Scleroderma Genomics and Health Disparities Unit is focused on enhancing our understanding of the genetic risk factors involved in scleroderma pathogenesis. Scleroderma (systemic sclerosis) is a chronic multisystem disease that is clinically characterized by progressive fibrosis of the skin and internal organs, vasculopathy, and autoimmunity. Scleroderma causes significant morbidity and mortality, and the only treatment options are organ based and primarily symptom management. Scleroderma is a health disparity in African Americans who have a higher prevalence of scleroderma than European Americans. African Americans with scleroderma have an earlier age of onset and are more likely to manifest diffuse skin involvement, interstitial lung disease (ILD), and pulmonary arterial hypertension (Table 1).
Family studies have suggested a role for genetic etiological factors in this disease with an increased sibling recurrence risk (λs) for scleroderma in African Americans than European Americans. Candidate gene and genome-wide association studies (GWAS) conducted mostly in European American scleroderma patients have revealed autoimmune disease susceptibility loci but these loci are not unique to scleroderma. Our understanding of genetic susceptibility in African American scleroderma is very limited and restricted to Human leukocyte antigen (HLA), due to a lack of systematic and comprehensive studies in the African American scleroderma population. We hypothesize that African-ancestry derived variants may explain the increased frequency and severity of scleroderma in African Americans, and admixture mapping is an effective tool for identifying such ancestry-specific effects (Figure 1).
Thus, we have established the “Genome Research in African American Scleroderma Patients” (GRASP) consortium comprising of 24 centers across the United States to enroll African American patients with scleroderma (Figure 2).
We are taking a comprehensive approach to test both rare and common genetic variants in scleroderma and are utilizing cutting edge technologies to understand scleroderma with the following three approaches:
1. Discover common variants leading to scleroderma susceptibility
The aim is to identify previously unrecognized multi-ethnic scleroderma susceptibility loci, and perhaps to identify African ancestry-specific variants increasing scleroderma genetic risk that could have a major impact in this underserved population with a more severe disease burden. Scleroderma samples from the GRASP cohort and controls are being genotyped on the Illumina Multi-Ethnic Global Array (MEGA) which contains 1.7 million markers, and a custom Illumina OmniExpressExome array that contains 1 million markers. Data from these arrays will be extracted and undergo quality control including population stratification and relatedness analysis.
Genome-wide association analysis will be conducted after performing SNP imputation and cross-platform validation of the top hits (Figure 3). Fine-mapping disease loci, admixture analysis, and utilizing publicly available expression quantitative trait loci (eQTL) datasets such as HaploReg and GTEx for in silico eQTL analysis will be performed. We will use pathway analysis approaches and machine learning methods to identify a combination of common variants that increase scleroderma susceptibility. Functional characterization of these non-coding variants that are likely regulatory in function will be performed utilizing the Encyclopedia Of DNA Elements (ENCODE) dataset. Since Class II HLA genes are the strongest genetic risk factor in scleroderma, elucidating the role of MHC molecules in antigen recognition, peptide presentation and autoimmunity induction will be another major focus of the lab.
2. Discover rare and low frequency variants leading to scleroderma susceptibility
Scleroderma has a unique phenotype and is a relatively rare disease. Rare and low frequency variants increasing scleroderma susceptibility will likely not be seen in other individuals or diseases. We are generating whole exome sequencing (WES) and targeted resequencing data. These data will be combined with detailed phenotypic and autoantibody information from the GRASP cohort to stratify scleroderma patients into subsets for gene-level testing and pathway analysis (Table 2). Each of the genes enriched in rare and low frequency variants has its own unique story and may involve fibrosis, cytokine signaling, inflammatory pathways or epithelial to mesenchymal transition. Functional characterization of the role of rare and low frequency variants will be performed using the CRISPR/Cas9-mediated precise genome editing system to introduce single variant changes in the cell line of interest.
3. Identify de novo dominant or rare recessive alleles
We are studying scleroderma families and trios and extreme phenotypes of scleroderma and utilizing whole exome sequencing (WES) and whole genome sequencing (WGS) for the discovery of high-penetrance mutations that may provide insight into the function of the implicated gene, it’s role in fibrosis, and ultimately shed some light on the pathogenesis of scleroderma.
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