Genomic investigation of primary immunodeficiency
Primary immunodeficiencies (PIDs) are a collection of rare diseases which effect one or more components of the human immune system and are typically considered monogenic. PID presents with features including increased susceptibility to infection, autoimmunity, autoinflammation, atopy and malignancy. The list of genes associated with these inborn errors of immunity continues to expand. However, the majority of patients clinically effected with PID still remain without a genetic diagnosis. In this thesis, I have investigated three novel monogenic associations with PID, and also explored the impacts of common genetic variation in PID-associated genes with common diseases. From analysis of whole-genome sequence data of over 800 PID probands within the NIHR BioResource Rare Disease PID cohort, I identified novel monogenic associations between PID and rare deleterious variants in SOCS1, IVNS1ABP and TRAF3. In two families with autoimmunity and immunodeficiency I investigated the impacts of heterozygous deleterious variants in SOCS1. Patients showed reduced suppressor of cytokine signalling 1 (SOCS1) protein leading to enhanced signal transducer and activator of transcription 1 (STAT1) phosphorylation. Also, due the reduction in the E3 ligase action of SOCS1, patient cells showed increased Toll-like receptor cytokine responses and hyperactivity of the Akt pathway. Thus, dysregulation of multiple immune pathways leads to autoimmunity and immunodeficiency in affected individuals. I then examined the functions and role of Influenza virus NS1A-binding protein (IVNS1ABP) in immunity through the study of three patients with IVNS1ABP haploinsufficiency. These patients presented with warts and autoimmune disease with low CD4+ T cells and aberrant expression of PD-1 and CD127. Study of patient T cells, IVNS1ABP knockdown Jurkat cell lines, and CRISPR/Cas9-mediated IVNS1ABP knockdown in primary human T cells demonstrated that reduced IVNS1ABP leads to T cell hyperactivation. Development of Ivns1abpEM1/+ haploinsufficient mice corroborated these human findings, with Ivns1abpEM1/+ mice displaying Cd4+ lymphopenia and developing an immune phenotype consistent with that of affected humans with age and following host-pathogen interactions. Finally, I investigated seven individuals from three families with heterozygous deleterious variants in TRAF3. Affected individuals clinically presented with bacterial infections and autoimmunity, predominantly early-onset Sjögren’s syndrome. Reduced tumour necrosis factor receptor-associated factor 3 (TRAF3) in B cells led to increased NF-B2 activity resulting in polyclonal hypergammaglobulinaemia and auto-antibody production. Increased NF-B2 activity promoted mitochondrial respiration and consequently B cell activity. TRAF3 is frequently somatically mutated in B cell malignancies, and I showed that somatic loss of TRAF3 has similar biological effects in B cells to those observed in the monogenic PID patients. Utilising the phenotypes of the monogenic TRAF3 haploinsufficient patients I identified common variants in TRAF3 which, via actions as expression quantitative trait loci, reduce expression of TRAF3 and increased the risk of B cell malignancy, systemic lupus erythematosus, and bacterial infections in the general population. Thus, the work in this thesis demonstrates how the study of rare monogenic PID can inform on the roles of specific genes in human immunity, and also how common variants in these human PID-associated genes may infer disease risks, albeit at a far lower relative risk to the individual, across the wider population.
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