Background/Purpose: Anti-nuclear antibody (ANA) positivity represents a complex ‘At-Risk’ state for development of connective tissue disease (CTD). ANA may become positive years in advance of clinically emergent CTD but only a small fraction of ANA positive individuals in the wider community ultimately develop symptomatic autoimmune disease. Complex immune disturbances including plasmacytoid dendritic cell exhaustion are evident even among ANA positive individuals who do not ultimately progress to overt CTD. We have shown that a validated blood IFN-Score could stratify progression from At-Risk ANA positivity to classifiable SLE. However, the wider transcriptional fingerprint of the At-Risk state and broader factors modulating risk of progression are unknown. We hypothesise that diverse immune processes, interacting and independent of IFN pathway activation, could modulate risk of progression. Here we investigate the peripheral blood immune cell transcriptional signatures derived by RNA Seq which distinguish At-Risk ANA positivity from healthy subjects and associate with progression or non-progression to clinically apparent SLE.

Methods: Bulk RNASeq was performed on peripheral blood mononuclear cells (PBMCs) isolated from healthy volunteers (n =15) and at baseline from ANA-positive At-Risk individuals (n =35) demonstrating ≤1 clinical criterion for classifiable CTD, symptom duration < 12 months and naive of glucocorticoid or immunosuppressive therapy. Progression from ANA-positivity was prospectively adjudicated at 12 months and defined as accrual of clinical/ immunological criteria sufficient to meet SLICC 2012 classification for SLE with 3 years total follow up. Differential gene expression was analysed using edgeR in R Bioconductor with Benjamini-Hochberg multiple testing correction. Reactome and Gene Ontology enrichment were examined in g:Profiler.

Results: As compared with healthy subjects, 101 genes were uniquely upregulated (log₂FC > 1.0, FDR < 0.05) at baseline in At-Risk subjects who subsequently progressed to SLE. These were highly enriched for IFNa /b signalling (FDR =5.95x10^-11) and epigenetic regulation of gene expression (FDR = 2.32×10^-9). 126 genes were uniquely upregulated at baseline in At-Risk non-progressors and these displayed pathway enrichment for IL-4 and IL-13 signalling (FDR =1.18×10^-5). Compared with healthy controls, ANA-positive At-Risk subjects, irrespective of subsequent progression status displayed significant downregulation (log₂FC < -1.0, FDR < 0.05) of 102 genes which were highly enriched for oxidative phosphorylation (FDR =5.3x10^-11).

Conclusion: We identify transcriptomic signatures implicated in SLE disease initiation. We show (i) baseline IFN-pathway activation is a strong transcriptomic risk marker of progression from ANA-positivity; ii) differential cytokine activation may modulate progression risk and iii) even in the absence of manifest autoimmune disease ANA positivity is transcriptionally associated with immune cell metabolic reprogramming.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/blood-rna-sequencing-reveals-complex-immune-dysregulation-in-ana-positive-individuals-with-distinct-profiles-preceding-progression-to-sle-versus-stable-autoimmunity/