Comparative Transcriptome Analysis Identifies Core and Species Driven Host pathways involved in fungal keratitis

Fungal keratitis is a significant cause of ocular morbidity, particularly in developing countries like India. Approximately 95% of fungal corneal infections are caused by filamentous fungi, primarily Fusarium spp. and Aspergillus spp. (Brown et al., 2021). This condition can progress to severe complications, including corneal ulceration, opacification, and, in rare cases, endophthalmitis (Brown et al., 2021). Clinically, Fusarium keratitis presents with feathery margins, grey infiltrates, active and resolving edges, ring infiltrates, and dry plaques (Donovan et al., 2022). Currently, both Fusarium and Aspergillus flavus keratitis are treated exclusively with antifungal agents, primarily Natamycin and Voriconazole (Venkatesh Prajna et al., 2013). However, the response to treatment, particularly for Aspergillus-induced ulcers, remains poor. Recent studies suggest that targeting the host immune system may be crucial for improving outcomes in patients with fungal keratitis. A deeper understanding of the protective host immune response, including the roles of antimicrobial proteins (AMPs), cytokines, and immune cells, is essential for developing effective antifungal immunotherapies. Recognition of fungal pathogens by pattern recognition receptors, such as Toll-like receptors and C-type lectins, initiates immune responses (Tarabishy et al., 2008). Research has identified differential AMP expression in Fusarium and A. flavus infections, with decreased mBD-3 expression in A. flavus infections (Mallela et al., 2021). In contrast, Fusarium infection has been associated with increased mBD-3 expression and more severe symptoms in mice lacking this protein (Kolar et al., 2013). Other immune components, such as factor H-like (FHL) protein and zinc alpha-2 glycoprotein, have been differentially expressed in tears of keratitis patients, depending on the fungal species involved (Shait Mohammed et al., 2020; Ananthi et al., 2013). We hypothesized that the pathophysiology of Fusarium keratitis and Aspergillus flavus keratitis is intrinsically different, with species-specific immune responses influencing disease progression and treatment outcomes. We employed an unbiased transcriptional profiling approach to investigate the host immune response in human corneal samples infected with Fusarium and A. flavus to test this. Our analysis revealed differentially expressed RNA transcripts and identified key genes involved in core and species-specific immune processes. These findings offer potential pathways for species-specific immunotherapies in fungal keratitis management.