Single cell RNA-seq mapping of nasal and tracheobronchial airways in human healthy volunteers

The respiratory tract constitutes an elaborated line of defense based on a unique cellular ecosystem. Single-cell profiling methods enable the investigation of cell population distributions and transcriptional changes along the airways. We have explored cellular heterogeneity of the human airway epithelium in 10 healthy living volunteers by single-cell RNA profiling. 77,969 cells were collected by bronchoscopy at 35 distinct locations, from the nose to the 12th division of the airway tree. The resulting atlas is composed of a high percentage of epithelial cells (89.1%), but also immune (6.2%) and stromal (4.7%) cells with peculiar cellular proportions in different sites of the airways. It reveals differential gene expression between identical cell types (suprabasal, secretory, and multiciliated cells) from the nose (MUC4, PI3, SIX3) and tracheobronchial (SCGB1A1, TFF3) airways. By contrast, cell-type specific gene expression was stable across all tracheobronchial samples. Our atlas improves the description of ionocytes, pulmonary neuro-endocrine (PNEC) and brush cells, which are likely derived from a common population of precursor cells. We also report a population of KRT13 positive cells with a high percentage of dividing cells which are reminiscent of “hillock” cells previously described in mouse. Robust characterization of this unprecedented large single-cell cohort establishes an important resource for future investigations. The precise description of the continuum existing from nasal epithelium to successive divisions of lung airways and the stable gene expression profile of these regions better defines conditions under which relevant tracheobronchial proxies of human respiratory diseases can be developed.EGA study EGAS00001004082

呼吸道依托独特的细胞生态系统，构建了一套精密的防御体系。单细胞谱分析（single-cell profiling）技术可用于探究气道内的细胞群体分布与转录组变化。本研究通过单细胞RNA谱分析（single-cell RNA profiling），对10名健康活体志愿者的人体气道上皮细胞异质性进行了探究。研究通过支气管镜检在35个不同位点采集了77969个细胞，采样范围覆盖从鼻腔至气道树第12级分支的全段气道。最终构建的细胞图谱中，上皮细胞占比高达89.1%，同时还包含免疫细胞（6.2%）与基质细胞（4.7%），且不同气道位点的细胞占比存在显著差异。该图谱揭示了鼻腔与气管支气管气道中同种细胞类型（基上层细胞、分泌细胞及多纤毛细胞）的基因表达差异：鼻腔相关细胞的特征基因为MUC4、PI3、SIX3，而气管支气管相关细胞的特征基因为SCGB1A1、TFF3。相较而言，所有气管支气管样本中的细胞类型特异性基因表达均保持稳定。本图谱完善了离子细胞、肺神经内分泌细胞（pulmonary neuro-endocrine, PNEC）以及刷状细胞的注释信息，上述细胞大概率起源于同一群前体细胞。本研究还报道了一群KRT13阳性细胞，其中处于增殖状态的细胞占比极高，该细胞群与此前在小鼠中报道的“丘状细胞（hillock cells）”特征相似。对这一前所未有的大规模单细胞队列的精准表征，为后续相关研究提供了重要的基础资源。对鼻腔上皮至肺气道各级分支的连续细胞谱系的精准描述，以及这些区域的稳定基因表达谱，进一步明确了构建人类呼吸道疾病相关气管支气管替代模型的适宜条件。EGA研究编号：EGAS00001004082