Single-cell RNA-seq reveals cell type-specific molecular and genetic associations to lupus
Systemic lupus erythematosus (SLE) is a heterogeneous autoimmune disease. Knowledge of circulating immune cell types and states associated with SLE remains incomplete. We profiled more than 1.2 million peripheral blood mononuclear cells (162 cases, 99 controls) with multiplexed single-cell RNA sequencing (mux-seq). Cases exhibited elevated expression of type 1 interferon-stimulated genes (ISGs) in monocytes, reduction of naïve CD4+ T cells that correlated with monocyte ISG expression, and expansion of repertoire-restricted cytotoxic GZMH+ CD8+ T cells. Cell type-specific expression features predicted case-control status and stratified patients into two molecular subtypes. We integrated dense genotyping data to map cell type-specific cis-expression quantitative trait loci and to link SLE-associated variants to cell type-specific expression. These results demonstrate mux-seq as a systematic approach to characterize cellular composition, identify transcriptional signatures, and annotate genetic variants associated with SLE.
Single-cell RNA-seq reveals cell type–specific molecular and genetic associations to lupus
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Analysis Portals
Project Label
Single-cellRNA-seqrevealscelltype-specificmoleculaSpecies
Homo sapiens
Sample Type
specimens
Anatomical Entity
blood
Organ Part
blood
Selected Cell Types
peripheral blood mononuclear cell
Disease Status (Specimen)
systemic lupus erythematosus
Disease Status (Donor)
systemic lupus erythematosus
Development Stage
Library Construction Method
10x 3' v2
Nucleic Acid Source
single cell
Paired End
falseFile Format
fastq
Cell Count Estimate
UnspecifiedDonor Count
261