Blood RNA-sequencing across the continuum of ANA-positive autoimmunity reveals insights into initiating immunopathology

Lucy Marie Carter; Md Yuzaiful Md Yusof; Zoe Wigston; Darren Plant; Stephanie Wenlock; Adewonuola Alase; Antonios Psarras; Edward M Vital

doi:10.1136/ard-2023-225349

Blood RNA-sequencing across the continuum of ANA-positive autoimmunity reveals insights into initiating immunopathology

Ann Rheum Dis. 2024 May 13:ard-2023-225349. doi: 10.1136/ard-2023-225349. Online ahead of print.

Authors

Lucy Marie Carter¹, Md Yuzaiful Md Yusof^{1

2}, Zoe Wigston¹, Darren Plant³, Stephanie Wenlock⁴, Adewonuola Alase¹, Antonios Psarras^{1

5}, Edward M Vital^{6

2}

Affiliations

¹ Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK.
² NIHR Leeds Musculoskeletal Biomedical Research Unit, Leeds Teaching Hospitals NHS Trust, Leeds, UK.
³ Division of Musculoskeletal and Dermatological Sciences, The University of Manchester, Manchester, UK.
⁴ Cambridge Genomic Sciences, University of Cambridge, Cambridge, UK.
⁵ Kennedy Institute of Rheumatology, University of Oxford, Oxford, UK.
⁶ Leeds Institute of Rheumatic and Musculoskeletal Medicine, University of Leeds, Leeds, UK e.m.j.vital@leeds.ac.uk.

PMID: 38740438
DOI: 10.1136/ard-2023-225349

Abstract

Objective: Mechanisms underpinning clinical evolution to systemic lupus erythematosus (SLE) from preceding antinuclear antibodies (ANA) positivity are poorly understood. This study aimed to understand blood immune cell transcriptional signatures associated with subclinical ANA positivity, and progression or non-progression to SLE.

Methods: Bulk RNA-sequencing of peripheral blood mononuclear cells isolated at baseline from 35 ANA positive (ANA+) subjects with non-diagnostic symptoms was analysed using differential gene expression, weighted gene co-expression network analysis, deconvolution of cell subsets and functional enrichment analyses. ANA+ subjects, including those progressing to classifiable SLE at 12 months (n=15) and those with stable subclinical ANA positivity (n=20), were compared with 15 healthy subjects and 18 patients with SLE.

Results: ANA+ subjects demonstrated extensive transcriptomic dysregulation compared with healthy controls with reduced CD4+naïve T-cells and resting NK cells, but higher activated dendritic cells. B-cell lymphopenia was evident in SLE but not ANA+ subjects. Two-thirds of dysregulated genes were common to ANA+ progressors and non-progressors. ANA+ progressors showed elevated modular interferon signature in which constituent genes were inducible by both type I interferon (IFN-I) and type II interferon (IFN-II) in vitro. Baseline downregulation of mitochondrial oxidative phosphorylation complex I components significantly associated with progression to SLE but did not directly correlate with IFN modular activity. Non-progressors demonstrated more diverse cytokine profiles.

Conclusions: ANA positivity, irrespective of clinical trajectory, is profoundly dysregulated and transcriptomically closer to SLE than to healthy immune function. Metabolic derangements and IFN-I activation occur early in the ANA+ preclinical phase and associated with diverging transcriptomic profiles which distinguish subsequent clinical evolution.

Keywords: Autoantibodies; Autoimmunity; Lupus Erythematosus, Systemic; Risk Factors.