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J. Allergy Clin. Immunol., Feb 25 2026, S0091-6749(26)00130-2 | https://doi.org/10.1016/j.jaci.2026.02.019 Single-cell profiling of paired nasal brushing and tissue samples reveals distinct cellular landscapes and immune phenotypes

Gyeongyeob Kim MS ^a,b, Sol Lee BS ^a,b, Min-Seok Koo BS^a,b, Sungmin Moon PhD^a,b, Dachan Kim MD, MS ^b, Hyung-Ju Cho MD, PhD ^b,c, Chang-Hoon Kim MD, PhD ^b,c, Min-Seok Rha MD, PhD ^b,c

^aThe Graduate School, Yonsei University College of Medicine, Seoul, Republic of Korea
^bDepartment of Otorhinolaryngology, Yonsei University College of Medicine, Seoul, Republic of Korea
^cThe Airway Mucus Institute, Yonsei University College of Medicine, Severance Hospital, Seoul, Republic of Korea

Corresponding author Min-Seok Rha, MD, PhD

Abstract

Background
Since the COVID-19 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).

Objective
To directly compare the cellular composition and immune cell responses of NB and NT samples.

Methods
Paired NB and NT samples were collected from the same anatomical site. The frequency, phenotype, and effector functions of epithelial and immune cells were analyzed using single-cell RNA sequencing and flow cytometry.

Results
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 CD56bright NK 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, SARS-CoV-2–specific T cells were significantly less frequent in NB samples than in NT.

Conclusions
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 to NT. These findings highlight the importance of selecting sampling methods that align with the specific objectives of a study.

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