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.

现代狗品种的巨大表型多样性代表了人工和自然选择中> 15，000年实验的终点。每个品种都经历了强烈的人工选择，其中狗敌人为许多特征选择，包括身体大小，毛皮类型，颜色，头骨形状甚至行为，以创造出新的品种。采用品种障碍规则，即没有狗可以成为繁殖的注册成员，除非其大坝和父亲都是注册成员，否则可以确保每个品种内有相对封闭的遗传池。结果，在包括品种相关的遗传疾病在内的品种中存在强大的表型同质性。今年，我们在研究犬膀胱癌的研究中取得了重大进步，确定了肿瘤中常见的可药物靶标。我们已经确定了在犬传播肿瘤中突变的途径，这使我们能够确定肿瘤如何避免免疫监测。我们还继续研究犬的起源。犬类癌我们最近对狗病的遗传研究集中在癌症上，我们认为这是人类癌症遗传的强大模型（Davis and Ostrander，2015年）。每年在美国有20,000例新病例，膀胱的犬侵入性过渡细胞癌（INVTCC）是一种常见的，天然发生的恶性肿瘤，与人类肌肉侵入性膀胱癌具有重要的组织学，生物学和临床表型。为了鉴定犬InvTCC的体细胞驱动器，我们确定了RNASEQ的多个肿瘤的完整转录组（Decker等，2015）。我们发现，所有肿瘤均具有与人BRAF（V600E）突变同源的体细胞突变，并且在62个额外的犬InvTCC肿瘤中，有87％存在相同的突变。在所有用突变阳性肿瘤测试的狗的尿液沉积物中也可以检测到该突变。功能实验表明，像人类肿瘤一样，犬激活BRAF突变会有力刺激MAPK途径。与野生型BRAF相比，具有突变的细胞系具有磷酸化的MEK水平升高。通过应用BRAF（V600E）抑制剂vemurafenib可以减少这种效果。这些发现为犬类INVTCC作为评估BRAF靶向疗法的强大系统奠定了基础，以及旨在克服耐药性的疗法，可以增强对人类和犬癌的治疗。犬传播性肿瘤（CTVT）。犬可传播性静脉肿瘤（CTVT）是一种寄生癌克隆，通过恶性细胞的性转移已经传播了数千年（Rev：Ostrander，Davis，Davis，Ostrander，Ostrander，提交）。除南极以外，它都处于地方性。因为关于将古代肿瘤转化为世界上最古老的持续传播细胞谱系的机制几乎没有理解，所以我们创建了犬类全基因组变异的最大现有目录，其中包含99％的犬类基因组变异的99％（Decker等，2015）。我们将其与两个CTVT基因组序列进行了比较，从而将源自创始人基因组的等位基因与克隆透射性的体细胞驱动因素分离。我们表明，CTVT对其可传播的同种异体移植属裂持续适应，并在免疫监视的每个步骤中都有重叠的突变，尤其是自我抗原表现和凋亡。我们还确定了可能代表克隆传播性的关键启动者的肿瘤生成和免疫相关基因中的年代早期体细胞突变。因此，我们为CTVT在世界各地的犬科动物上的毅力基础的特定基因组畸变提供了第一个见解。可以在（Parker and Ostrander，2014年）中找到我们其他癌症研究的摘要。犬基因组学在组装来自家犬和野生犬科动物的186个整个基因组序列的过程中，我们意识到，几乎没有工作，我们几乎可以捕捉到当今现代狗的大部分变化。现在，我们正在研究我们正在研究的大约300个整个基因组序列的目录（戴维斯在准备中）。这使我们能够鉴定基因和基因家族在犬种驯化和繁殖中很重要。其他人则分享了这一兴趣，并且有许多合作以攻击这个问题。我们与（Freedman等人，2014年）合作，确定了狗驯化的遗传变化，并重建了其早期进化史。我们从三只灰狼中产生了高质量的基因组序列，其中一个来自三个推定的狗驯化中心，两个基底狗谱系（Basenji和Dingo）和一个金色jack狼作为外组。对这些序列的分析支持了一个人口统计学模型，在该模型中，狗和狼在涉及谱系和传播后基因流中涉及种群瓶颈的动态过程中差异。我们将初始狗驯化日期的合理范围缩小到跨越11-16千年前的间隔，早于农业的兴起。关于狗的地理起源，发现假定的驯化中心的现存狼谱系与狗的关系更紧密，而采样的狼则形成了姐妹的单属枝条。在驯化过程中，该结果与狗狼混合结合了混合，表明需要对过去关于狗起源的假设进行重新评估。形态学在过去的4 - 6年中，我们的大多数狗论文揭示了我们对犬类基因组组织的越来越多及其与品种之间形态变化的关系的越来越多。我们最新的形态学研究途径旨在了解颅骨形状变异的遗传基础（Schoenebeck，2014年），该概念在各种品种之间变化很大。为了量化这种变化，我们使用Microscribe数字化器从51个地标从533个博物馆头骨收集了数据。由此产生的主成分分析（PCA）表明，前四个PC占各种品种颅骨方差的77％。我们继续在该地区取得进步，并写了一份审查来总结该领域的状态（Schoenebeck and Ostrander 2014）。开发DNA以及有关葡萄牙水犬的测量和临床信息的数据存储库也大大努力。这项工作都是与犹他大学的K. Gordon Lark和Kevin Chase合作完成的。这种非凡的品种允许体型和外套颜色的差异很大。多年来，Lark Lab建立了我们自己的实验室不断受益的大量测量和GWAS数据资源。现在，我们正在深入研究该数据集，以开始研究代谢和血液化学的遗传学，并继续我们的形态学工作。