Investigation of the role of copy number variation in the susceptibility to systemic lupus erythematosus

Abstract

Systemic lupus erythematosus (SLE) is a chronic systemic autoimmune disease characterised by immune complex deposition and production of autoantibodies against nuclear antigens (ANA). The aetiology of SLE is complex; however, twin and genome-wide association (GWA) studies clearly indicate that SLE has a strong genetic component. Most recently, Copy Number Variations (CNVs) have been shown to be ubiquitously present in unrelated healthy subjects and contribute substantially to phenotypic variation in the human population. Furthermore, there is increasing evidence that CNVs contribute to the pathogenesis in autoimmune diseases such as Type 1 diabetes, psiorasis and SLE. In order to investigate SLE-associated genes with CNVs, Affymetrix Human Genome-wide SNP array 5.0 analysis was performed across 66 samples from our APOSLE (Australian Point Mutations in SLE) cohort. 24, 094 CNVs were identified, however, low log2R values suggested many were likely to be false positive CNVs. For this reason, we used a filtering approach to identify positive CNVs reducing the number to 981. Out of these 981CNVs, we selected 13 CNVs based on the selection criteria list developed to be able to detect the CNV most likely associated with SLE disease. We used qRT-PCR to verify gene CN in firstly the individuals of interest and then the larger human DNA cohorts. CNVs in the CFHR1/3, RASGRP3, WNK1 and PTPN7 were verified as true positive results. We screened two different human cohorts, the APOSLE and European, for the presence or absence of these CNVs, to determine if these CNVs showed a different trend in SLE patients (divided into those with and without nephritis) compared to healthy control subjects. Using this method, we identified three genes, CFHR 1/3, WNK1 and RASGRP3, where loss of CN was more frequently found in SLE patients without nephritis. Thus the results presented in this thesis suggest CNVs in the CFHR1/3, WNKl and RASGRP3 may act as a protective factor against development of nephritis in patients with SLE.