Deprez et al. - 2020 - A Single-Cell Atlas of the Human Healthy Airways

AnnData object of the single-cell atlas Rationale: The respiratory tract constitutes an elaborate line of defense that is based on a unique cellular ecosystem. Objectives: We aimed to investigate cell population distributions and transcriptional changes along the airways by using single-cell RNA profiling. Methods: We have explored the cellular heterogeneity of the human airway epithelium in 10 healthy living volunteers by single-cell RNA profiling. A total of 77,969 cells were collected at 35 distinct locations, from the nose to the 12th division of the airway tree. Measurements and Main Results: 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 distinct cellular proportions in different regions 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 is stable across all tracheobronchial samples. Our atlas improves the description of ionocytes, pulmonary neuroendocrine cells, and brush cells and identifies a related population of NREPpositive cells. We also report the association of KRT13 with dividing cells that are reminiscent of previously described mouse “hillock” cells and with squamous cells expressing SCEL and SPRR1A/B. Conclusions: Robust characterization of a single-cell cohort in healthy airways establishes a valuable resource for future investigations. The precise description of the continuum existing from the nasal epithelium to successive divisions of the 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. Keywords: single-cell RNAseq; epithelium; nose; trachea; bronchus单细胞图谱的AnnData对象 研究背景：呼吸道依托独特的细胞生态系统，构筑了一套精密的防御屏障。 研究目的：本研究旨在采用单细胞RNA谱分析（single-cell RNA profiling）技术，探究气道内细胞群分布与转录组变化规律。 研究方法：本研究针对10名健康活体志愿者的人类气道上皮细胞开展单细胞RNA谱分析以探究其细胞异质性；共从鼻腔至气道树第12级分支的35个不同位点采集了77,969个细胞。 检测与主要结果：本研究获得的图谱包含高比例的上皮细胞（89.1%），同时还包含免疫细胞（6.2%）与基质细胞（4.7%），且不同气道区域的细胞占比存在显著差异。研究揭示了来自鼻腔（MUC4、PI3、SIX3）与气管支气管（SCGB1A1、TFF3）气道的同类细胞类型（基上层细胞、分泌细胞及多纤毛细胞）之间存在差异基因表达现象；相较而言，所有气管支气管样本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、肺神经内分泌细胞与刷细胞的特征描述，并鉴定出一群NREP阳性的相关细胞群。此外，本研究还报道了KRT13与一类此前被描述的小鼠“丘状细胞”样增殖细胞，以及表达SCEL和SPRR1A/B的鳞状细胞之间的关联。 研究结论：本研究对健康气道内的单细胞队列进行了精准表征，为后续研究提供了宝贵的资源。本研究精准描述了从鼻腔上皮到气道各级分支的连续转录组变化特征，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。 关键词：单细胞RNA测序（single-cell RNAseq）；上皮细胞；鼻腔；气管；支气管