Genome-wide dissection of Mendelian susceptibility to mycobacterial disease

描述（由申请方提供）：孟德尔分枝杆菌病易感性（MSMD）是一种原发性免疫缺陷综合征，其特征是在其他健康患者中由弱毒力分枝杆菌（如BCG疫苗和环境分枝杆菌）引起的严重疾病。患有MSMD的患者也容易患结核病和沙门氏菌病，尽管其他感染很少见。MSMD的发病机制在20世纪50年代首次在临床上描述，直到1996年才被阐明，当时它的第一个遗传病因是在儿童干扰素受体1（IFN-R1）缺乏症中被破译。在过去的十五年中，对MSMD的遗传解剖已经鉴定出六个致病基因，包括五个常染色体（IFNGR 1、IFNGR 2、STAT 1、IL 12 B、IL 12 RB 1）和一个X连锁（NEMO）基因。在这六个位点的等位基因异质性的高水平，导致多达13个不同的疾病的定义。在患有这些疾病的患者中MSMD的发病机制涉及受损的白细胞介素-12（IL-12）依赖性IFN-免疫。然而，在我们实验室测试的600名患者中，只有大约一半携带这些遗传缺陷。我们假设其他患者的MSMD是由其他单基因先天性免疫缺陷引起的，可能但不一定涉及IL-12-IFN-通路。一种基于假设的候选基因方法，重点关注IL-12-IFN-通路中涉及的基因和与已知的MSMD致病基因相关的基因，该方法由NIH资助1 R 01 AI 089970。因此，本申请中描述的工作的主要目标是通过遵循互补的、产生假设的、全基因组（GW）筛选方法来鉴定新的MSMD致病基因。在目前的GW方法中，我们将通过GW连锁（X连锁和常染色体隐性遗传性状）和GW深度测序（通过全外显子组测序）来搜索和表征导致MSMD的基因。在实验室中开发了一种新的GW连锁方法，并且我们的实验室在其他感染性疾病中开创了全外显子组深度测序。根据这种方法，我们已经获得了强有力的初步证据，五个新的MSMD致病基因，在X连锁CYBB和常染色体TYK 2，JAK 2，ISG 15和AP 4 E1的隐性突变。这五个发现都非常令人惊讶，每一个都以独特的方式，它们一起巧妙地说明了GW方法的力量，特别是全外显子组测序。因此，我们的项目具有高度的创新性和可行性，并得到了强有力的初步证据的支持。从基本的生物学观点来看，这项研究将为分枝杆菌免疫机制提供相当多的新见解。阐明MSMD的分子遗传学基础也将有助于阐明分枝杆菌病的发病机制，为患者提供分子诊断和为家庭提供遗传咨询。这一新的信息将为使用IFN-γ或其他细胞因子治疗分枝杆菌疾病铺平道路，除了抗生素。最后，MSMD的基因解剖将为在其他健康儿童中进行严重结核病的基因解剖铺平道路。 公共卫生相关性：已知的孟德尔易感性的遗传病因分枝杆菌病（MSMD）损害干扰素（IFN）介导的免疫。近一半的MSMD患者缺乏遗传病因。我们假设这些患者的MSMD也是由先天性免疫缺陷引起的，我们的目标是使用无假设的GW方法来确定。

DESCRIPTION (provided by applicant): Mendelian susceptibility to mycobacterial disease (MSMD) is a primary immunodeficiency syndrome characterized by severe disease caused by weakly virulent mycobacteria, such as BCG vaccines and environmental mycobacteria, in otherwise healthy patients. Patients with MSMD are also vulnerable to tuberculosis and salmonellosis, though other infections are rare. First described clinically in the 1950s, the pathogenesis of MSMD remained unclear until 1996, when its first genetic etiology was deciphered in children with interferon- receptor 1 (IFN-R1) deficiency. Genetic dissection of MSMD over the last fifteen years has identified six morbid genes, including five autosomal (IFNGR1, IFNGR2, STAT1, IL12B, IL12RB1) and one X- linked (NEMO) gene. The high level of allelic heterogeneity at these six loci has led to the definition of up to 13 distinct disorders. The pathogenesis of MSMD in patients with these disorders involves impaired interleukin-12 (IL-12)-dependent IFN- immunity. However, only about half of the 600 patients tested in our laboratory carried any of these genetic defects. We hypothesize that MSMD in other patients results from other monogenic inborn errors of immunity, possibly but not necessarily involving the IL-12-IFN- circuit. A hypothesis-based, candidate gene approach focused on genes involved in the IL-12-IFN- circuit and related to the known MSMD-causing genes is being funded by the NIH grant 1R01AI089970. Therefore, the principal objective of the work described in this application is to identify new MSMD-causing genes by following a complementary, hypothesis-generating, genome-wide (GW) screening approach. In the present, GW approach, we will search for and characterize MSMD-causing genes by GW linkage (for both X-linked and autosomal recessive traits) and GW deep sequencing (by whole-exome sequencing). A novel method of GW linkage has been developed in the lab and whole-exome deep sequencing has been pioneered by our lab for other infectious diseases. Following this approach, we have obtained strong preliminary evidence of five novel MSMD-causing genes, with recessive mutations in X-linked CYBB and autosomal TYK2, JAK2, ISG15, and AP4E1. These five discoveries are very surprising, each in a unique way, and together they neatly illustrate the power of GW approaches and whole-exome sequencing in particular. Our project is therefore highly innovative, feasible, and supported by strong preliminary evidence. From a basic biological standpoint, this research will provide considerable and novel insights into the mechanisms of immunity to mycobacteria. Elucidation of the molecular genetic basis of MSMD will also shed light on the pathogenesis of mycobacterial disease, making it possible to provide molecular diagnoses for patients and genetic counseling for families. This new information will pave the way for the use of IFN- or other cytokines for the treatment of mycobacterial diseases, in addition to antibiotics. Finally, the genetic dissection of MSMD will pave the way for the genetic dissection of severe tuberculosis in otherwise healthy children. PUBLIC HEALTH RELEVANCE: The known genetic etiologies of Mendelian susceptibility to mycobacterial disease (MSMD) impair interferon (IFN)--mediated immunity. Nearly half the patients with MSMD lack a genetic etiology. We hypothesize that MSMD in these patients also results from inborn errors of immunity, which we aim to identify using hypothesis- free, GW approaches.