Positional identification and functional analysis of genes regulating autoimmune arthritis

The major histocompatibility complex (MHC) is the most gene-dense and polymorphic region in the human genome with strong associations to many autoimmune disorders, including rheumatoid arthritis (RA). However, even the genetic association between MHC and RA was known more than 40 years ago, we still have not fully explained the functional roles of the MHC genes and identified the underlying specific polymorphisms. This thesis describes some of our research aimed for a better understanding of this topic, which can largely be divided into three parts as follows. First, we made use of a panel of MHC class II (MHC-II) congenic strains to evaluate the functional roles of MHC-II polymorphisms in arthritis. By performing an extensive genetic and functional analysis, we showed that MHC-II RT1-B (the rat orthologs of HLA-DQ) determines the onset and severity of experimental arthritis, possibly due to the amino acid variations in the P1 pocket of RT1-B. In addition, we showed that natural allelic variants in Tap2, another gene in the MHC-II region, regulates the thymic selection of CD8+ T cells. Second, in order to investigate whether other MHC genes also contribute to arthritis susceptibility, we assessed arthritis development in congenic strains mapped to other parts of the MHC region. We identified a second arthritis-regulatory QTL in the MHC class III region, that regulates not only the onset and severity, but also chronicity of arthritis. We subsequently mapped this effect to a conserved, 33-kb large haplotype Ltab-Ncr3 comprising five polymorphic genes. Interestingly, unlike other positionally-identified arthritis genes in rats, Ltab-Ncr3 regulates only adjuvant arthritis models but not autoimmunity triggered by specific tissue antigens, such as type II collagen. Furthermore, we found that gene expression and alternative splicing of the Ltab-Ncr3 genes correlate remarkably with arthritis severity and some of the gene expression differences were reproduced in a cohort of RA patients and healthy controls. Third, the MHC-II gene expression is regulated by class II transactivator (CIITA or C2TA), and in humans, genetic variation in CIITA has been associated with differential expression of MHC-II and susceptibility to autoimmune diseases. Using a congenic mouse strain with an allelic variant in the type I promoter of C2ta, we demonstrate that whereas genetic polymorphisms in C2ta promoter result in differential MHC-II expression and antigen presentation, these do not necessarily have a strong impact on autoimmune diseases such as arthritis. In summary, these studies demonstrate how the congenic approach remains powerful to conclusively identify and characterise genes regulating a complex disease like arthritis. LIST OF SCIENTIFIC PAPERS I. Positional identification of RT1-B (HLA-DQ) as susceptibility locus for autoimmune arthritis Sabrina Haag*, Jonatan Tuncel*, Soley Thordardottir, Daniel E. Mason, Anthony C. Y. Yau, Doreen Dobritzsch, Johan Bäcklund, Eric C. Peters, & Rikard Holmdahl J Immunol. 2015 Mar 15;194(6):2539-50 II. Class II major histocompatibility complex–associated response to type XI collagen regulates the development of chronic arthritis in rats Jonatan Tuncel, Sabrina Haag, Stefan Carlsén, Anthony C. Y. Yau, Shemin Lu, Harald Burkhardt, Rikard Holmdahl Arthritis Rheum. 2012 Aug;64(8):2537-47 III. Natural polymorphisms in Tap2 influence negative selection and CD4∶CD8 lineage commitment in the rat Jonatan Tuncel, Sabrina Haag, Anthony C. Y. Yau, Ulrika Norin, Amelie Baud, Erik Lönnblom, Klio Maratou, A Jimmy Ytterberg, Diana Ekman, Soley Thordardottir, Martina Johannesson, Alan Gillet, EURATRANS Consortium, Pernilla Stridh, Maja Jagodic, Tomas Olsson, Alberto Fernandez-Teruel, Roman A. Zubarev, Richard Mott, Timothy J Aitman, Jonathan Flint, Rikard Holmdahl PLoS Genet. 2014 Feb 20;10(2):e1004151 IV. Conserved 33-kb haplotype in the MHC class III region regulates chronic arthritis Anthony C. Y. Yau, Jonatan Tuncel, Sabrina Haag, Ulrika Norin, Miranda Houtman, Leonid Padyukov, Rikard Holmdahl Proc Natl Acad Sci U S A. 2016 Jun 28;113(26):E3716-24 V. MHC class III Ltab-Ncr3 haplotype regulates adjuvant-induced but not antigen-dependent autoimmunity Anthony C. Y. Yau, Jonatan Tuncel, Rikard Holmdahl Manuscript (Under Revision) VI. Effects of C2ta genetic polymorphisms on MHC class II expression and autoimmune diseases. Anthony C. Y. Yau, Fredrik Piehl, Tomas Olsson, Rikard Holmdahl Manuscript (Under Revision) * These authors contributed equally.