Background/Purpose: Early immune events leading to clinical autoimmune disease are complex and the pathways involved remain incompletely defined. Anti-nuclear antibody (ANA) positivity is a feature of several autoimmune diseases; however, up to 20% of healthy women are ANA+, and most will never develop clinical autoimmune disease. We have previously evaluated T cells in healthy ANA+ individuals, and found differences by race. European American (EA) ANA+ subjects, at lower risk for transition to autoimmunity, had T cells with a decreased interferon (IFN) gene signature compared to ANA- healthy and EA SLE patients. T Cells of ANA+ African Americans (AA) had greater expression of IFN and activation markers. The current project evaluated the impact of race on gene expression in B Cells and myeloid cells of healthy ANA – and ANA+ individuals as well as SLE patients.

Methods: scRNA-seq and CITE-seq was performed on healthy EA and AA ANA- (n=12), and ANA+ (n=12) people, and SLE patients (n=12). CD2 depleted peripheral blood mononuclear cells were used to determine B cell and myeloid cell subset frequencies and identify differential gene signatures. Library preparation was done on a 10X Genomics® Chromium instrument and sequencing was completed on Illumina NextSeq. Analyses using Seurat package in R were used to identify and visualize distinct cell clusters, while clusterProfiler was used for gene enrichment and pathway analyses.

Results: Cells from all subjects clustered into 14 unique B cell populations and 6 distinctive myeloid cell populations. IgE+ B cells and several naïve B cell clusters frequencies were elevated in B cells of ANA+ healthy people compared to ANA- controls. Gene enrichment analyses revealed greater neutrophil activation and degranulation in AA ANA+ and SLE patients (Q< 0.0025), and greater expression of T cell stimulatory signals (CD52, HLA-Class I and II, ISG) (Q< 0.00006) in classical monocytes (CD14+CD16-) than EA subjects. Both EA and AA patients with SLE had gene enrichment in transcription initiation, viral transcription, and protein targeting to the endoplasmic reticulum (Q< 0.0005) with modest enrichment found in ANA+ healthy individuals (Q< 0.01). EA ANA+ healthy individuals also had enrichment of gene pathways involved in regulation of viral life cycle (Q=0.01), regulation of viral entry into the host cell (Q=0.01), and negative regulation of the viral process (Q=0.01). Expression of these pathways was reduced in SLE patients and not found in AA ANA+ healthy samples. S100 gene expression was increased with disease in both EA and AA SLE patients (Q< 0.00007); however, AA ANA+, AA SLE patients (Q< 0.002) and even AA ANA- controls (Q< 0.0007) had higher expression of genes in the S100 pro-inflammatory family than EA subjects.

Conclusion: In healthy ANA+ individuals, gene expression pathways in myeloid and B cell subsets are altered. Healthy ANA+ African Americans exhibit heightened gene expression in cellular activation pathways and decreases in certain viral regulatory networks, suggesting an ongoing struggle with viral-like stimuli which may enhance their risk for progression to clinical autoimmunity.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/myeloid-and-b-cell-transcriptional-phenotypes-reveal-race-dependent-differences-in-early-autoimmunity/