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Introduction Sjögren’s disease (SjD) is a systemic, rheumatic autoimmune disorder evidenced by broad organ-specific manifestations, predominantly exocrine gland-impairment, which disproportionally affects females. The golden-standard tool for diagnosing disease-associated pathology includes a microscopic evaluation of minor salivary gland (MSG) biopsies. Approximately 25% of the patients exhibit germinal centre (GC)-like structures within their salivary glands, which have been associated with an increased risk of B cell lymphoma and infiltration of T follicular helper (Tfh) cells.Objective We aimed to explore spatial signalling patterns associated with the Tfh cell and ectopic GC-like structure formation.Materials and methods Novel duplex-chromogenic RNAscope in situ hybridisation was employed on MSGs of 20 male and female SjD patients, alongside 20 non-SjD sicca tissue controls where mRNA levels of B cell stimulating factor (BAFF) were visualised and quantified alongside IL-21R, CXCL13 and CXCR5.Results Digital quantifications in Qupath revealed a positive correlation between cells containing BAFF and IL-21R mRNA-signals (p<0.05). Also, the spatial mRNA expression of IL-21R, CXCL13 and CXCR5 was predominantly localised within focal infiltrates, with significantly higher transcript abundance observed in the GC +-group (p<0.001). Additional evaluation of salivary flow-related immunopathological changes showed that increased BAFF-positive ductal epithelial cells were associated with hyposalivation (p<0.05). Moreover, elevated atrophy of the MSGs displayed a negative correlation with BAFF-expressing immune cells within focal infiltrates (p<0.001).Conclusion Spatial localisation of key Tfh cell-related cytokines in relation to ectopic GC-like formations may explain the immunopathological alterations and symptoms involved in SjD pathogenesis.