Genome-Wide Dissection of Mendelian Susceptibility to Mycobacterial Disease

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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.