Single-nucleus RNA sequencing identifies conserved structural cell programs in allergic lung inflammation.

Background: Lung structural cells contribute to allergic airway inflammation; however, the lung cell type that mounts the most vigorous early transcriptional response to allergen exposure remains unclear. In this study, we used single-nucleus RNA sequencing to define early allergen-induced transcriptional programs across major lung structural cell populations. Objective: We sought to identify the lung structural cell type that exhibits a unique and robust transcriptional response following allergen challenge. Methods: Wild-type C57BL/6J mice were sensitized and challenged with cat dander extract. Lung tissues were collected 4 hours postchallenge to capture early transcriptional events and 72 hours to assess allergic inflammation. Single-nucleus RNA sequencing was performed on nuclei from frozen lung tissue. Transcript quantification, cell-type annotation, and differential gene expression analyses were conducted using Cell Ranger, CellTypist, iDEP, and gene set enrichment analysis. Results: Allergen challenge induced early transcriptional responses across lung structural cell populations. Capillary endothelial cells displayed the greatest number of unique allergen-induced genes and showed enrichment of transcriptional programs related to DNA damage, oxidative stress, and pathways associated with expansion of GATA-3 Conclusions: Capillary endothelial cells represent a dominant and early transcriptionally specialized responder to allergen exposure, characterized by coordinated activation of DNA damage/repair, oxidative stress, and T