The exact cause of systemic lupus erythematosus (SLE) is unknown; however, increasing evidence indicates that genetics play a significant role. A gene contains information for making, or encoding, a specific protein, and researchers have identified approximately 100 risk genes in which mutations, or variations in the gene, are associated with SLE; however, how many of these genetic mutations impact the encoded protein is unknown. Cells in the immune system use a process called alternative splicing to adapt, differentiate, and respond to foreign pathogens. Alternative splicing occurs when a product of a gene, which typically produces a single protein, is cut and joined in different combinations to encode different proteins with distinct structures and functions. This leads to drastic functional consequences, as this indicates that even though two individuals carry the same gene, their immune cells could be expressing different proteins, altering the immune response. Recent evidence suggests that genetic mutations in or near SLE risk genes may impact alternative splicing underlying SLE; however, how this process affects immune function is unknown. To determine how splicing disruptions promote autoimmunity, Dr. Gutierrez-Arcelus will investigate the impact of alternative splicing disruptions in B cells, an immune cell type that produces antibodies and is highly dysfunctional in SLE.

Dr. Gutierrez-Arcelus will determine whether mutations in previously identified SLE risk genes affect alternative splicing in B cells. To understand the consequence of splicing disruptions caused by SLE risk variants, Dr. Gutierrez-Arcelus will induce the specific splicing events in B cells and measure changes in the B cell activation state. SLE is a complex disease with heterogeneous clinical features. To determine whether alternative splicing variability contributes to clinical heterogeneity in SLE, Dr. Gutierrez-Arcelus will identify genes whose alternative splicing variation correlates with clinical features, including autoantibody production and organ damage, in 120 SLE patients. Heterogeneity in clinical manifestations of SLE is considered a significant contributor to the high failure rate of clinical trials. Identifying alternative splicing disruptions that contribute to SLE heterogeneity will enable the development of precision therapies for SLE.

What this study means for people with lupus:

Alternative splicing is an understudied molecular process, and how mutations in many SLE risk genes cause autoimmunity is poorly understood. Overall, this study will establish the role of splicing disruptions in B cells and how this process impacts the immune response. By highlighting the importance of alternative splicing in SLE, Dr. Gutierrez-Arcelus hopes the research team’s findings will enable the development of targeted therapies for patients with specific genetic variants.

Systemic lupus erythematosus (SLE) is an autoimmune disease for which only a few new drugs have been approved in over 60 years. Design of future therapies will require new insights into disease pathogenesis. Splicing disruption by non-coding genetic variants can cause severe alterations in protein function and lead to disease (e.g. CTLA4 isoform in SLE). Recent advancements in drug development allow for efficient repair of splicing defects, making causal disease genes with abnormalities in splicing excellent targets for therapy. However, alternative splicing remains and under-studied transcriptomic phenotype due to its extra analytical challenges.

The genetic contribution to SLE susceptibility is high (up to 66%), and B cell dysfunction is a main driver of disease. Within the >100 susceptibility loci for SLE, most likely causal variants are non-coding, and are believed to affect gene regulation, but for the vast majority of them we haven’t found their regulatory effects and target genes.

The PIs preliminary data suggests that (A) non-coding SLE variants often cause alternative splicing disruption of genes, and (B) SLE patients have an abnormal isoform profile in a pathogenic B cell subset. In this proposal we will (1) characterize the splicing disruption caused by SLE risk variants and its consequences, and (2) define altered isoform variability associated with SLE and its clinical manifestations in B cells. Overall, our comprehensive characterization of B cell splicing dysregulation in SLE will show new disease mechanisms and will point to new candidate targets for splicing modulator drugs.

The PIs long term goal is to use genetics and informative molecular phenotypes, such as alternative splicing, to predict SLE disease-­course and accelerate the application of precision medicine.