Genome-Wide Dissection of Mendelian Susceptibility to Mycobacterial Disease

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.

Grant Number: 5R01AI095983-15
NIH Institute/Center: NIH
Principal Investigator: Jean-Laurent Casanova