Mendelian randomization and single-cell transcriptomics prioritize CD7 and LAPTM5 in primary Sjögren's disease: an integrative multi-omics analysis.

BACKGROUND

Primary Sjögren's disease (pSD) is a chronic autoimmune condition marked by exocrine gland dysfunction. Emerging evidence indicates that lactylation modification may contribute to the pathogenesis of autoimmune diseases; however, its role in pSD has yet to be investigated.

METHODS

We conducted an integrated analysis combining single-cell RNA sequencing data (GSE157278), bulk transcriptome data (GSE51092), and whole-blood eQTL data with Mendelian randomization (MR) and colocalization analysis. Expanded single-cell quality-control analyses were performed, and lactylation-related gene-set scores (332 literature entries representing 330 unique genes) were quantified using five algorithms as an exploratory analysis, together with method-sensitivity and library-complexity-corrected analyses. RT-qPCR in peripheral blood mononuclear cells (PBMCs) was performed as an explohhratory analysis.

RESULTS

MR identified ten nominal associations between gene expression and an electronic health record-based sicca syndrome phenotype (PheCode 709.2), including CD7 (OR = 0.50, P = 0.0033) and LAPTM5 (OR = 1.29, P = 0.0088); colocalization analysis supported shared underlying variants at both loci, prioritizing CD7 and LAPTM5 as candidate genes; reverse MR was negative. In an additional disease-state expression analysis of the whole-blood GSE51092 cohort (190 patients, 32 controls), CD7 expression was significantly lower in patients (fold-change 0.74, q = 2.8 × 10-4), directionally concordant with its genetically predicted protective effect, as was a 12-gene megakaryocyte/platelet signature (standardized mean difference - 0.31, 95% CI - 0.56 to - 0.06; Welch q = 0.045). A megakaryocyte/platelet-like population was present in all ten single-cell donors and was supported by marker panels and differential-expression analysis. Exploratory lactylation-related gene-set scores were method-dependent and not robustly cell-type-specific after library-complexity correction; at the sample level, scores were nominally higher in patients' CD14 + monocytes (P = 0.016, q = 0.095) and NK cells (P = 0.032, q = 0.095), and within the megakaryocyte/platelet-like population, the score-associated transcriptional variation of CD7 and LAPTM5 was the largest among the six cell types. RT-qPCR in PBMCs (10 patients, 10 controls) showed directionally upward but statistically non-significant trends for LAPTM5 (median fold-change 2.9) and CD7 (median fold-change 1.7).

CONCLUSIONS

CD7 and LAPTM5 emerged as candidates at the intersection of pSD transcriptomic findings and genetic associations with a broader sicca/Sjögren spectrum phenotype, with distinct immunological pathway profiles, and whole-blood disease-state data corroborate the direction of the CD7 association. Megakaryocyte/platelet-lineage cells warrant further investigation in pSD. Lactylation-related transcriptomic scores are surrogates that require direct experimental validation, and studies in disease-relevant tissues are needed. Key Points • Characterization of a megakaryocyte/platelet-like population in peripheral blood: We characterized this population in pSD and control PBMCs using expanded quality control, marker panels, and differential-expression analysis, in line with prior flow-cytometric evidence of circulating megakaryocyte expansion in systemic autoimmune diseases. • Genetically prioritized candidate genes: By integrating Mendelian randomization with colocalization analysis and single-cell transcriptomics, we identified LAPTM5 and CD7 as candidate genes supported by convergent pSD transcriptomic findings and nominal genetic associations with a broader sicca phenotype. • Elucidation of functional pathways: We delineated the distinct immunological pathways linked to these genes, with LAPTM5 linked to Notch signaling and complement cascades, while CD7 is involved in antigen presentation and NK cell cytotoxicity.