Background/Purpose: Primary Sjögren’s syndrome (pSS) is a common, heterogeneous exocrinopathy.  Etiology involves complex environmental, genetic and genomic influences driving innate and adaptive autoimmune responses.  This study sought to integrate genome-wide association study (GWAS) and classical HLA allele associations in SS, and to explore this genetically complex region for insight into disease mechanisms through bioinformatic approaches.

Methods: Genotype data was collected for 1638 pSS cases and 6754 controls on Illumina Omni1-Quad or ImmunoChip arrays. HLA classical allele imputation was performed using HiBag with a certainty threshold of >80% to define relationships with single nucleotide polymorphisms (SNPs).  A set of 9122 pSS associated SNPs (P<5x10E-5) were tested for enrichment using GenomeRunner to determine if the set of SNPs co-localize with various functional genomic elements such as specific transcription factor binding sites.  A subset of SS associated SNPs that were significantly enriched in genomic locations near functional elements related to the transcriptional regulator, RFX5, were tested by expression quantitative trait locus (eQTL) analysis using the MATRIXeQTL package in R using transcript levels measured by Illumina WG-6 arrays in 133 subjects.

Results: After adjusting for the most significant GWAS variant (rs115575857 in HLA Class II; P=1.65x10E-114), we found a second independent effect peaking at rs116232857 (P=1.33x10E-96).  Imputation and regression analyses identified the previously reported ancestral haplotype including DQB1*0201 (P=1.38x10E-95), DQA1*0501 (P=8.50x10E-94), and DRB1*0301 (P=2.19x10E-84) and indicated rs115575857 was synonymous with this haplotype.  The association at rs116232857 persisted and accounted for DQB1*0501, but DQB1*0501 could not account for rs116232857, suggesting rs116232857 either tags multiple functional effects or, alternatively, DQB1*0501 is a false positive.  Statistically significant co-localization (P=1.53x10E-14) was observed showing that 160 HLA region variants are located within or near (100 bp) ChIP-seq peaks for RFX5, a key transcriptional regulator of HLA Class I and II loci.  Further analyses of RFX5 related variants identified multiple eQTLs (P-values between 8.31x10E-11 and 4.54x10E-33) in both the Class I and Class II HLA loci and include HLA-DRB6, HLA-C, HLA-DPB1, HLA-DQA1, and HLA-A.  Risk alleles for these eQTLs reside on both pSS associated haplotypes.

Conclusion: We conclude that the ancestral haplotype of DQB1*0201, DQA1*0501, and DRB1*0301 corresponds to our top GWAS effect, rs115575857 and the second independent effect at rs116232857 is novel.  RFX5 was identified as a novel potential functional candidate as the RFX5 binding elements were enriched for pSS associated variants affecting HLA Class I and II expression levels. This work suggests that complex functional elements in the HLA region involved in both transcriptional regulation and peptide binding impact SS.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/complex-functional-effects-within-the-hla-contribute-to-sjogrens-syndrome-pathogenesis-and-may-influence-both-transcriptional-regulation-and-peptide-binding/