Autoimmune diseases are clinical manifestations of a loss-of-tolerance of the immune system against the body’s own substances and healthy tissues. Primary Sjögren’s syndrome (pSS) and systemic lupus erythematosus (SLE) are two chronic inflammatory autoimmune diseases characterized by autoantibody production and an activated type I interferon system. Although the precise mechanisms leading to autoimmune processes are not well defined, recent studies suggest that aberrant DNA methylation and gene expression patterns may play a central role in the pathogenesis of these disorders. The aim of this thesis was to investigate DNA methylation and gene expression in pSS and SLE on a genome-wide scale to advance our understanding of how these factors contribute to the diseases and to identify potential biomarkers and novel treatment targets. In study I, differential DNA methylation was analyzed in multiple tissues from pSS patients and healthy controls. We identified thousands of CpG sites with perturbed methylation; the most prominent finding was a profound hypomethylation at regulatory regions of type I interferon induced genes in pSS. In study II, a cases-case study comparing DNA methylation in pSS patients with high fatigue to patients with low fatigue, we found methylation patterns associated to the degree of fatigue. In study III, RNA-sequencing was applied to investigate the transcriptome of B cells in pSS in comparison to controls. Increased expression of type I and type II interferon regulated genes in pSS was observed, indicating ongoing immune activation in B cells. In study IV, the impact of DNA methylation on disease susceptibility and phenotypic variability in SLE was investigated. We identified DNA methylation patterns associated to disease susceptibility, SLE manifestations and different treatments. In addition, we mapped methylation quantitative trait loci and observed evidence for genetic regulation of DNA methylation in SLE.   In conclusion, the results presented in this thesis provide new insights into the molecular mechanisms underlying autoimmunity in pSS and SLE. The studies confirm the central role of the interferon system in pSS and SLE and further suggest novel genes and mechanisms to be involved in the pathogenesis these autoimmune diseases.

This thesis comprised patients with chronic rheumatic diseases. The studies aimed to elucidate food sensitivity by measuring mucosal inflammatory reactivity and thereby a possible link between the gut and joints. In all the studies, the mucosal path technique was used to evaluate the rectal mucosal response to rectal challenge with gluten and/or cow’s milk protein (CM). In some patients with primary Sjögren’s syndrome (pSS) and the genetic susceptibility genes HLA DQ2, mucosal reactivity measured with nitric oxide (NO) was found after rectal gluten challenge without detectable serum antibodies to gluten or transglutaminase. This gluten sensitivity was not linked to coeliac disease. After rectal CM challenge, a rectal mucosal inflammatory response measured with NO and myeloperoxidase (MPO) was detected in 38% of pSS patients, all of whom fulfilled the criteria for irritable bowel syndrome. In a questionnaire study of self-experienced adverse reactions to food, 27% of patients with rheumatoid arthritis (RA) reported intolerance to various foods and CM in particular. After rectal CM challenge performed in RA patients (n=27), strong mucosal reactivity to CM was observed in a few patients and a moderate increase in 23%. After gluten challenge, a moderate increase in mucosal reactivity was found in 35% of patients. No correlation to self-perceived intolerance and mucosal reactivity measured with NO and MPO was seen. Inflammation of the gut is a prominent feature of spondyloarthropathies (SpA). After rectal challenges with CM protein and gluten, an increase in rectal NO production was seen in 26% and 19% respectively (p<0.001). An increase in the mucosal release of MPO as a sign of neutrophil activation was seen in the CM- and gluten-sensitive patients. NO production in SpA patients was more enhanced compared with RA and pSS patients and could contribute to the increased barrier permeability described in SpA patients.

Le syndrome de Gougerot-Sjögren (SGS) est une épithélite auto-immune caractérisée par des lésions des glandes exocrines et manifestations systémiques. Une des complications majeures est la survenue chez 5% des malades, d’un lymphome non-hodgkininen (NHL). La contribution majeure des lymphocytes B (LB) a récemment été démontrée. Dans ce travail, nous avons voulu aborder des sujets cliniques et fondamentaux concernant le rôle des LB dans le SGS. Dans un premier temps, nous avons démontré que des LB mémoires sont visibles dans des infiltrats des échantillons de la peau et sa présence peut aider au diagnostic. Dans un deuxième temps, nous avons démontré que la cytokine FLT3-L augmentée (une cytokine impliquée dans l’ontogenèse des LB et lympho-prolifération) est associée à une distribution anormale des LB dans les malades. En plus, le rôle prolifératif de FLT3-L sur les LB pourrait expliquer l’évolution vers le NHL. Dans un troisième temps, nous avons étudié une autre cytokine dérégulée dans le SGS (la cytokine BAFF) et nous avons confirmé le rôle d’un nouveau variant de BAFF produit par l’épissage alternatif de l’exon 4 (∆4BAFF) comme un facteur de transcription de son propre gène. Ce nouveau variant est beaucoup plus exprimé au cours des maladies autoimmunes, et son expression est contrôlée par l’interferon gamma et la protéine SC35. Tous ces données montrent pour la première fois, un nouveau concept à savoir la possibilité pour une cytokine d’être régulée par un variant provenant de l’épissage alternatif de son propre gène. Ensemble, ces résultats montrent le rôle des cytokines impliquées dans l’ontogenèse et la survie des LB, dans la physiopathologie du SGS. / Primary Sjögren’s Syndrome (pSS) is a systemic autoimmune disease characterized by sicca symptoms and a broad variety of systemic manifestations. The most severe complication of the disease is the development of non-Hodgkin’s lymphoma (NHL) in 5% of patients. Recent evidence indicates a major contribution of B cells. In this work, we developed clinical and basic research subjects, related to the role of B-cell in the pathogenesis of pSS. In the first section, we showed that memory B-cell infiltrates are present in pSS and may be used as an additional diagnostic and follow-up tool. In the second section, we showed that high serum levels of the cytokine called FLT3-L (a cytokine implicated in B-cell ontogenesis and lymphoproliferation) are associated with abnormal B-cell distribution, characteristic of pSS; and disease clinical activity. In addition, this cytokine may explain the development of lymphoma. In the third section, we demonstrated that ∆4BAFF (a new variant of BAFF, due to the alternative splicing of exon 4) is a transcription factor of its own gene. Interestingly, this new variant is mainly detected in autoimmune diseases and its expression is regulated by IFN-y and SC35 protein (one of the proteins implicated in the splicing machinery). This finding provides an expanded conceptual view of BAFF gene regulation in autoimmune diseases, and contributes to a better understanding of the mechanisms involved in BAFF up-regulation in autoimmunity. Collectively, these results are of clinical and fundamental basic interest in pSS, in the diagnostic, physiopathology and therapeutic contexts.