ArticleNature genetics2025
Deciphering state-dependent immune features from multi-layer omics data at single-cell resolution.
Article in Nature genetics, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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Who cites it
7 citing papers in PubMed.
- From Genome-Wide Association Study Signal to Mechanism in Rheumatoid Arthritis: Lessons From a Single Risk Locus.Arthritis & rheumatology (Hoboken, N.J.) · 2026Article
- Single-cell catalogue of immune cells from Japanese individuals.Communications biology · 2026Article
- A multi-ethnic reference map of T cell receptor germline diversity reveals evidence of natural selection on alpha chain genes.Nature communications · 2026Article
- Pathogenic CGG expansions in oculopharyngodistal myopathy exhibit distinct characteristics of each causative gene on the flanking sequences as well as methylation status.Genome medicine · 2026Article
- Somatic loss of the Y chromosome complements polygenic risk scores for type 2 diabetes risk prediction.Nature medicine · 2026Article
- Genetic regulation across germline and somatic variation on the Y chromosome contributes to type 2 diabetes.Nature medicine · 2026Article
- Reframing brain aging: neuroinflammation as an interconnected network process.Frontiers in aging · 2026Review
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Authors and funding
41 authors.
Funding
Abstract
Current molecular quantitative trait locus catalogs are mostly at bulk resolution and centered on Europeans. Here, we constructed an immune cell atlas with single-cell transcriptomics of >1.5 million peripheral blood mononuclear cells, host genetics, plasma proteomics and gut metagenomics from 235 Japanese persons, including patients with coronavirus disease 2019 (COVID-19) and healthy individuals. We mapped germline genetic effects on gene expression within immune cell types and across cell states. We elucidated cell type- and context-specific human leukocyte antigen (HLA) and genome-wide associations with T and B cell receptor repertoires. Colocalization using dynamic genetic regulation provided better understanding of genome-wide association signals. Differential gene and protein expression analyses depicted cell type- and context-specific effects of polygenic risks. Various somatic mutations including mosaic chromosomal alterations, loss of Y chromosome and mitochondrial DNA (mtDNA) heteroplasmy were projected into single-cell resolution. We identified immune features specific to somatically mutated cells. Overall, immune cells are dynamically regulated in a cell state-dependent manner characterized with multiomic profiles.
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