Integrative GWAS and snRNA-seq Reveal a Mesenchymal-Like Endothelial Signature in Moyamoya Disease
Yudai Hirano1,2, Satoru Miyawaki1, Kyuto Sonehara2,3,4,5
1Faculty of Medicine, Department of Neurosurgery (Y.H., S.M., H. Imai, H.H., H.O., S.O., S.T., Y. Sakai, D.S., T.T., S.H., S. Koizumi, S.D., Y. Shinya, S. Kiyofuji, H.N., N.S.), The University of Tokyo, Japan.
Background:
Moyamoya disease (MMD) has a strong genetic basis, with the rare RNF213 p.Arg4810Lys variant (rs112735431) representing a major risk factor, while the broader genetic architecture and disease-relevant vascular cell types remain incompletely understood.
Methods:
We conducted a genome-wide association study in Japanese individuals (n=47 656; 401 MMD cases and 47 255 controls). Population-level features at MMD risk loci were examined by regional allele frequency and haplotype analyses. We performed single-nucleus RNA-seq of superficial temporal arteries from patients with MMD (n=3). Cell type-specific enrichment of genome-wide association study signals was assessed using the Single-Cell Disease Relevance Score. Endothelial signatures were validated by integration with publicly available single-cell data sets from controls (n=5) and immunohistochemistry for candidate markers (n=1).
Results:
Beyond rs112735431, we identified a genome-wide significant signal in the HDAC9-TWIST1 region (rs12530920; P=3.3×10-14; odds ratio, 1.77). Conditional analysis on rs112735431 revealed a protective RNF213 missense variant, p.Asp1331Gly (rs8074015; P=3.7×10-9; odds ratio, 0.53), whose minor allele was mutually exclusive with rs112735431-A on haplotypes. Population analysis revealed geographic variation and extended haplotype structure of the rs112735431-A allele in Japan. Single-nucleus RNA-seq identified a mesenchymal-like endothelial cell (MEC) population with selective FN1 expression. Genome-wide association study-prioritized disease genes were strongly enriched in MECs. MECs showed mesenchymal pathway activation with a regulatory program distinct from canonical endothelial states. The proportion of MECs was markedly increased in MMD (72% versus 28% in controls), and fibronectin 1 (FN1) expression in endothelial regions was confirmed by immunohistochemistry.
Conclusions:
Our findings identify a protective RNF213 p.Asp1331Gly variant (rs8074015) that is mutually exclusive with the known rs112735431-A allele. Genetic risk converges on an MEC state markedly expanded in MMD.
Insights
Moyamoya disease (MMD) genetic risk is linked to a protective RNF213 variant, distinct from the major risk allele. This genetic risk converges on an expanded mesenchymal-like endothelial cell (MEC) state in MMD patients.
Area of Science:
- Genetics
- Vascular Biology
- Genomics
Background:
- Moyamoya disease (MMD) has a significant genetic component, primarily linked to the RNF213 variant rs112735431.
- The complete genetic architecture and involved vascular cell types in MMD are not fully understood.
Purpose of the Study:
- To investigate the broader genetic landscape of Moyamoya disease.
- To identify novel genetic risk factors and understand the cellular mechanisms underlying MMD pathogenesis.
Main Methods:
- Genome-wide association study (GWAS) in a large Japanese cohort (47,656 individuals).
- Single-nucleus RNA sequencing (snRNA-seq) of superficial temporal arteries from MMD patients.
- Cell type-specific enrichment analysis using the Single-Cell Disease Relevance Score.
- Immunohistochemistry for validation of candidate markers.
Main Results:
- Identified a novel genome-wide significant signal in the HDAC9-TWIST1 region associated with MMD risk.
- Discovered a protective RNF213 missense variant (p.Asn1331Gly, rs8074015) mutually exclusive with the major risk allele on haplotypes.
- snRNA-seq revealed an expanded population of mesenchymal-like endothelial cells (MECs) in MMD patients, characterized by selective FN1 expression and mesenchymal pathway activation.
- GWAS-prioritized genes were significantly enriched in MECs.
Conclusions:
- A protective RNF213 variant was identified, which is inversely associated with the major risk allele rs112735431.
- Genetic risk in Moyamoya disease converges on an expanded mesenchymal-like endothelial cell (MEC) state, highlighting its critical role in pathogenesis.
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