Genetics of systemic autoimmunity and comorbidities

Abstract: Sjögren‘s syndrome (SS) is a systemic autoimmune disease that typically affects the salivary and lacrimal glands leading to dry eyes and dry mouth, but the patients may also have systemic involvement. Most patients with SS carry autoantibodies, most often to the Ro (SSA) and La (SSB) proteins. During pregnancy, these autoantibodies can pass over from affected mothers to the fetus, who is then at risk of developing a congenital heart block (CHB). There is a prominent gender bias in systemic autoimmunity overall, particularly in SS where the ratio of women to men is approximately 14:1. While some genetic susceptibility factors for SS have been identified, much about the interplay between genetics, sex and the varying clinical presentation of this disease needs further study. In order to identify genetic associations with SS, we performed targeted sequencing of 1853 immune-related loci in over a thousand clinically well characterized SS patients and population controls. After subgrouping the patients by clinical manifestations, we identified three independent genetic signals in the HLA locus for Ro/La autoantibody positive SS, that were absent in the antibody negative group. The two top associations further indicated higher risk of severe manifestations, including purpura, major salivary gland swelling and lymphadenopathy. Our findings demonstrate that two distinct subgroups of patients with SS can be defined by the presence or absence of Ro/La antibodies and genetic markers. We and others have identified genetic variants associated with SS and/or the partially overlapping disease systemic lupus erythematosus (SLE). The frequency of these variants is the same in women and men in the general population. However, as the vast majority of patients are women, the risk of developing SS or SLE is much higher if the carrier is female. Genetic variants may contribute to different phenotypes via differential gene regulation, so called expression quantitative trait loci (eQTL). We hypothesized that sex may influence the eQTL effects of SS/SLE-associated genetic variants differentially in women and men, and discovered several associated variants that had sex-specific effects on the expression of nearby genes in CD19+ B cells. We also specifically studied the SS/SLE-associated FAM167A-BLK locus on chromosome 8, since the associated variants in this locus have prominent eQTL effects on the unknown gene FAM167A. We found the gene to be evolutionarily conserved, with one additional family member, but no other homologies in the genome, and the proteins to have a high level of intrinsic disorder. The gene is expressed in B cells, and we further found high expression in the lung of both mice and humans. We named the FAM167 encoded proteins Disordered Autoimmunity 1 and 2 (DIORA1 and 2), and will continue our efforts to further characterize their function. CHB affects 1-3% of anti-Ro/La autoantibody exposed pregnancies, with a recurrence rate of approximately 12-16%. The relatively low recurrence rate, despite persistent maternal autoantibodies, suggests fetal susceptibility factors are important. We performed a genome-wide association study in patients with CHB and controls. We found genetic associations with variants in the HLA region, KCNT2 on chromosome 1, and several suggestive signals. Most women with Ro/La autoantibodies have a steady state interferon activation, and to study the interferon in anti-Ro/La autoantibody positive pregnancy, we sampled anti-Ro/La positive mothers and their neonates at the time of birth, as well as healthy control mother-child pairs, and analyzed cellular profiles and cytokine- and gene expression. We found that anti-Ro/La exposed neonates had measurable type I and II interferon in plasma, and increased NK cell frequencies. Intracellular interferon detected by flow cytometry in neonatal NK and T cells indicates the neonates may produce the interferon, and we confirmed neonatal cell ability for interferon production in vitro. Notably, the genes near the CHB-associated signals were enriched for interferon regulation, suggesting an interplay between interferon activation and fetal genetic susceptibility factors in the pathogenesis of CHB. In summary, this thesis presents novel insight into genetic associations with SS and CHB, and begins to delineate how genetic susceptibility interacts with biological context such as sex or intrauterine exposure to maternal immune factors to lead to disease. The results will be important in clinical practice for personalized treatment and follow-up strategies, and as a basis for future therapy development.