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Objectives Systemic lupus erythematosus (SLE) is preceded by an at-risk stage of disease that can be marked by the presence of antinuclear antibodies (ANA). We aimed to create a detailed single-cell profile in ANA+ individuals at-risk of developing SLE. Using single-cell RNA-sequencing and CITEseq, we longitudinally profiled ANA+ at-risk individuals signifying changes in immunobiology of the at-risk stage.Methods PBMCs from patients with active SLE (n = 20), inactive SLE (n = 23), at-risk individuals before (n = 23) and after (n = 23) developing SLE (progressors), at-risk individuals (n =23) who never progressed to SLE (non-progressors), and healthy donors (n = 17). Eight-sample pools were generated by combining equal numbers of viable cells. Sorted pools were loaded onto the 10x Genomics Chromium X. Gene expression and feature barcoding were prepared using the Chromium GEM-X platform. Final libraries were pooled and sequenced on the Illumina NovaSeq X system. Clustering, differential abundance, and differential expression were performed by computational analysis.Results Pseudobulk analysis of single-cell data highlighted the distinct transcriptomic profile of the ANA+ at-risk individuals against the healthy controls. The cellular composition across the samples significantly varied among the patient groups and within the progressors at baseline. The largest differences in cellular abundance were observed in the myeloid and B cell compartments highlighting an expansion of specific cell subsets at baseline in the ANA+ at-risk individuals prior to the development of SLE. The highest effect size of differential expressed genes in progressors was also seen in myeloid and B cell subsets. Pathway analysis revealed that type I and II interferon responses, complement activation, chemokine receptor binding were highly associated with progression to SLE, whilst negative regulation of other inflammatory and metabolic pathways appeared to reversely correlate with progression to SLE from the at-risk stage.Conclusions We created a detailed single-cell atlas of PBMCs from ANA+ patients at-risk of SLE highlighting subtle changes in cellular abundance and transcriptomic profile. Our novel findings signified the pathogenesis of the ANA+ at-risk stage supporting the concept that disease onset occurs much earlier than clinically overt SLE. This extensive immune resource can enable further interactive tools for subsequent investigations.