Comparative Mammalian Genomics

比较哺乳动物基因组学

基本信息

批准号：
9152747
负责人：
elaine ostrander
金额：
$ 112.75万
依托单位：
NATIONAL HUMAN GENOME RESEARCH INSTITUTE
依托单位国家：
美国
项目类别：
财政年份：
资助国家：
美国
起止时间：
至
项目状态：
未结题

来源：
https://reporter.nih.gov/project-details/9152747
关键词：
Accounting Admixture Adoption Agriculture Alleles Allografting Antarctica Antigen Presentation Apoptosis Autoantigens BRAF gene Behavior Biology Bladder Neoplasm Blood Chemical Analysis Body Size Breeding Canis familiaris Cataloging Catalogs Cell Line Cell Lineage Clinical Collaborations Color Communities DNA Data Data Set Databases Deltastab Development Dog Diseases Ensure Evaluation Evolution Gene Expression Profile Gene Family Genes Genetic Genetic study Genome Genomics Gray Wolf Health Hereditary Disease Histologic Human Immune Immunologic Monitoring Immunologic Surveillance In Vitro Individual Jackals Laboratories Life Cycle Stages MAP Kinase Gene MEKs Malignant Neoplasms Malignant neoplasm of urinary bladder Maps Measurement Metabolism Modeling Morphology Muscle Museums Mutate Mutation Natural Selections Paper Pathway interactions Population Preparation Principal Component Analysis Process Recording of previous events Research Resistance Resources Role Sampling Scientist Sequence Analysis Shapes Sister Somatic Cell Somatic Mutation Staging System Techniques Testing Transitional Cell Carcinoma United States Universities Urine Utah Variant Veterinary Venereal Tumors Water Wolves Work Writing bladder transitional cell carcinoma cancer cell cancer genetics cancer genome cancer risk clinical phenotype companion animal comparative cranium dog genome genetic variant genome sequencing genome wide association study genome-wide genomic variation human data inhibitor/antagonist insight interest member novel pressure programs research study skeletal targeted treatment therapy design trait transcriptome sequencing tumor tumorigenesis

