Background/Purpose: Both plasmacytoid dendritic cells (pDCs) and switched memory B cells (SMBCs) are considered to be key effector cells in systemic lupus erythematosus.  It seems likely that within these classical cell lineages, additional diversity of function will exist that will contribute to disease pathogenesis.  To explore this question, we performed single-cell RNA sequencing in pDCs and SMBCs from SLE patients and controls to assess gene expression patterns and cellular sub-groupings within these lineages.

Methods: pDCs and SMBCs from SLE patients (n=10) and Healthy controls (n=5) were purified by magnetic separation. For deep sequencing, we used the Fluidigm C1 HT system with 800 capture site chips to capture single cells.  Single cell capture was verified by direct visualization using the Array Scan system, allowing us to remove empty wells and wells with multiple cells.  After quality control and adaptor trimming, the data was analyzed using SeqGeq software. pDCs and SMBCs were clustered using UMAP and pseudo-time analysis was performed using the Monocle program.  Type I IFN activity in SLE plasma was measured using reporter cell assay.

Results: A total of 2774 pDCs and 2578 SMBCs from SLE and healthy controls passed the quality control and were used for further analysis.  In pDCs, we observed unique clusters for patients with high interferon, low interferon, and controls, indicating that the IFN response is a major determinant of overall gene expression patterns in SLE patient pDCs.  IFN signature in pDCs correlated with circulating type I IFN activity in the SLE patients measured at the same time.   Other genes upregulated in pDCs included the type I interferon regulator AXL and MACC1.  The SMBCs were heterogeneous in patients and controls, and in contrast to the pDCs, the overall clustering pattern was independent of the IFN score. SMBC clusters were predominantly defined by genes indicating cellular activation or proliferation such as HLA-DRs and CREB1, or genes associated with nucleic acid processing such as DNASE1 and SNORD3B-1.

Conclusion: We find distinct clusters of cells defined transcriptionally within the pDC and SMBC lineages, and the transcripts which define these subgroups differ between cell lineages.  Type I IFN induced transcripts are important to pDC diversity, while in SMBCs transcripts related to cellular activation and nucleic acid processing are critical markers of transcriptional heterogeneity.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/single-cell-transcriptome-analysis-of-circulating-plasmacytoid-dendritic-cells-and-switched-memory-b-cells-in-sle-patients-reveals-transcriptional-subsets-within-the-classical-cell-lineages/