Defining the cistrome and quantitative transcriptome of virus-transformed cells using massively parallel sequencing

和人类一样，包括鸡在内的许多动物都会患上癌症。然而，与人类不同的是，鸡的大多数癌症是由病毒引起的。马立克氏病(MD)是鸡的一种常见疾病，涉及瘫痪，通常死于高度恶性T淋巴瘤(白血球癌症)的生长。马立克氏病是由一种传播性病原体--马立克氏病病毒引起的。MDV具有很强的传染性，是全球家禽业的主要威胁。据估计，这种疾病在全球造成的总损失高达20亿GB。目前，它是通过接种疫苗来控制的，每年使用近220亿剂疫苗试图控制这种疾病。尽管广泛接种疫苗，但这种疾病的威胁正在增加，需要进行更多基础性研究，以了解这种病毒导致癌症的机制，以制定更有效的控制方案。另一种在英国不太常见的鸡致癌病毒称为网状内皮组织增生症病毒(REV)，是一个非常好的癌症模型。利用这种病毒研究癌症的机制的好处是，可以在从鸟类采集的鸡细胞上进行诱发癌症的实验。我们使用了这个模型，并研究了细胞转化为癌细胞时的分子变化。我们发现正常癌细胞之间的基因和22个核苷酸的小分子的表达发生了非常重要的变化，这表明这些变化与癌症的发生有关。在这项由动物卫生研究所(康普顿)和方舟基因组学研究所(罗斯林研究所)联合进行的新拨款提案中，我们希望扩展这些研究，以获得使用新的RNA-Seq技术的基因表达变化的详细信息，该技术将提供关于转化过程中基因表达的更详细、更全面的图景。类似地，我们还将检查基因组中病毒癌蛋白可以直接与DNA结合以改变基因表达从而导致癌症的序列。我们的目标是使用这个优秀的模型系统和马立克氏病癌症模型来获得详细的基因表达数据，以了解和预测癌症的分子途径。这项研究对于了解这些病毒致癌的机制非常重要，其中一些机制对于了解包括人类在内的其他物种的癌症非常有价值。最后，该项目的发现将对开发控制致癌病毒引起的癌症的新方法非常有价值。

As in humans, many animals including chickens, develop cancer. However, unlike in humans, most of the cancers in chickens are caused by viruses. Marek's disease (MD) is a common disease of chickens involving paralysis and commonly death from the growth of highly malignant T lymphomas (cancers of white blood cells). MD is caused by a transmissible agent, Marek's disease virus (MDV). MDV is very contagious and is a major threat to the poultry industry worldwide. The estimated total loss from this disease worldwide is up to £ 2 billion. Presently, it is controlled by vaccination, and nearly 22 billion vaccine doses a year are used in an attempt to control the disease. Despite widespread vaccination, the threat from this disease is on the increase, and more fundamental studies to understand the mechanisms by which this virus cause cancer is needed to develop more effective control programmes. Another cancer inducing virus of chickens less common in the UK called Reticuloendotheliosis virus (REV) is a very good model for cancer. The advantage of using this virus for studying the mechanisms of cancer is that the experiments to induce cancer can be done on chicken cells collected from birds. We have used this model and examined the molecular changes to the cells while it is transformed into cancer cells. We have identified very important changes in the expression of genes and small 22-nucleotide microRNAs molecules between normal cancer cells, suggesting that these changes contribute to cancer. In this new grant proposal, to be carried out jointly between the Institute for Animal Health (Compton) and ARK-Genomics (Roslin Institute), we want to extend these studies to obtain detailed information on the changes in the expression of genes using the new RNA-Seq technology that will provide a much detailed comprehensive picture on the expression of genes during the transformation process. Similarly, we will also examine the sequences in the genomes where viral oncoproteins can directly bind to the DNA to change the gene expression to cause cancer. We aim to use this excellent model system and Marek's disease cancer model to obtain detailed gene expression data to understand and predict the molecular pathways to cancer. The study is very important to understand the mechanisms by which these viruses induce cancer, some of which are valuable in understanding cancer in other species including humans. Finally, the findings from the project will be very valuable in developing new approaches for the control of cancers caused by oncogenic viruses.