Background/Purpose: Systemic juvenile idiopathic arthritis (sJIA) is a genetically complex inflammatory condition. It can be marked by severe systemic inflammation that resembles the hereditary periodic fever syndromes (HPF). Sometimes that inflammation leads to macrophage activation syndrome (MAS), a secondary form of hemophagocytic lymphohistiocytosis (HLH). To date, studies have attempted to identify whether variants in HPF and familial HLH (fHLH) genes contribute to the pathophysiology of sJIA; however, they lacked sufficient statistical power to reach generalizable conclusions. Our goal was to determine whether rare variation in these genes contributes to the risk of developing sJIA.

Methods: Targeted sequencing of HPF (MEFV, MVK, NLRP12, NLRP3, NOD2, PSTPIP1, TNFRSF1A) and fHLH (LYST, PRF1, RAB27A, STX11, STXBP2, UNC13D) genes was performed in sJIA cases and control subjects from the International Childhood Arthritis Genetics Consortium cohort using Illumina Nextera Custom Capture Assays and Illumina sequencers. Sequence reads were aligned to human genome assembly hg19 with the Burrows-Wheeler Aligner. Data processing and quality control were performed using the Genome Analysis Toolkit. Variants were filtered to retain rare (minor allele frequency < 0.01), protein-altering variation that mapped to Ensembl canonical transcripts. The distribution of rare variants among sJIA cases was compared to the distribution among INCHARGE healthy controls or simulated data from the 33,370 Non-Finnish European (NFE) reference subjects from the Exome Aggregation Consortium (ExAC) using rare variant association testing (RVT). RVT was performed in R using the data-adaptive sum test and the sequence kernel association test. Significance was evaluated at a threshold of p < 0.05 after 100,000 permutations.

Results: Targeted sequencing was performed in 525 sJIA cases and 366 control subjects. Patients were excluded for meeting genetic criteria for HPF (n=4) or fHLH (n=2), and if their ancestry was dissimilar from the rest of the cohort by principal component analysis (39 cases, 1 control). Sequencing of the remining 480 sJIA cases identified 78 rare fHLH gene variants and 62 rare HPF gene variants. RVT comparing the distribution of rare variants of sJIA cases with that of the ExAC NFE population revealed significant rare variant associations between sJIA and LYST, STXBP2, UNC13D and MEFV. We also discovered recurrent, ultra-rare mutations of STXBP2, UNC13D, and MEFV among the sJIA cohort, including several that were not observed in the ExAC population. A sub-analysis of 123 sJIA cases with known MAS status (32 with MAS, 91 without MAS) identified a significant association between rare variation of UNC13D and the development of MAS in sJIA (SKAT p=0.024).

Conclusion: The observations of this study connect HPF and fHLH genes to the pathophysiology of sJIA. These results highlight the potential value of studying rare genetic variation in sJIA. To expand this approach, we have established a collaborative infrastructure to perform an exome sequencing-based study of rare variation across all protein-coding genes in sJIA.

« Back to ACR Convergence 2022

ACR Meeting Abstracts - https://acrabstracts.org/abstract/large-scale-targeted-sequencing-study-links-systemic-juvenile-idiopathic-arthritis-with-rare-variants-of-mefv-lyst-stxbp2-unc13d/