Background/Purpose:

Our previous gene expression studies in sorted immune cell populations in SLE has shown that different cell types from the same blood sample demonstrate diverse gene expression parameters.  These studies also suggested that heterogeneity in gene expression runs deeper than major immune cell subsets.  In this study, we examine IFN signatures in single monocytes isolated from SLE patients.

Methods:

CD14⁺⁺CD16^– classical monocytes (CLs) and CD14^dimCD16⁺ non-classical monocytes (NCLs) from 14 SLE patients were purified by magnetic separation.  The Fluidigm single cell capture and pre-amplification  System was used for single cell capture and target gene pre-amplification.  Fluidigm Biomark system (Rt-PCR system) was used to quantify expression of 87 monocyte-related genes.  IFN-induced genes in monocytes were identified by culturing monocytes isolated from whole blood of healthy controls with or without IFN-α. Genes significant up-regulated by IFN were identified as IFN-induced genes in current study. Limit of Detection (LOD) of Rt-PCR was set at 28 cycles.  An individual cell IFN score was given based upon the sum of expression of IFN-induced genes. Hierarchical clustering was generated by using Cluster 3.0 and Java Treeview. 

Results: Both CLs and NCLs demonstrated a wide range of expression of IFN-induced genes, and NCL monocytes had higher IFN scores than CL monocytes. Hierarchical clustering of all cells displayed clustering of cells in subsets within the CL and NCL lineages, as well as expression patterns that were shared by both lineages.  We found four gene sets that clustered monocytes functionally.  These included an IFN-induced gene set, two inflammatory gene sets, and one immunosuppressive gene set.  Interestingly, we could define a large subset of NCL monocytes with upregulation of suppressive transcripts (including TGF-β and PDL1) and IFN-induced transcripts were also upregulated, while the two inflammatory gene sets were down-regulated.  These cells were highly over-represented in a patient with inactive disease who was on immunosuppressants at the time of blood draw.  The proportion of anti-inflammatory gene set expressing NCLs was inversely correlated with anti-dsDNA titers (rho = -0.77, p=0.0051) and positively correlated with C3 complement (rho = 0.68, p=0.030) in the SLE patient group, suggesting that these cells are also associated with serological quiescence.  

Conclusion: Using single cell gene expression, we have identified a unique population of NCL monocytes in SLE patients with upregulation of a combination of anti-inflammatory and IFN-induced transcripts.  These cells correspond with clinical and serological quiescence.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/single-cell-gene-expression-studies-in-lupus-patient-monocytes-reveal-a-unique-anti-inflammatory-population-of-non-classical-monocytes-associated-with-clinical-quiescence/