项目摘要

The tremendous phenotypic diversity of modern dog breeds represents the end point of a >15,000-year experiment in artificial and natural selection. Each breed has undergone strong artificial selection, in which dog fanciers selected for many traits including body size, fur type, color, skull shape, and even behavior, to create novel breeds. The adoption of the breed barrier rule that no dog may become a registered member of a breed unless both its dam and sire are registered members ensures a relatively closed genetic pool within each breed. As a result, there is strong phenotypic homogeneity within breeds including breed-associated genetic disease. This year we have made significant advances in our studies of canine bladder cancer, identifying a common druggable target in tumors. We have identified pathways that are mutated in canine transmissible tumors, which has allowed us to determine how tumors avoid immune surveillance. We have also continued our studies of canine origins. Canine Cancer Our recent genetic studies of dog disease have focused on cancer, which we argue is a strong model for human cancer genetic (Davis and Ostrander, 2015). With 20,000 new cases in the United States each year, canine invasive transitional cell carcinoma of the bladder (InvTCC) is a common, naturally occurring malignancy that shares significant histologic, biologic, and clinical phenotypes with human muscle invasive bladder cancer. In order to identify somatic drivers of canine InvTCC, we determined the complete transcriptome for multiple tumors by RNAseq (Decker et al., 2015). We found that all tumors harbored a somatic mutation that is homologous to the human BRAF(V600E) mutation, and an identical mutation was present in 87% of 62 additional canine InvTCC tumors. The mutation was also detectable in the urine sediments of all dogs tested with mutation-positive tumors. Functional experiments suggest that, like human tumors, canine activating BRAF mutations potently stimulate the MAPK pathway. Cell lines with the mutation have elevated levels of phosphorylated MEK, compared with a line with wild-type BRAF. This effect can be diminished through application of the BRAF(V600E) inhibitor vemurafenib. These findings set the stage for canine InvTCC as a powerful system to evaluate BRAF-targeted therapies, as well as therapies designed to overcome resistance, which could enhance treatment of both human and canine cancers. Canine Transmissible Venereal Tumor (CTVT). Canine transmissible venereal tumor (CTVT) is a parasitic cancer clone that has propagated for thousands of years via sexual transfer of malignant cells (Rev: Ostrander, Davis, Ostrander, Submitted). It is endemic everywhere except Antarctica. Because so little has been understood about the mechanisms that converted an ancient tumor into the world's oldest known continuously propagating somatic cell lineage, we created the largest existing catalog of canine genome-wide variation, which contains greater then 99% of canine genomic variation (Decker et al., 2015). We compared it against two CTVT genome sequences, thereby separating alleles derived from the founder's genome from somatic drivers of clonal transmissibility. We show that CTVT has undergone continuous adaptation to its transmissible allograft niche, with overlapping mutations at every step of immunosurveillance, particularly self-antigen presentation and apoptosis. We also identified chronologically early somatic mutations in oncogenesis- and immune-related genes that may represent key initiators of clonal transmissibility. Thus, we provide the first insights into the specific genomic aberrations that underlie CTVT's perseverance in canids around the world. A summary of our other cancer studies can be found in (Parker and Ostrander, 2014). Canine Genomics In the process of assembling 186 whole genome sequences from domestic dogs and wild canids, we realized that with little more work we could capture most of the variation present in modern dogs today. We now have a catalog of about 300 whole genome sequences that we are studying (Davis In Preparation). This is allowing us to identify genes and gene families important in canine domestication and breed development. Others share this interest and a number of collaborations have sprung up to attack this problem. We worked with (Freedman et al. 2014) To identify genetic changes underlying dog domestication and reconstruct their early evolutionary history. We generated high-quality genome sequences from three gray wolves, one from each of the three putative centers of dog domestication, two basal dog lineages (Basenji and Dingo) and a golden jackal as an outgroup. Analysis of these sequences supports a demographic model in which dogs and wolves diverged through a dynamic process involving population bottlenecks in both lineages and post-divergence gene flow. We narrow the plausible range for the date of initial dog domestication to an interval spanning 11-16 thousand years ago, predating the rise of agriculture. Regarding the geographic origin of dogs, none of the extant wolf lineages from putative domestication centers was found to be more closely related to dogs, and, instead, the sampled wolves form a sister monophyletic clade. This result, in combination with dog-wolf admixture during the process of domestication, suggests that a re-evaluation of past hypotheses regarding dog origins is necessary. Morphology A majority of our dog papers over the past 4-6 years reveal our growing understanding of canine genome organization and its relationship to morphologic variation between breeds. Our newest avenue of morphologic study is aimed at understanding the genetic underpinning of skull shape variation (Schoenebeck, 2014) which varies dramatically across breeds. To quantify the variation, we collected data from 533 museum skulls at 51 landmarks using a microscribe digitizer. The resulting principal components analysis (PCA) showed that the top four PCs account for about 77% of skull variance across breeds. We continue to make advances in this region and have written a review to summarize the state of the field (Schoenebeck and Ostrander 2014). Significant effort has also gone into developing a data repository of DNA and measurements and clinical information on Portuguese Water Dogs. This work is all being done in collaboration with K. Gordon Lark and Kevin Chase at the University of Utah. This remarkable breed is allowed considerable variation in body size and coat color. Over the years the Lark lab has built a tremendous resource of measurements and GWAS data that our own lab has continually benefitted from. We are now digging deeper into that dataset to begin studies of the genetics of metabolism and blood chemistries and to continue our work on morphology.

