Background/Purpose: The genetic and environmental factors underlying pathogenesis of systemic lupus erythematosus (SLE) are incompletely resolved. While inherited genetic variation has been extensively queried in lupus, post-zygotically acquired somatic mutations remain largely unexplored. Somatic lesions are continually generated in all cells by physiologic processes and exogenous exposures, rendering every human a genetic mosaic. Lymphocytes are especially prone to mutagenesis in part due to programmed genomic instability during antigen receptor maturation. We therefore sought to survey somatic single nucleotide variants (sSNVs) in lymphocytes towards testing the hypothesis that mosaicism contributes to impaired self-tolerance in autoimmunity.

Methods: Subjects aged 6 – 21 years who met 2019 ACR/EULAR SLE classification criteria (n = 22) and unaffected controls (JIA, n = 6; low-titer ANA positive without disease, n = 4) were recruited from Stanford Pediatric Rheumatology clinics between August 2023 and October 2024. Peripheral blood mononuclear cells were obtained from controls at one timepoint and from SLE cases during active (n = 14, SLEDAI >4) and/or quiescent disease (n = 14). B cells, CD4 and CD8 T cells, and monocytes were isolated via fluorescence-activated cell sorting and sSNVs were detected via deep cell type-specific exome sequencing (~300X coverage).

Results: We discovered 9,650 candidate sSNVs with median variant allele frequency (VAF) of 3.4% (range 1.9 – 20.1%) across 112 exome datasets representing 4 cell types and 38 samples from 32 subjects. Based on sequencing synthetic mixtures of well-characterized cell lines, our workflow recovered SNVs with VAF ≥1.5% with precision >95% and recall >60%. B cells in active SLE were enriched for non-synonymous sSNVs relative to quiescent lupus and controls (median 62 vs. 40 – 52, p = 0.028, Mann-Whitney U test). Similarly, CD8 T cells in active SLE carried more sSNVs than in quiescent disease or in controls (median 65 vs. 40 – 41, p = 0.004, Mann-Whitney U test). Differences in age-stratified sSNV burden and cell type-specific VAFs were not significant. Genes harboring sSNVs in SLE lymphocytes included JAK1, STAT3, and RELB. Pooled analysis of non-synonymous sSNVs in SLE lymphocytes identified enrichment of survival signaling pathway genes (p < 0.001, hypergeometric test, Bonferroni corrected).

Conclusion: Interim analysis of immunogenetic mosaicism identified frequent protein-coding candidate sSNVs in peripheral B and T cells in clinically active SLE. Together with ongoing validation of sSNVs, sequencing of additional pediatric and adult subjects, and longitudinal analyses, we expect that future mechanistic studies will clarify the role of somatic variation in lupus pathogenesis and heterogeneity.

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ACR Meeting Abstracts - https://acrabstracts.org/abstract/protein-coding-somatic-genetic-variation-in-lymphocytes-in-systemic-lupus-erythematosus/