Identify Rare Pathogenic Variants and their Functional Consequences in SLE

Medical University Of South Carolina, Charleston SC

Investigators

Abstract

Systemic lupus erythematosus (SLE) is a chronic autoimmune disease characterized by episodic flares, significant morbidity, and higher mortality. Since >1 million Americans have SLE, the economic impact is $50 billion/year, with the most disease burden on women of non-white ancestry. Few effective treatments exist for SLE, largely because etiology is incompletely understood, but the disease is likely to occur in genetically susceptible individuals upon environmental triggers. Patients with childhood-onset SLE (cSLE) have more severe and aggressive disease than those with adult-onset. While genetic investigations of cSLE could yield important insights to SLE pathogenesis, most studies have focused on adult-onset SLE patients. We studied two African American families, each having two sons affected with cSLE, using whole exome sequencing. In each family, a private loss-of-function (LOF) variant of SAT1 co-segregated with the SLE disease status of the affected sibling, exhibiting an X-linked recessive pattern. SAT1, encoding the spermidine/spermine-N1- acetyltransferase (SSAT1), a rate-limiting enzyme in polyamine catabolism, was not known as a genetic association with SLE. We showed disease causation of the frameshift LOF variant in CRISPR/Cas9-edited (knock in, KI) C57BL/6 (B6) mice. Young hemizygous male and homozygous female mice spontaneously develop lupus-like characteristics, highlighting potential monogenic contribution in multiplex families with cSLE, an understudied resource. Here we propose to 1) apply whole genome sequencing on 30 SLE multiplex, 62 simplex families, and an additional 35 cSLE patients enriched for early disease onset (< 10-year-old), familial aggregation, and non-European ancestry, to define polygenic risk scores of each individual and to identify novel, ultra-rare, pathogenic coding and non-coding variants; (2) test the evolutionally conserved, pathogenic coding variant candidates for their ability to induce either spontaneous or apoptotic cell-induced lupus in conditional KI mice on B6 mouse background and to assess differentially expressed genes and pathways that are altered in diseased tissues and cell types; and (3) test the functional consequences of pathogenic coding variants from Aim 2 and predicted non-coding candidate risk alleles in differentiated human immune cells derived from genome-edited induced pluripotent stem cells (iPSCs). Our proposed studies are likely to discover novel monogenic lupus variants and validate causality of new and/ or prior monogenic lupus-associated variants in isogenic non-autoimmune mice and iPSCs, which will gain insights into disease causal pathways and pave the way for the new development of targeted therapies in disease management of patients affected with SLE.