.
The individual test kit of suffering from liver cancer probability of detecting described in 12. claims 10, wherein, this performance degree is detected by quantitative reverse transcriptional PCR (qRT-PCR) or Microrna array chip analysis method.
The individual test kit of suffering from liver cancer probability of detecting described in 13. claims 10, wherein this oligonucleotide is the introduction pair shown in recognition sequence numbers 6 or 7.
The individual test kit of suffering from liver cancer probability of detecting described in 14. claims 13, wherein this oligonucleotide is for the performance degree with quantitative reverse transcriptional PCR (qRT-PCR) detecting miR-129-2.
The individual test kit of suffering from liver cancer probability of detecting described in 15. claims 10, wherein this biological specimen comprises hepatic tissue, blood, serum or blood plasma.
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