Genome-wide association studies and targeted genetic scans performed by Dr. Gaffney and others in the field have now identified >120 genetic loci that are associated with increased SLE susceptibility. Such studies leverage the genetic phenomenon of linkage disequilibrium to identify risk haplotypes, e.g. a set of risk alleles that are inherited together and, therefore, cannot be statistically distinguished in association studies. Each risk haplotype can carry tens, if not hundreds, of associated alleles. Further, the majority of associated risk alleles are in non-protein-coding regulatory regions of the genome that have the potential to influence gene expression locally or at a distance through three-dimensional chromatin looping.
Dr. Gaffney has dedicated a significant amount of his research to identifying, prioritizing, and functionally characterizing the causal variants of autoimmune disease. His research team uses bioinformatic approaches to prioritize variants for study based on their positions in areas of enriched for epigenetic modifications indicative of promoters, active enhancers, and/or transcription factor binding. Then, using several different in vitro assays including EMSAs, luciferase transactivation assays, 3C-qPCR, ChIP-qPCR, and gene-editing technologies, they investigate the functional effects of specific risk alleles on nuclear protein binding, enhancer/promoter activity, and chromatin looping.
Using these approaches, they have identified two causal variants in an enhancer element that engages the TNFAIP3 promoter to influence A20 expression in immune cells (Wang, et al. PLoS Genet 2013; Wang, et al. Genes Immun 2016) and two risk alleles in the promoter of BLK that influence BLK expression in a cell type- and development-specific manner (Guthridge, et al. Am J Hum Genet 2014).
In more recent work, Dr. Gaffney and his team systematically characterized the function of multiple risk alleles carried on the TNIP1 haplotype and determined that, for this specific haplotype, it is the collective effect of multiple risk alleles, rather than a single allele, that drives hypomorphic TNIP1 expression in the immune cells of SLE patients (Pasula, et al. Arthritis Rheumatol 2020).