现代犬种的巨大表型多样性代表了超过 15,000 年的人工和自然选择实验的终点。每个品种都经过了严格的人工选择，养狗者根据身体大小、毛皮类型、颜色、头骨形状甚至行为等许多特征进行选择，创造出新的品种。采用品种壁垒规则，除非其母亲和父亲都是注册成员，否则任何狗都不能成为该品种的注册成员，这确保了每个品种内相对封闭的遗传库。因此，品种内存在很强的表型同质性，包括品种相关的遗传病。今年，我们在犬膀胱癌的研究中取得了重大进展，确定了肿瘤中常见的药物靶点。我们已经确定了犬传染性肿瘤中的突变途径，这使我们能够确定肿瘤如何逃避免疫监视。我们还继续研究犬科动物的起源。犬癌我们最近对狗疾病的遗传学研究主要集中在癌症上，我们认为这是人类癌症遗传学的强大模型（Davis 和 Ostrander，2015）。美国每年新增病例 20,000 例，犬浸润性膀胱移行细胞癌 (InvTCC) 是一种常见的自然发生的恶性肿瘤，与人类肌肉浸润性膀胱癌具有显着的组织学、生物学和临床表型。为了确定犬 InvTCC 的体细胞驱动因素，我们通过 RNAseq 确定了多个肿瘤的完整转录组（Decker 等，2015）。我们发现所有肿瘤都含有与人类 BRAF(V600E) 突变同源的体细胞突变，并且在另外 62 个犬 InvTCC 肿瘤中 87% 存在相同的突变。在所有患有突变阳性肿瘤的狗的尿液沉积物中也可以检测到这种突变。功能实验表明，与人类肿瘤一样，犬类激活 BRAF 突变可有效刺激 MAPK 通路。与具有野生型 BRAF 的细胞系相比，具有突变的细胞系的磷酸化 MEK 水平升高。通过应用 BRAF(V600E) 抑制剂维莫非尼 (vemurafenib) 可以减弱这种影响。这些发现为犬类 InvTCC 奠定了基础，成为评估 BRAF 靶向疗法以及旨在克服耐药性的疗法的强大系统，这可以增强人类和犬类癌症的治疗。犬传染性性病肿瘤（CTVT）。犬传染性性病肿瘤 (CTVT) 是一种寄生性癌症克隆，通过恶性细胞的性转移传播了数千年（修订版：Ostrander、Davis、Ostrander、已提交）。除南极洲外，它在其他地方都有流行。由于人们对将古老肿瘤转变为世界上已知最古老的连续繁殖体细胞谱系的机制知之甚少，因此我们创建了现有最大的犬类全基因组变异目录，其中包含超过 99% 的犬类基因组变异（Decker）等人，2015）。我们将其与两个 CTVT 基因组序列进行比较，从而将源自创始人基因组的等位基因与克隆遗传性的体细胞驱动因素分开。我们发现 CTVT 对其可传播的同种异体移植物生态位进行了持续适应，在免疫监视的每一步，特别是自身抗原呈递和细胞凋亡中都存在重叠突变。我们还发现了肿瘤发生和免疫相关基因中按时间顺序排列的早期体细胞突变，这些突变可能代表克隆传播性的关键启动子。因此，我们首次深入了解了 CTVT 在世界各地犬科动物中持久存在的特定基因组畸变。我们其他癌症研究的总结可以在（Parker 和 Ostrander，2014）中找到。犬基因组学在组装来自家养狗和野生犬科动物的 186 个全基因组序列的过程中，我们意识到，只需做更多的工作，我们就可以捕获当今现代狗中存在的大部分变异。我们现在拥有大约 300 个正在研究的全基因组序列的目录（戴维斯准备中）。这使我们能够识别在犬类驯化和品种发育中重要的基因和基因家族。其他人也有同样的兴趣，并且已经出现了许多合作来解决这个问题。我们与（Freedman et al. 2014）合作，识别狗驯化背后的遗传变化，并重建它们的早期进化历史。我们从三只灰狼（三个假定的狗驯化中心各一只）、两个基础狗谱系（巴森吉犬和野狗）以及作为外群的金豺中生成了高质量的基因组序列。对这些序列的分析支持了一个人口统计模型，在该模型中，狗和狼通过涉及谱系和分化后基因流的种群瓶颈的动态过程而分化。我们将狗最初驯化日期的合理范围缩小到 11-16000 年前，即农业兴起之前。关于狗的地理起源，没有发现来自假定驯化中心的现存狼谱系与狗有更密切的关系，相反，样本狼形成了一个姐妹单系进化枝。这一结果与驯化过程中的狗与狼的混合相结合，表明有必要重新评估过去有关狗起源的假设。形态学我们在过去 4-6 年中发表的大多数关于狗的论文都揭示了我们对犬基因组组织及其与品种间形态变异的关系的日益了解。我们最新的形态学研究旨在了解头骨形状变异的遗传基础（Schoenebeck，2014），不同品种的头骨形状变异差异很大。为了量化差异，我们使用 microscribe 数字化仪收集了 51 个地标的 533 个博物馆头骨的数据。由此产生的主成分分析 (PCA) 显示，前 4 个 PC 约占不同品种头骨差异的 77%。我们继续在这一领域取得进展，并撰写了一篇综述来总结该领域的现状（Schoenebeck 和 Ostrander 2014）。我们还投入了大量精力开发葡萄牙水犬的 DNA、测量数据和临床信息数据库。这项工作全部是与犹他大学的 K. Gordon Lark 和 Kevin Chase 合作完成的。这个非凡的品种允许体型和毛色有相当大的变化。多年来，Lark 实验室已经建立了巨大的测量和 GWAS 数据资源，我们自己的实验室也不断从中受益。我们现在正在深入挖掘该数据集，开始研究新陈代谢和血液化学的遗传学，并继续我们在形态学方面的工作。