Background/Purpose:

One hallmark of the autoimmune disease Systemic lupus erythematosus (SLE) is the presence of antinuclear antibodies (ANAs). While the specificities and levels can indicate characteristics of SLE status, many individuals acquire ANAs either years prior to clinical diagnosis of SLE or fail to develop any further symptoms. At present, the mechanisms controlling further autoimmune progression in ANA+ healthy individuals remain unknown.

Methods:

To ascertain potential differences in immune cell populations and/or their transcriptional state, we performed single cell RNA-seq on peripheral blood mononuclear cells from 30 patients, including African and European American individuals which were healthy ANA⁺ individuals with no other SLE criteria (n=10), active SLE patients (n=10), and healthy controls (n=10) with no autoantibodies. Transcriptomes were analyzed using canonical correlation analysis, followed cell population identification and by tSNE cluster visualization and differential gene expression within each cell population was assessed.

Results:

Distinct cell population clusters could be identified for each of the disease classifications. EA ANA⁺ individuals showed an increase in the number of NK cells relative to SLE and healthy individuals while, in contrast, AA ANA⁺ individuals had lower numbers of NK cells. Specific populations of B cells could be identified for each disease classification in both AA and EA patients. For EA patients, stress response related genes such as JUN and PPP1R15A were upregulated in ANA⁺-specific B cells while SLE-specific B cells were marked by upregulation of pro-survival/proliferation genes such as TCL1A, PCDH9 and RALGPS2. AA SLE patients demonstrated a proportional enrichment of plasma cells relative to both ANA+ and healthy individuals while FCRL5, a marker of dysfunctional B cells, was increased in SLE memory B cells. Overall, AA ANA⁺ cell populations showed an upregulation in a number of heat shock genes in ANA+ (HSPA6, HSPA1A, DNAJB1). Comparison of a list of candidate regulatory factors demonstrated dysregulation of several genes, including an upregulation of TGFB across all AA ANA+ cell clusters and a similar increase in CD46 in EA ANA+ clusters.

Conclusion:

These data indicate that substantial transcriptional and cell population differences exist among immune cells from ANA⁺, SLE, and healthy individuals, including an apparent activated stress response programs in the cells from ANA⁺ individuals. Our results suggest that cells from ANA⁺ individuals may be actively regulating a response to autoantigen stimulation, whereas an exhaustion of that response may allow for transition to SLE.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/single-cell-rna-seq-analysis-of-ana-healthy-and-sle-patients-show-variations-in-activated-stress-response-and-regulatory-pathways/