Human Genetics of Tuberculosis

Project Summary Tuberculosis (TB) caused by Mycobacterium tuberculosis (Mtb) is a major health problem. About a quarter of the world population is infected, yet only a minority develop TB, either during primary infection, or later during secondary infection or reactivation of latent Mtb. Genetic epidemiological evidence strongly suggests that TB is

driven by human genetic predisposition. Its molecular basis has been dissected since 2000. We discovered 2 types of inborn errors of immunity (IEI) underlying TB, both impairing interferon (IFN)-γ immunity: (i) rare IEI, such as autosomal recessive complete IL-12Rβ1 and TYK2 deficiencies, found in a few TB patients, and (ii) a

common IEI due to homozygosity for the TYK2 missense P1104A variant that selectively disrupts IL-23- dependent IFN-γ immunity, accounting for up to 1% of European TB cases. These findings provided proof of principle that there are both rare and common monogenic etiologies of human TB, in specific ethnicities, and

established that TYK2-dependent IFN-γ production is essential for protective immunity to Mtb. However, the vast majority of TB patients lack a genetic etiology. We hypothesize that TB is the consequence of a diverse collection of monogenic or digenic IEI, with incomplete or more rarely complete penetrance, and in a sizeable proportion

of populations of diverse ancestries. To discover these variants, our project will combine a candidate gene approach focused on rare and common coding TYK2 variants with a genome-wide search for rare and common variants in other genes. TB patients will be recruited in Haiti with a specific focus on patients belonging to families

with at least two TB-affected siblings, and/or with recurrent forms of TB, as these patients are more likely to carry IEI. Our project will also take advantage of our previously recruited TB patients in Haiti and worldwide (>1,500), following a strategy combining: (i) a comprehensive genetic study based on next generation sequencing (>900

samples with whole exome sequencing data already available) to search for candidate TB-causing variants using cutting-edge computational analyses under different genetic hypotheses (genetic heterogeneity or homogeneity, monogenic or digenic inheritance), and (ii) in-depth functional studies to biochemically characterize the proteins

encoded by the newly discovered candidate variants, and to validate their causal role immunologically at the molecular and cellular levels. We will also test whether the effects of these IEI may be influenced by Mtb strains using a specific host-pathogen interaction study in Haitian patients. Our preliminary data indicate that this

approach is fruitful, as we already identified strong candidate genotypes, including both bi-allelic loss-of-function rare variations in TYK2, TNF, BTN2A2, and PDCD1, and mono- or bi-allelic common variations in IL10RA and HLA-DRB1. Our search for rare and common variants underlying monogenic or digenic IEI that govern the

development of TB with high penetrance will decipher mechanisms of protective immunity to Mtb in humans. This approach will also pave the way to new preventive or therapeutic approaches, aiming to rescue genetically deficient immune responses in patients at risk of, or with TB.