Ikaros family genes and lupus susceptibility across ethnically diverse populations

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Project Summary Systemic lupus erythematosus (SLE) is a complex autoimmune disease with a substantial genetic component. Recent genome-wide association studies (GWAS) have identified SLE associated loci, including IKZF1 and IKZF2, encoded for ikaros and helios proteins, respectively. These proteins play important roles in regulation of differentiation of immune cells important in SLE development and drugs which regulate these protein levels are used to treat refractory cutaneous lupus and nephritis making a strong case for the importance of these genes in SLE. Our recent ImmunoChip-based association study in Asians firmly established IKZF1-SLE association and detected additional independent variants (10-24<p<10-8). While IKZF1 results are also well-supported in non-Asian populations, due to poor SNP coverage, European-GWAS identified IKZF2 (1.2x10-13) could not be thoroughly assessed in our study. However, our bioinformatics data predicted several IKZF1-2 variants as eQTLs, again indicating their regulatory roles in expression. Despite solid evidence of association, a gap exists in defining mechanisms with IKZF1-2 variants, hence, the functional effects of IKZF1-2 risk alleles in SLE remains largely unaddressed. Since SLE is 3-5 times more prevalent in individuals of non-European ancestry, a comprehensive, sequence-based trans-ethnic mapping (TEM) approach will be informative to both identify additional causal variants, and understand SLE clinical heterogeneity across ethnicities. We have successfully applied TEM in SLE, and our research team has the expertise, resources and infrastructure necessary to move beyond GWAS and accelerate discovery and analysis of functional variants. We successfully identified causal variants and their functional consequences in ITGAM, BLK, IFIH1 and NCF2. We will apply our expertise in new variant discovery, localizing functional variants, and correlation of functional risk variants in IKZF1-2 on cellular and molecular surrogates associated with SLE. In Aim 1, we will localize additional SLE-predisposing variants from IKZF1-2 by performing comprehensive trans-ethnic mapping across four ethnically diverse populations (N>20,000 from Asian, African-American, European-American, and Hispanic descent). Promising variants, especially imputed and low frequency variants, will be validated by confirmatory genotyping. We will also correlate genetic and clinical heterogeneity using clinical sub-phenotypes and autoantibody profiles. In Aim 2, we will use cutting-edge approaches to directly identify functional variants in the enhancers of IKZF1-2 important for regulating expression using a novel allele-specific reporter system which works in the native chromatin context and in relevant cell types. This enables direct experimental validation of the most important variants in a human model cell system. Data generated will provide answers about SLE disease mechanisms influenced by IKZF1-2 variants, and the understanding of function of molecular variants on regulation of this pathway may enable precision application of existing treatments targeting this pathway and elucidate of new targets without the serious adverse events and limitations of these current thalidomide family-based therapies.