极具潜力的癌症分子标志物：DNA 甲基化 临床上，原发性肝细胞癌（hepatocellularcarcinoma ）目前仅有两个常用的分子标志物AFP （甲胎蛋白）和SF （铁蛋白），均是上世纪60 、70 年代发现的。在找肝癌分子标志物的相关研究中，很大一部分都是找基于遗传物质的分子标志物，但是很难将这些分子标志物与临床的预后及治疗结合起来。 DNA 甲基化异常是肿瘤发生发展过程中的标志性事件之一。人类基因启动子区的CpG 岛通常是非甲基化的状态，在癌症中CpG 岛会发生明显的高甲基化现象（CpG island methylator phenotype ，CIMP ），可能会导致一些重要的抑癌基因、DNA 修复基因的转录沉默，同时全基因通常呈现出去甲基化的状态（genome-wide hypo-methylation ），与基因组的稳定性有很大关联。这两种异常变化均与肿瘤的发生发展密切相关。2015 年Villanueva A（Hepatology 2015） 等人对肝细胞癌患者异常甲基化的研究显示 ， 68% 的探针存在低甲基化，32% 的探针存在高甲基化的现象，且这些高甲基化的探针大部分都位于Promoter 区的CpG 岛上。 为了进一步研究肝癌DNA异常甲基化的情况，我们首先用基于分位数的方法分析了TCGA 的50 个肝细胞癌患者的癌组织和癌旁的全基因组DNA 甲基化数据， 可以明显的观察到上述两种肝癌DNA 异常甲基化的现象（图1，左图为全基因组甲基化水平中值，可观察到显著的全基因组去甲基化现象；右图为CpG岛甲基化高四分位值，可观察到显著的CIMP现象） 。 图1 TCGA 样本全基因组及CpG 岛甲基化状态 随后，我们广泛收集了公开发表的三组DNA 甲基化数据集，并与北京协和医院合作新检测了一些临床样本，共计646 个tumor 样本和134 个non-tumor 样本的甲基化数据，令人兴奋的是，仅提取以上两个特征对tumor/non-tumor 构建分类器，就实现了很好的分类效果（如下图）！ 我们接下来对所收集样本的甲基化数据和基因表达数据进行了系统的整合分析，结果表明： 肝细胞癌患者基因启动子区的少数高甲基化位点即可区分癌和非癌组织的分子标志物 （如下图）。这些结果表明， DNA甲基化是肝癌极好的候选生物标志物 ，其应用前景还需在血液检测中进一步进行验证。 同时，我们的分析还发现： 通过对DNA甲基化数据及基因表达数据的相关性分析，找到了一些与免疫反应及代谢过程相关的表观遗传分子标志物； 从生存期分析的结果来看，SFN, SPP1 和TKT等基因与肝癌病人的预后密切相关。 （ 作者 ：黄倩倩 修改 ：古槿） 数据 1： http://bioinfo.au.tsinghua.edu.cn/member/jgu/hcc-dnameth 数据 2：HCCdb http://bioinfo.au.tsinghua.edu.cn/database/hccdb Briefings in Bioinformatics 2016, Advanced Access Genome-wide DNA methylation analysisidentifies candidate epigenetic markers and drivers of hepatocellular carcinoma Yongchang Zheng1,*, Qianqian Huang2,*,Zijian Ding2, Tingting Liu3, Chenghai Xue3,4, Xinting Sang1, Jin Gu2,# The alteration of DNA methylation landscapeis a key epigenetic event in cancer. As the accumulation of large-scalegenome-wide DNA methylation data from clinical samples, we are able tocharacterize the patterns of DNA methylation alterations for identifyingcandidate epigenetic markers and drivers. In this survey, we takehepatocellular carcinoma (HCC) as an example to show the basic steps ofanalyzing the DNA methylation patterns in cancer across multiple datasets. Wecollected three genome-wide DNA methylation datasets with ~800 clinical samplesand the corresponding gene expression datasets. Firstly, by quantitativelyanalyzing two global methylation alterations, it is found that about 90% tumorsacquire either genome-wide DNA hypo-methylation (GDH) or CpG island methylatorphenotype (CIMP). Secondly, probe-level analysis identified 267, 228 and 197hyper-methylated sites in promoter regions for the three datasets,respectively. These local hyper-methylated patterns are highly consistent: 84sites (from 61 promoters) are hyper-methylated in all the three studieddatasets, including many previously reported genes, such as CDKL2, TBX15 andNKX6-2. Then, these hyper-methylated sites were used as candidate markers toclassify tumor and non-tumor samples. The classifiers based on only 10 selectedprobes can achieve high discriminative ability across different datasets.Finally, by integrative analyzing DNA methylation and gene expression data, weidentified 222 candidate epigenetic drivers, which are enriched in inflammatoryresponse and multiple metabolic pathways. A set of high-confidence candidates,including SFN, SPP1 and TKT, are significantly associated with patients’overall survivals. In summary, this study systematically characterized the DNAmethylation alterations and their impacts on gene expressions in HCCs based onmultiple datasets.
