Functional genomics implicates natural killer cells as potential key drivers in the pathogenesis of ankylosing spondylitis

Objective: 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. In this study, we aimed to identify the key cell types mediating the genetic risk in AS using an unbiased integrative functional genomics approach. Methods: We integrated GWAS data with epigenomic and transcriptomic datasets of immune cells in healthy humans. To quantify enrichment of cell type-specific open chromatin regions or gene expression in AS risk loci, we used three published methods which have identified cell types for other diseases. Additionally, we performed co-localization analyses between GWAS risk loci and genetic variants associated with gene expression (eQTL) to find putative target genes of AS risk variants. Results: Natural killer (NK) cell-specific open chromatin regions are significantly enriched in heritability for AS, compared to other immune cell types such as T cells, B cells, and monocytes. This finding was consistent between two AS GWAS. Using RNA-seq data, we validated that genes in AS risk loci are enriched in NK cell-specific gene expression. Expression levels of AS-associated genes, such as RUNX3, TBX21, TNFRSF1A, and NPEPPS, were found to be highest in NK cells compared to five T cell subsets. Using the human Space-Time Gut Cell Atlas we found significant upregulation of AS-associated genes predominantly in NK cells. Co-localization analysis revealed four AS risk loci affecting regulation of candidate target genes in NK cells: two known loci, ERAP1 and TNFRSF1A, and two under-studied loci, ENTR1 (aka SDCCAG3) and B3GNT2. Conclusion: Our results point to NK cells as potential key drivers in the development of AS and highlight four putative target genes for functional follow-up in NK cells. ### Competing Interest Statement The authors have declared no competing interest. ### Funding Statement This study was supported by a seed grant from the Spondyloarthritis Research and Treatment Network (SPARTAN) and a microgrant from the Joint Biology Consortium (1P30AR070253-01). PAN was supported by P30AR070253 and R01AR073201. JE was supported by NIH Grant R21 AR076040-01 and an ASPIRE grant from Pfizer. MGA was supported by P30AR070253, the Arthritis National Research Foundation, the Lupus Research Alliance, and the Gilead Sciences Rheumatology Research Scholars Award. ### Author Declarations I confirm all relevant ethical guidelines have been followed, and any necessary IRB and/or ethics committee approvals have been obtained. Yes The details of the IRB/oversight body that provided approval or exemption for the research described are given below: IRB of Boston Children's Hospital gave ethical approval of this work. I confirm that all necessary patient/participant consent has been obtained and the appropriate institutional forms have been archived, and that any patient/participant/sample identifiers included were not known to anyone (e.g., hospital staff, patients or participants themselves) outside the research group so cannot be used to identify individuals. Yes I understand that all clinical trials and any other prospective interventional studies must be registered with an ICMJE-approved registry, such as ClinicalTrials.gov. I confirm that any such study reported in the manuscript has been registered and the trial registration ID is provided (note: if posting a prospective study registered retrospectively, please provide a statement in the trial ID field explaining why the study was not registered in advance). Yes I have followed all appropriate research reporting guidelines, such as any relevant EQUATOR Network research reporting checklist(s) and other pertinent material, if applicable. Yes All data used so far is publicly available in the URLs provided below. Data produced in the future will be made publicly available.