Single-cell profiling of paired nasal brushing and tissue samples reveals distinct cellular landscapes and immune phenotypes.

Abstract

Since the coronavirus disease 2019 pandemic, local immune responses in the nasal mucosa have become an area of growing research interest. In this context, studies using noninvasive nasal brushing (NB) samples have increased markedly. However, it remains unclear whether NB samples accurately reflect the immune landscape of the nasal tissue (NT). A study was conducted to directly compare the cellular composition and immune cell responses of NB and NT samples. Paired NB and NT samples were collected from the same anatomic site. The frequency, phenotype, and effector functions of epithelial and immune cells were analyzed by single-cell RNA sequencing and flow cytometry. NB samples contained a significantly higher proportion of epithelial cells than NT samples, while fibroblasts, endothelial cells, and B cells were significantly less abundant. Within the epithelial compartment, NB showed an enrichment of ciliated and secretory cells, whereas basal cells were less frequent and glandular basal/secretory cells were rarely detected. Additionally, CD103⁺ tissue-resident memory T cells and CD56^bright natural killer cells were more abundant in NB samples than in NT samples. Functional analyses revealed distinct T-cell effector profiles between the two sample types. Notably, severe acute respiratory syndrome coronavirus 2-specific T cells were significantly less frequent in NB samples than in NT. NB is well suited for sampling cells located near the epithelial surface but captures fewer cells from deeper mucosal layers. Additionally, NB samples display distinct T-cell effector profiles and virus-specific T-cell frequencies compared with NT. These findings highlight the importance of selecting sampling methods that align with the specific objectives of a study.