Dissecting the genetics of autoimmune diseases

Autoimmune diseases occur when the immune system mistakenly attacks its own healthy tissue. There are more than 80 different types of autoimmune diseases and they are classified as either systemic or tissue specific depending on the antigen/s targeted and the effector mechanism involved. Although not necessarily pathological, autoimmunity may lead to clinically relevant tissue damage in some individuals. Three-point-five percent of Western populations are afflicted, causing a huge burden on the country's resources. Many of the diseases are related with members of a cluster commonly occurring in an individual or a family suggesting some commonality in inheritance. Uncovering genes involved in one autoimmune disease may therefore also be relevant in other autoimmune diseases as well as in their underlying mechanisms. The "candidate gene" approach was for many years the only option for tackling the genetics of complex diseases but although biologically sound it led to initial elation at discovering a gene being turned to disappointment when it didn't stand up to scrutiny and/or could not be replicated by independent researchers. As the effects of a single gene may be small and the disease or animal model often pleiotropic with overlapping phenotypes, family based linkage studies too have achieved only limited success, mainly due to limitations in identifying common variants with modest effects. In the course of this thesis, I have used mouse models of disease with previously identified linkage regions and the powerful tools of a positional cloning approach coupled with microarray gene expression analyses to identify genes contributing to an important immuno-regulatory cell type, NKT cell number, as well as genes contributing to experimental autoimmune gastritis. Candidate genes identified were subsequently validated by real time PCR and FACS analyses on new sample sets and polymorphic differences in gene structure were identified between strains positive for the phenotype compared to those phenotypically negative for it as a possible explanation for the observed differential expression patterns. To this end, thirty-nine sub-congenic mouse lines of the gastritis linkage region on chromosome 4 were produced and microarray gene expression analyses were carried out on the most informative of these to reveal at least four chromosomal regions contributing to the gastritis phenotype. Two of these regions contain a single candidate gene: Cap1 and Apitd1 that are both involved in apoptosis. A subcongenic approach to identifying NKT cell genes revealed a minimum of four candidates, with at least one on chromosome 1 and three or more on chromosome 2. One of the candidate genes, Slamf1, was subsequently confirmed through transgenic complementation, while a previously unknown role for peroxisomes in NKT cell biology identified by microarray analyses and confirmed using a knock-out mouse system