Genome-wide dissection of Mendelian susceptibility to mycobacterial disease

描述(申请人提供)：孟德尔对分枝杆菌病的易感性(MSMD)是一种原发免疫缺陷综合征，其特征是由弱毒力分枝杆菌引起的严重疾病，如卡介苗和环境分枝杆菌，在其他健康的患者中。MSMD患者也容易感染结核病和沙门氏菌病，尽管其他感染很少见。MSMD在20世纪50年代首次在临床上被描述，其发病机制直到1996年才被阐明，当时它的第一个遗传学病因是在干扰素受体1(IFN-R1)缺乏的儿童中被破译。在过去的15年中，对MSMD的遗传解剖已经发现了6个致病基因，其中包括5个常染色体(IFNGR1、IFNGR2、STAT1、IL12B、IL12RB1)和1个X连锁(NEMO)基因。这六个基因座的高度等位基因异质性导致了多达13种不同疾病的定义。这些疾病患者的MSMD的发病机制涉及依赖IL-12(IL-12)的干扰素免疫功能受损。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基因缺陷。我们假设，其他患者的MSMD是由其他单基因先天免疫缺陷引起的，可能但不一定涉及IL-12-干扰素回路。一种基于假设的候选基因方法专注于参与IL-12-干扰素循环的基因，并与已知的导致MSMD的基因相关，正由NIH拨款1R01AI089970资助。因此，本申请中描述的工作的主要目标是通过遵循互补的、假设生成的、全基因组(GW)筛选方法来识别导致MSMD的新基因。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性状)和GW深度测序(通过全外显组测序)来寻找和表征MSMD的致病基因。本实验室已开发出一种新的GW连锁方法，并率先对其他传染病进行了全外显子组深度测序。按照这种方法，我们已经获得了5个新的MSMD致病基因的强有力的初步证据，这些基因在X连锁的CYBB和常染色体TYK2、JAK2、ISG15和AP4E1中存在隐性突变。这五个发现非常令人惊讶，每个发现都以独特的方式，它们一起巧妙地说明了GW方法的力量，特别是整个外显子组测序。因此，我们的项目是高度创新、可行的，并得到了强有力的初步证据的支持。从生物学的基本观点来看，这项研究将对分枝杆菌的免疫机制提供相当多和新颖的见解。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成为可能。这一新信息将为除抗生素外，使用干扰素或其他细胞因子治疗分枝杆菌疾病铺平道路。最后，MSMD的基因解剖将为在其他健康的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：孟德尔人对分枝杆菌病(MSMD)易感性的已知遗传病因损害了干扰素(干扰素)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也是由先天性免疫错误引起的，我们的目标是使用无假设的GW方法来识别这些错误。

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.