A Cross-Tissue Transcriptome-Wide Association Study Identifies Novel Susceptibility Genes for Juvenile Idiopathic Arthritis in Asia and Europe

Large-scale integrative analysis of juvenile idiopathic arthritis for new insight into its pathogenesis

BACKGROUND

Juvenile idiopathic arthritis (JIA) is one of the most prevalent rheumatic disorders in children and is classified as an autoimmune disease (AID). While a robust genetic contribution to JIA etiology has been established, the exact pathogenesis remains unclear.

METHODS

To prioritize biologically interpretable susceptibility genes and proteins for JIA, we conducted transcriptome-wide and proteome-wide association studies (TWAS/PWAS). Then, to understand the genetic architecture of JIA, we systematically analyzed single-nucleotide polymorphism (SNP)-based heritability, a signature of natural selection, and polygenicity. Next, we conducted HLA typing using multi-ethnicity RNA sequencing data. Additionally, we examined the T cell receptor (TCR) repertoire at a single-cell level to explore the potential links between immunity and JIA risk.

RESULTS

We have identified 19 TWAS genes and two PWAS proteins associated with JIA risks. Furthermore, we observe that the heritability and cell type enrichment analysis of JIA are enriched in T lymphocytes and HLA regions and that JIA shows higher polygenicity compared to other AIDs. In multi-ancestry HLA typing, B*45:01 is more prevalent in African JIA patients than in European JIA patients, whereas DQA1*01:01, DQA1*03:01, and DRB1*04:01 exhibit a higher frequency in European JIA patients. Using single-cell immune repertoire analysis, we identify clonally expanded T cell subpopulations in JIA patients, including CXCL13+BHLHE40+ TH cells which are significantly associated with JIA risks.

CONCLUSION

Our findings shed new light on the pathogenesis of JIA and provide a strong foundation for future mechanistic studies aimed at uncovering the molecular drivers of JIA.

Integrative Analysis of Transcriptome-Wide Association Study and Gene-Based Association Analysis Identifies In Silico Candidate Genes Associated with Juvenile Idiopathic Arthritis

Genome-wide association study (GWAS) of Juvenile idiopathic arthritis (JIA) suffers from low power due to limited sample size and the interpretation challenge due to most signals located in non-coding regions. Gene-level analysis could alleviate these issues. Using GWAS summary statistics, we performed two typical gene-level analysis of JIA, transcriptome-wide association studies (TWAS) using FUnctional Summary-based ImputatiON (FUSION) and gene-based analysis using eQTL Multi-marker Analysis of GenoMic Annotation (eMAGMA), followed by comprehensive enrichment analysis. Among 33 overlapped significant genes from these two methods, 11 were previously reported, including TYK2 (PFUSION = 5.12 × 10−6, PeMAGMA = 1.94 × 10−7 for whole blood), IL-6R (PFUSION = 8.63 × 10−7, PeMAGMA = 2.74 × 10−6 for cells EBV-transformed lymphocytes), and Fas (PFUSION = 5.21 × 10−5, PeMAGMA = 1.08 × 10−6 for muscle skeletal). Some newly plausible JIA-associated genes are also reported, including IL-27 (PFUSION = 2.10 × 10−7, PeMAGMA = 3.93 × 10−8 for Liver), LAT (PFUSION = 1.53 × 10−4, PeMAGMA = 4.62 × 10−7 for Artery Aorta), and MAGI3 (PFUSION = 1.30 × 10−5, PeMAGMA = 1.73 × 10−7 for Muscle Skeletal). Enrichment analysis further highlighted 4 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways and 10 Gene Ontology (GO) terms. Our findings can benefit the understanding of genetic determinants and potential therapeutic targets for JIA.