Positional identification and functional analysis of genes regulating autoimmune arthritis

Abstract: 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