Genome-Wide Dissection of Mendelian Susceptibility to Mycobacterial Disease

项目摘要 分枝杆菌病（MSMD）的孟德尔易感性是一种遗传和选择性的临床易感性， 由弱毒性分枝杆菌引起的疾病，如卡介苗（BCG）疫苗， 环境分枝杆菌（EM）。MSMD患者偶尔易受其他巨噬细胞内 病原体（例如沙门氏菌）。MSMD的发病机制一直不清楚，直到1996年，当它的第一个遗传 干扰素-γ受体1（IFN-γR1）缺乏症患儿的病因已被阐明。遗传学研究 在过去的25年中，已经鉴定了16种引起MSMD的基因，包括14种常染色体基因（IFNG，IFNGR 1，IFNGR 2， STAT 1、IL 12 B、IL 12 RB 1、IL 12 RB 2、IL 23 R、IRF 8、SPPL 2A、RORC、ISG 15、TYK 2、JAK 1）和2个X连锁基因 (NEMO，CYBB）。在这些基因座的等位基因异质性的高水平已经定义了31个不同的疾病。有 然而，由于所有疾病都损害IFN-γ免疫性，因此其具有生理均一性。5个基因突变（RORC， ISG 15、TYK 2、JAK 1、STAT 1）可能是具有相关表型的非典型综合征形式的MSMD的基础。 事后看来，MSMD是一个用词不当，因为大多数遗传病因显示MSMD的不完全遗传。这 偶然发现了真正的结核病的遗传病因。值得注意的是，只有大约一半 在我们实验室研究的900名国际患者中，外显子和侧翼内含子中携带导致MSMD的病变 在这16个基因座中的任何一个。在这个更新申请中，我们假设无法解释的MSMD病例可以 由新的单基因先天性免疫缺陷引起，可能但不一定涉及IFN-γ介导的 免疫力我们的目标是通过全基因组（GW）方法，基于 主要但不限于全外显子组测序（WES）。我们将招募至少50名MSMD患者， 年我们将通过检验遗传同质性的假设来寻找新的遗传病因，即寻找 两个或两个以上家族的基因突变。我们还将测试遗传异质性的假设，即搜索 一个家族的基因突变这项研究将受益于我们长达12年的计算发展， 分析WES的工具。将建立候选基因型与MSMD之间的因果关系 在分子、细胞和免疫学水平上进行了深入的机制实验， 尖端技术和我们对MSMD长达25年的研究。在无候选基因型的患者中， WES，我们将在已知和未知的MSMD致病基因中寻找候选调控变异， 基因组测序（WGS）。我们的初步结果令人兴奋，因为我们已经确定了导致MSMD的突变 在已知对IFN-γ免疫至关重要的基因（TBX 21、IRF 1）和其他可能破坏IFN-γ的基因中 新机制免疫（ZNFX 1，MCTS 1）。从免疫学的角度来看，这项研究将提供 人类对分枝杆菌免疫机制的新见解。从医学的角度来看，这项工作 将为MSMD患者提供分子诊断，为家庭提供遗传咨询，同时提供使用 治疗性IFN-γ，至少在那些遗传性疾病不能消除对IFN-γ的细胞反应的患者中。

Project Summary Mendelian susceptibility to mycobacterial disease (MSMD) is a genetic and selective predisposition to clinical disease caused by weakly virulent mycobacteria, such as Bacillus Calmette-Guérin (BCG) vaccines and environmental mycobacteria (EM). Patients with MSMD are occasionally vulnerable to other intra-macrophagic pathogens (e.g. salmonella). The pathogenesis of MSMD remained unclear until 1996, when its first genetic etiology was deciphered in children with interferon-γ receptor 1 (IFN-γR1) deficiency. Genetic studies over the last 25 years have identified 16 MSMD-causing genes, including 14 autosomal (IFNG, IFNGR1, IFNGR2, STAT1, IL12B, IL12RB1, IL12RB2, IL23R, IRF8, SPPL2A, RORC, ISG15, TYK2, JAK1) and 2 X-linked genes (NEMO, CYBB). The high level of allelic heterogeneity at these loci has defined 31 distinct disorders. There is however physiological homogeneity, as all disorders impair IFN-γ immunity. Mutations in 5 genes (RORC, ISG15, TYK2, JAK1, STAT1) can underlie an atypical, syndromic form of MSMD, with an associated phenotype. With hindsight, MSMD is a misnomer, as most genetic etiologies show incomplete penetrance for MSMD. This serendipitously led to the discovery of genetic etiologies of bona fide tuberculosis. Remarkably, only about half of the 900 international patients studied in our lab carry MSMD-causing lesions in the exons and flanking intron regions at any of these 16 loci. In this renewal application, we hypothesize that unexplained MSMD cases can result from novel monogenic inborn errors of immunity, possibly but not necessarily involving IFN-γ mediated immunity. We aim to identify new MSMD-causing genes by following a genome-wide (GW) approach, based primarily but not exclusively on whole-exome sequencing (WES). We will enroll at least 50 MSMD patients each year. We will search for novel genetic etiologies by testing a hypothesis of genetic homogeneity, i.e. searching for genes mutated in two or more families. We will also test a hypothesis of genetic heterogeneity, i.e. searching for genes mutated in a single family. This search will benefit from our 12-year-long development of computational tools to analyze WES. Causal relationships between candidate genotypes and MSMD will be established experimentally in great mechanistic depth at the molecular, cellular, and immunological levels, taking advantage of cutting-edge technologies and our 25-year-long study of MSMD. In patients without candidate genotypes by WES, we will search for candidate regulatory variations in known and unknown MSMD-causing genes by whole genome sequencing (WGS). Our preliminary results are exciting, as we have identified MSMD-causing mutations in genes known to be crucial for IFN-γ immunity (TBX21, IRF1) and in other genes that probably disrupt IFN-γ immunity by novel mechanisms (ZNFX1, MCTS1). From an immunological standpoint, this research will provide novel insights into the mechanisms of human immunity to mycobacteria. From a medical standpoint, this work will provide molecular diagnoses for MSMD patients and genetic counseling for families, while offering the use of therapeutic IFN-γ, at least in patients whose genetic disorder does not abolish cellular responses to IFN-γ.