用临床样本做的实验更真实，临床样本的获得相对更困难，特别是样本量大的时候整个实验更是艰难。大量临床样本做成的实验往往可以被接受发表到高影响的杂志。动物模型离真实的疾病更远，取样相对容易，实验的成本更低。动物模型做的实验往往被编辑和审稿人认为是低一等的实验。实际情况真的是这样吗？这得从标志物的定义说起。 标志物的最重要的特性是变化，尿里，呼气里都有大量的变化，汗液等也应该有很多的变化，血里变化少些。我们提出应该在变化比较多的地方找标志物。标志物第二个重要的特性是找到的变化必需和疾病 相关 。所以标志物的研究中能体现 确定的相关性 的实验应该被认为是好实验。到底临床实验还是动物实验更能体现相关性呢？临床实验的影响因素很多，尿液受到各种生理的病理的药理的因素影响，所以要找到和疾病确切的相关的标志物，比较困难。需要巨大量的数据。特别是疾病和药物因为伦理上的愿意很难分开，即便大数据理论上也没法分开。所以找到的很多变化有时无法确定是和疾病相关还是和药物相关，因为药物也影响尿液。相比之下，动物模型做的研究往往可以用严格的对照控制影响因素。这样动物模型做的实验找到的变化往往和疾病的相关性更确定。其实这类的研究对于找到有用的标志物更有贡献。虽然动物模型找到的线索还需要在临床样本上验证，但是这并不能改变动物模型实验得出的线索与疾病的相关性更确定的事实。所以强烈建议编辑和审稿人在评价生物标志物发现阶段的研究时，考虑到相关性的确定性，并依此做出判断。不要只看是不是用的临床样本，用了多少例，实验是不是困难来确定是不是接受投稿。 这种认识的改变有利于促进生物标志物领域的发展。 这个观点发表在一个没有什么影响的新杂志。我更喜欢没有影响的杂志，它让人可以真正得到发表的自由，而不是受到编辑和审稿人的限制。这种给编辑和审稿人的进言在高影响的杂志上可能都未必被允许。居高临下的审稿制度在限制着思想的自由表达和创新。开发的互联网发表渠道还没有改变科学发表。但愿以后能连开放获取的费用也省掉，只要发表在各自的博客上可以检索到就能得到同行的认可。 http://medcraveonline.com/MOJPB/MOJPB-02-00035.pdf Are Human Biomarker Studies Always More Valuable than Animal Ones.pdf
亥姆霍兹慕尼黑中心及德国糖尿病中心王瑞博士所在的团队率先发现并在最新一期《分子系统生物学》杂志上报导了三种可用于诊断早期糖尿病的生物标志物。此前尚从未有人找出过可供早期糖尿病诊断的相应标志物。 这是一个由王瑞所负责的亥姆霍兹慕尼黑中心的分子表观遗传学团队与该中心 Jerzy Adamski教授负责的 基因组分析中心暨代谢组学平台的 共同合作的成果。两种标志物可以用于判断患病风险。 http://www.helmholtz-muenchen.de/en/news/press-releases-2012/press-release/article/19841/index.html Wang-Sattler, R et al.(2012) Novel biomarkers for pre-diabetes identified by metabolomics, Molecular Systems Biology (8): doi:10.1038/msb.2012.43 —————————————————————— First diagnostic markers for pre-diabetes discovered Neuherberg, 25.09.2012. Detecting a predisposition to type 2 diabetes and preventing the disease before it develops is possible based on a current study by scientists at the Helmholtz Zentrum München. In the latest edition of Molecular Systems Biology they describe for the first time three biomarkers that can indicate pre-diabetes. Image: (from the left side to the right): Dr. Ana Messias, Prof. Annette Peters, Dr. Rui Wang-Sattler The current study by scientists at the Helmholtz Zentrum München and the German Center for Diabetes Research, which appears in the latest edition of the renowned journal Molecular Systems Biology, reports for the first time on new biomarkers of pre-diabetes. Up to now, no specific biomarkers have been available for the early form of diabetes, one of the most important common diseases. headed by Dr. Rui Wang-Sattler, who leads a working group in the Research Unit of Molecular Epidemiology, and Professor Jerzy Adamski, Head of Genome Analysis Center and the metabolomics platform at Helmholtz Zentrum München, identified identified three new biomarkers of pre-diabetes, two of which predicted the risk of the disease in individuals. “As the concentration of the biomarkers in blood are indicative of pre-diabetes, our study suggests that preventive measures can be taken,” says corresponding author Dr. Wang-Sattler, explaining the impact of the new discovery. If type 2 diabetes is diagnosed in early stages, such as pre-diabetes, disease development can be arrested or even prevented. Between about 8-10% of the German population suffers from type 2 diabetes mellitus, a disorder of glucose metabolism. New approaches to the diagnosis, therapy and prevention of this common disease are the scientific objectives of the Helmholtz Zentrum München. For