The role of microRNAs in complex diseases of the ocular surface: pathogenetic insights and translational implications

Autoimmune ocular surface diseases represent a major cause of chronic morbidity, yet reliable biomarkers and targeted therapeutic strategies remain limited. MicroRNAs (miRNAs) have emerged as crucial post-transcriptional regulators of inflammation, immune homeostasis, and fibrotic remodeling, making them promising candidates for precision diagnostics and intervention. This thesis investigates miRNA dysregulation directly at the ocular surface across three immune-mediated disorders with distinct anatomical and pathogenic features: primary Sjögren’s syndrome (pSS), ocular mucous membrane pemphigoid (oMMP), and Basedow–Graves orbitopathy (BGO). Conjunctival epithelial samples were collected through minimally invasive impression cytology. In pSS and oMMP, global miRNA expression was profiled using NanoString technology, followed by bioinformatic functional analysis and literature mapping. In parallel, a panel of four miRNAs implicated in orbital inflammation and adipogenesis (miR-21, miR-146a-5p, miR-192, miR-96) was validated by qRT-PCR in BGO. pSS was characterized by a distinct pro-inflammatory miRNA signature, with significant upregulation of miR-548 family members. Pathway analysis supported their role in modulating NF-κB and interferon-driven epithelial immune activation, suggesting disruption of mucosal tolerance. In oMMP, miRNA dysregulation was more pronounced: miR-223-3p emerged as a dominant signal (≈16-fold increase), forming a high-confidence interaction network enriched for DNA damage response, MAPK signaling, and oxidative stress pathways, indicating its involvement in chronic fibro-inflammatory injury. In contrast, the only downregulated transcript, miR-99, targeted antifibrotic regulators (FGFR3/MAPK axis, inflammasome control), revealing a key vulnerability predisposing to irreversible conjunctival scarring. Despite clinically significant ocular surface alterations in BGO, none of the selected miRNAs showed significant dysregulation in conjunctival cells, reflecting the orbit-centric nature of disease and highlighting tissue-specific miRNA regulation. Collectively, these findings reveal disease-specific miRNA signatures that reflect distinct anatomical patterns and immune mechanisms across three major ocular autoimmune disorders. miRNAs such as miR-548j-3p, miR-223-3p, and miR-99 emerge as promising candidates for non-invasive diagnostics and targeted molecular therapy. This work supports the integration of ocular-surface miRNA profiling into future biomarker panels and precision-medicine strategies aimed at preserving epithelial integrity and preventing fibrosis in immune-mediated ocular disease.