Single-cell analysis of human airway epithelium identifies cell-type-specific responses to <i>Aspergillus</i> and <i>Coccidioides</i>

Respiratory fungal infections pose a significant threat to human health. Animal models do not fully recapitulate human disease, necessitating advanced models to study human-fungal pathogen interactions. In this study, we utilized primary human airway epithelial cells (hAECs) to recapitulate the lung environment <i>in vitro</i> and investigate cellular responses to two diverse, clinically significant fungal pathogens, <i>Aspergillus fumigatus</i> and <i>Coccidioides posadasii</i>. To understand the mechanisms of early pathogenesis for both fungi, we performed single-cell RNA sequencing of infected hAECs. Analysis revealed that both fungi induced cellular stress and cytokine production. However, the cellular subtypes affected and specific pathways induced differed between fungi, with <i>A. fumigatus</i> and <i>C. posadasii</i> triggering protein-folding-related stress in ciliated cells and hypoxia responses in secretory cells, respectively. This study represents one of the first reports of single-cell transcriptional analysis of hAECs infected with either <i>A. fumigatus</i> or <i>C. posadasii</i>, providing a vital data set to dissect the mechanism of disease and potentially identify targetable pathways.IMPORTANCEFungal infections in the lungs are lethal complications for those with compromised immune systems and have limited treatment strategies available. These options are restricted further by the increased prevalence of treatment-resistant fungi. Many studies focus on how our immune systems respond to these pathogens, yet airway epithelial cells remain an understudied component of fungal infections in the lungs. Here, the authors provide a transcriptional analysis of primary human airway epithelial cells stimulated by two distinct fungal pathogens, <i>Aspergillus fumigatus</i> and <i>Coccidioides posadasii</i>. These data will enable further mechanistic studies of the contribution of the airway epithelium to initial host responses and represent a powerful new resource for future investigations.