Deep resequencing identifies candidate functional genes in leprosy GWAS loci

Leprosy is the second most prevalent mycobacterial disease globally. Despite the existence of an effective therapy, leprosy incidence has consistently remained above 200,000 cases per year since 2010. Numerous host genetic factors have been identified for leprosy that contribute to the persistently high case numbers. In the past decade, genetic epidemiology approaches, including genome-wide association studies (GWAS), identified more than 30 loci contributing to leprosy susceptibility. However, GWAS loci commonly encompass multiple genes, which poses a challenge to define causal candidates for each locus. To address this problem, we hypothesized that genes contributing to leprosy susceptibility differ in their frequencies of rare protein-altering variants between cases and controls. Using deep resequencing we assessed protein-coding variants for 34 genes located in GWAS or linkage loci in 555 Vietnamese leprosy cases and 500 healthy controls. We observed 234 nonsynonymous mutations in the targeted genes. A significant depletion of protein-altering variants was detected for the IL18R1 and BCL10 genes in leprosy cases. The IL18R1 gene is clustered with IL18RAP and IL1RL1 in the leprosy GWAS locus on chromosome 2q12.1. Moreover, in a recent GWAS we identified an HLA-independent signal of association with leprosy on chromosome 6p21. Here, we report amino acid changes in the CDSN and PSORS1C2 genes depleted in leprosy cases, indicating them as candidate genes in the chromosome 6p21 locus. Our results show that deep resequencing can identify leprosy candidate susceptibility genes that had been missed by classic linkage and association approaches.

Case Report: Reactive Lymphohistiocytic Proliferation in Infant With a Novel Nonsense Variant of IL2RG Who Received BCG Vaccine

We present here a male young infant with X-linked severe combined immunodeficiency (MIM#300400) due to the novel nonsense variant of IL2RG (interleukin 2 receptor, gamma; MIM#308380), NM_000206.2(IL2RG):c.820_823dup p.Ser275Asnfs*29. He developed aggressive reactive lymphohistiocytic proliferation after receiving the live-attenuated Bacillus Calmette-Guérin (BCG) vaccine at birth. This report advocates for modifying the current practice of early use of BCG. The natural history of his disease also suggests considering IL2RG variants as a potential cause of “X-linked recessive Mendelian susceptibility to mycobacterial disease” (MSMD). His reactive lymphohistiocytic proliferation and massive hepatosplenomegaly simulated hemophagocytic lymphohistiocytosis (HLH, likely triggered by the BCG disease). This entity was masked by the absence of fever and markedly elevated inflammatory biomarkers. Thus, his findings stimulate discussion on the need to modify the diagnostic criteria of HLH, in order to accommodate conditions, such IL2RG variants that block systemic inflammation.

Phenotypic and immune functional profiling of patients with suspected Mendelian Susceptibility to Mycobacterial Disease in South Africa

Background Mendelian Susceptibility to Mycobacterial Disease (MSMD) is a primary immunodeficiency (PID) characterised by a predisposition to infection by weakly-pathogenic mycobacteria. In countries with a high prevalence of tuberculosis (TB), individuals with MSMD are also prone to infections by Mycobacterium tuberculosis. Several MSMD-associated genes have been described, all resulting in a disruption of IL-12 and IFN-γ cytokine axis, which is essential for control of mycobacterial infections. An accurate molecular diagnosis, confirmed by phenotypic and functional immune investigations, is essential to ensure that the patient receives optimal treatment and prophylaxis for infections. The aim of this study was to implement a set of functional assays to assess the integrity of the IL-12-IFN-γ cytokine pathways in patients presenting with severe, persistent, unusual and/or recurrent TB, mycobacterial infections or other clinical MSMD-defining infections such as Salmonella. Methods Blood was collected for subsequent PBMC isolation from 16 participants with MSMD-like clinical phenotypes. A set of flow cytometry (phenotype and signalling integrity) and ELISA-based (cytokine production) functional assays were implemented to assess the integrity of the IL-12-IFN-γ pathway. Results The combination of the three assays for the assessment of the integrity of the IL-12-IFN-γ pathway was successful in identifying immune deficits in the IL-12-IFN-γ pathway in all of the participants included in this study. Conclusions The data presented here emphasise the importance of investigating PID and TB susceptibility in TB endemic regions such as South Africa as MSMD and other previously described PIDs relating to TB susceptibility may present differently in such regions. It is therefore important to have access to in vitro functional investigations to better understand the immune function of these individuals. Although functional assays alone are unlikely to always provide a clear diagnosis, they do give an overview of the integrity of the IL-12-IFN-γ pathway. It would be beneficial to apply these assays routinely to patients with suspected PID relating to mycobacterial susceptibility. A molecular diagnosis with confirmed functional impairment paves the way for targeted treatment and improved disease management options for these patients.

Disseminated Salmonellosis in a child with IL12Rß1 deficiency – Case report and review of literature.

Mendelian susceptibility to mycobacterial disease (MSMD) is a group of genetic disorders characterized by a defect in interferon γ (IFN γ)–mediated immunity, with predisposition to infections caused by atypical and low virulent mycobacteria and other intra-macrophagic organisms like Salmonella, Klebsiella, Listeria etc. A 10-year-old boy, second born of a consanguineously (third-degree) married Indian couple, presented with left inguinal and submandibular lymphadenopathy with low grade fever for 10 days. Past history was significant as the child had been unwell from infancy. At the age of 4 months and 5 years, he was diagnosed to have tubercular axillary lymphadenitis and was treated with anti-tubercular drugs on each occasion and he responded to the same. On examination, he had left submandibular and inguinal lymphadenopathy and mild splenomegaly. Chest radiograph showed enlarged mediastinal nodes. He underwent left inguinal lymph node biopsy that reported granulomatous lymphadenitis. However, culture from the biopsy showed a growth of Salmonella enterica sensitive to ceftriaxone. Genetic evaluation showed pathogenic homozygous mutation c.1791 + 2T > G in exon 15 of IL12Rß1 gene by whole exome sequencing. A diagnosis of Mendelian Susceptibility to Mycobacterial Disease (MSMD) was established and he was treated with intravenous ceftriaxone followed by oral cefixime. He responded promptly and lymphadenopathy resolved. He is currently being maintained on azithromycin prophylaxis. Children and adults presenting with disseminated infections with atypical mycobacteria and salmonella must be evaluated for MSMD. Disseminated salmonellosis is a peculiar manifestation in IL12Rß1 deficiency. A detailed review of literature on IL12RB1 deficiency was performed. Index case has been discussed in light of the previously published literature.

Severe mycobacterium bovis BCG infection in an infant with partial dominant interferon gamma receptor deficiency-a case report

Mendalian susceptibity to mycobacterial disease (MSMD) is a condition caused by selective susceptibility to weakly virulent bacteria in otherwise healthy patients without additional immunological abnormalities. It is an inherited, genetic disorder with variety of clinical presentation. Diagnosis is mandatory because the illness may get precipitated by BCG and other live vaccines. Estimating interleukin in serum can be considered as a diagnostic test. Immunological analysis is mandatory for confirming the diagnosis. Mutation analysis can be done to confirm the mutation and hence, prevent the disease in the next sibling by testing in utero. This condition can be treated with ATT as the first line treatment. If ineffective, can be given other modalities of treatment described. But relapses are common. Stem cell transplantation is the definitive treatment. We describe an infant diagnosed as partial dominant interferon gamma receptor deficiency (IFNGR1) deficiency, who responded to ATT