Journal Article

Single cell profiling of human airway identifies tuft-ionocyte progenitor cells displaying cytokine-dependent differentiation bias in vitro

Rajagopal, Jayaraj, Slyper, Michal, Lin, Brian, Bhagwat, Atharva, Yang, Lujia Cha Cha, Xu, Jiajie, Sun, Jiawei, Delorey, Toni M., Dionne, Danielle, Sun, Dawei, Kim, Sunghyun, Nguyen, Lan T., Tsankov, Alexander M., Xu, Ke, Lou, Wendy, Monga, Isha, Regev, Aviv, Shah, Viral S., Saladi, Srinivas Vinod, Surve, Manalee V., Rozenblatt-Rosen, Orit, Giotti, Bruno, Waghray, Avinash, Bairakdar, Mohamad, Cai, Peiwen, Muus, Christoph, Waldman, Julia, Park, Eric

2025

Overview

Human airways contain specialized rare epithelial cells including CFTR-rich ionocytes that regulate airway surface physiology and chemosensory tuft cells that produce asthma-associated inflammatory mediators. Here, using a lung cell atlas of 311,748 single cell RNA-Seq profiles, we identify 687 ionocytes (0.45%). In contrast to prior reports claiming a lack of ionocytes in the small airways, we demonstrate that ionocytes are present in small and large airways in similar proportions. Surprisingly, we find only 3 mature tuft cells (0.002%), and demonstrate that previously annotated tuft-like cells are instead highly replicative progenitor cells. These tuft-ionocyte progenitor (TIP) cells produce ionocytes as a default lineage. However, Type 2 and Type 17 cytokines divert TIP cell lineage in vitro, resulting in the production of mature tuft cells at the expense of ionocyte differentiation. Our dataset thus provides an updated understanding of airway rare cell composition, and further suggests that clinically relevant cytokines may skew the composition of disease-relevant rare cells. Human airway contains physiologically relevant yet rare cells, but their scarcity prevents thorough profiling and differentiation studies. Here the authors use single cell RNA sequencing to identify rare ionocytes and tuft cells, as well as a potential progenitor population with cytokine-guided differentiation into either the ionocytes or tuft cell lineage.

• Publisher: Nature Publishing Group UK,Nature Publishing Group,Nature Portfolio
• Subject: 13/100 / 13/31 / 13/51 / 14/19 / 38/39 / 38/91 / 631/136/142 / 631/208/514 / 631/250/127/1213 / 631/553/1833 / Cell Differentiation / Cell Lineage / Cells (biology) / Chemoreception / Composition / Cystic Fibrosis Transmembrane Conductance Regulator - metabolism / Cytokines / Cytokines - metabolism / Epithelial cells / Epithelial Cells - cytology / Epithelial Cells - metabolism / Epithelium / Gene sequencing / Humanities and Social Sciences / Humans / Lung - cytology / Lung - metabolism / multidisciplinary / Progenitor cells / Respiratory Mucosa - cytology / Respiratory Mucosa - metabolism / Respiratory tract / RNA-Seq / Science / Science (multidisciplinary) / Single-Cell Analysis - methods / Stem Cells - cytology / Stem Cells - metabolism