Unveiling the Role of IL-12A in Lupus: Linking Genetic Risk to B Cell Pathogenicity

Nada Abdel Aziz – Boston Children's Hospital,Harvard Medical School,Broad Institute of MIT and Harvard; Sara Djeddi – Boston Children's Hospital, Harvard Medical School, Broad Institute of MIT and Harvard; Yifei Liao – Brigham and Women's Hospital, Broad Institute of Harvard and MIT, Cambridge,Harvard Medical School; Daniela Fernandez-Salinas – Boston Children's Hospital, Harvard Medical School, Broad Institute of MIT and Harvard; Vitor Rezende Da Costa Aguiar – Boston Children's Hospital, Harvard Medical School, Broad Institute of MIT and Harvard; Benjamin E Gewurz – Brigham and Women's Hospital, Broad Institute of Harvard and MIT, Harvard Medical School, Harvard Program in Virology; Maria Gutierrez-Arcelus – Boston Children's Hospital, Harvard Medical School, 3Broad Institute of MIT and Harvard

Abstract Text: Systemic lupus erythematosus (SLE) is a complex autoimmune disease with over 200 risk loci identified through genome-wide association studies (GWAS). Among these, a risk locus harbouring the gene IL12A remains understudied. IL12A participates in the activation of the IFN-γ pathway. IFN-γ signalling drives B cell differentiation into IgD- CD27- CD21- CD11c+ (DN2) B cells, a likely pathogenic subset expanded in SLE patients.
We hypothesize that an SLE risk variant dysregulates IL12A, which impacts DN2 B cell differentiation. First, we narrowed down the candidate causal risk variants by their overlap with regulatory elements in a B cell line. We identified a single nucleotide polymorphism (SNP) within a strong enhancer region near IL12A. Using CRISPR inactivation, we showed that silencing this enhancer significantly reduces IL12A expression. Additionally, we used base editing to show that the risk allele of this SNP increases IL12A expression. Notably, this SNP overlaps an open chromatin region (ATAC-seq) in primary B cells activated in vitro with a DN2-inducing cocktail. To investigate IL-12A’s functional role, we performed CRISPR knockout of IL-12A in primary naïve B cells, which caused a decrease in DN2 population differentiation compared to the control. Conversely, treatment with recombinant IL-12A increased the DN2 population. Overall, our findings identify a likely causal SNP at the SLE IL12A locus, with the risk allele driving increased IL12A expression in a B cell line. Moreover, our data showed that IL12A plays a direct role in promoting DN2 B cell differentiation, linking this locus to pathogenic mechanisms in SLE.