the study, Dr. Wang-Sattler collaborated with several institutes at the Helmholtz Zentrum München, two partners from the German Center for Diabetes Research, the German Diabetes Center in Düsseldorf, and the German Institute of Human Nutrition in Potsdam-Rehbrücke. Further information Database and scientific team Metabolomics analysis was used to identify biomarkers from the KORA (Cooperative Health Research in the Augsburg Region) cohort and verified with data from the EPIC (European Prospective Investigation into Cancer and Nutrition) study. Dr. Rui Wang-Sattler and Mr. Zhonghao Yu of the Research Unit Molecular Epidemiology (acting Head, Prof. Annette Peters) cooperated with Dr. Ana Messias (Institute of Structural Biology), Prof. Thomas Meitinger (Director, Institute of Human Genetics), Prof. Martin Hrabě de Angelis (Director, Institute for Experimental Genetics), Prof. Jerzy Adamski (Head of the Genome Analysis Center) and Prof. Annette Peters (Director, Institute of Epidemiology II). The study was led by Dr. Christian Herder and Prof. Michael Roden at the German Diabetes Center in Düsseldorf. Original Publication Wang-Sattler, R et al.(2012) Novel biomarkers for pre-diabetes identified by metabolomics, Molecular Systems Biology (8): doi:10.1038/msb.2012.43 Link to specialist publication The Helmholtz Zentrum München , the German Research Center for Environmental Health, pursues the goal of developing personalized medicine, i.e. a customized approach to the diagnosis, treatment and prevention of widespread diseases such as diabetes mellitus and lung disease. To that end, it investigates the interaction of genetics, environmental factors and lifestyle. The Helmholtz Zentrum München is headquartered in Neuherberg in the north of Munich. It has about 2,000 staff members and is a member of the Helmholtz Association, Germany’s largest scientific organization, a community of 18 scientific-technical and medical-biological research centers with some 34,000 staff members. The Helmholtz Zentrum München is a partner in the German Center for Diabetes Research. www.helmholtz-muenchen.de The German Center for Diabetes Research e.V. is a noational network combining diabetes experts from basic research, epidemiology and clinical applications. The members of the association are Helmholtz Zentrum München German Research Center for Environmental Health, the German Diabetes Center in Düsseldorf, the German Institute of Human Nutrition in Potsdam-Rehbrücke, the Paul Langerhans Institute of the Carl Gustav Carus University Hospital in Dresden and Helmholtz Zentrums München’s Institute of Diabetes Research and Metabolic Diseases the Eberhard Karl University of Tübingen. The aim of the DZD is to find answers to unsolved questions in diabetes research by adopting a novel, integrative approach and to make a significant contribution towards improving the prevention, diagnosis and treatment of diabetes mellitus. _______________________________________________________________________________ Specialist contact Dr. Rui Wang-Sattler, Department of Molecular Epidemiology, Helmholtz Zentrum München – the German Research Center for Environmental Health (GmbH), Ingolstädter Landstr. 1, 85764 Neuherberg - Tel: +49 89-3187-3978 - Fax: +49 89-3187-2428 -
标签: 标志物
