Background/Purpose: Multiple lines of evidence indicate that ankylosing spondylitis (AS) is a lymphocyte-driven disease. However, which lymphocyte populations are critical in AS pathogenesis is not known. AS is a highly heritable disease, with estimates of the genetic contribution to AS ranging from 69 to 90%. Genome-wide association studies (GWAS) have identified >100 loci associated with AS, with the vast majority of likely causal variants being non-coding. In this study, we aimed to identify the key cell types mediating the genetic risk in AS using an unbiased multi-omics approach.

Methods: We integrated GWAS data with epigenomic and transcriptomic datasets in human lymphocytes to identify key cell subsets mediating genetic susceptibility to AS. We used public ATAC-seq on sorted peripheral immune cell subsets of healthy subjects, low-input RNA-seq on 7 sorted lymphocyte populations of healthy subjects, and single-cell RNA-seq from the human gut single-cell atlas. To link cell type-specific open chromatin regions or gene expression with GWAS we used 3 published methods: Linkage Disequilibrium Score-regression in Specifically Expressed Genes (LDSC-seg), SNPsea, and single-cell disease-relevance score (scDRS). We validated that these methods could identify T-cells as the main drivers of Rheumatoid Arthritis. Additionally, we performed co-localization analyses between GWAS loci and genetic variants associated with gene expression (eQTL) to find putative target genes of AS risk variants.

Results: LDSC-seg revealed that NK-specific open chromatin regions are significantly enriched in heritability for AS, while this was not the case for other cell types such as T cells, B cells, and monocytes. This finding was consistent between two AS GWAS, one using the ImmunoChip, and the other (UK biobank) using a genome-wide chip. Applying SNPsea to RNA-seq data, we validated that genes in AS risk loci are enriched in NK cell-specific gene expression, compared to 6 T cell subsets (CD4+ T, CD8+ T, MAIT, iNKT, and two gamma delta T cell subsets). Gene expression levels of AS-associated genes, such as RUNX3, TNFRSF1A, and NPEPPS, were found to be highest in NK cells. Additionally, scDRS analysis using the human gut single-cell atlas revealed significant upregulation of AS-associated genes predominantly in NK cells. With co-localization analyses using a large-scale NK cell transcriptomic study with genotyped subjects, we found putative target genes for AS risk variants, including the widely studied ERAP1, previously reported as likely target gene TNFRSF1A and two new understudied target genes.

Conclusion: Using a variety of published datasets and complementary analytical approaches, we consistently identified NK cells as the primary cell type with gene expression and open chromatin enriched in genetic risk variants for AS. These findings point to NK cells as key mediators of the genetic susceptibility to AS.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/integrative-functional-genomics-points-to-natural-killer-cells-as-key-drivers-in-the-pathogenesis-of-ankylosing-spondylitis/