[Single-cell transcriptome analysis reveals development atlas of mouse molar pulp cells].

Objective: Single-cell RNA sequencing (scRNA-seq) was used to analyze the developing mouse molars, in order to construct a spatiotemporal development atlas of pulp cells, and further to reveal the developmental process and regulatory mechanism of tooth development. Methods: Ten mandibular first molars from C57BL/6 mice in postnatal day (PN) 0 and 3 were respectively dissected and digested to obtain single-cell suspensions. scRNA-seq was performed on 10× Genomics platform. PN 7 mouse molar scRNA-seq data were obtained from our previous study. PN 0, 3, and 7 scRNA-seq data were integrated for following analysis. The initial quality control, mapping and single cell expression matrix construction were performed by Cell Ranger. Quality control, standardization, dimensional reduction and cluster analysis were performed by using Seurat. Monocle was used to generate the pseudotime trajectory. Scillus was used to perform gene ontology analysis. In order to detect the spatiotemporal change of different population of pulp cells, the marker genes of each cluster were demonstrated by RNAscope in situ hybridization. Results: There were twenty-six cell clusters within mouse molars, which were identified as eight different cell types, including dental pulp cells, dental follicle cells, epithelial cells, immune cells, endothelial cells, perivascular cells, glial cells and erythrocytes. We further re-clustered and analyzed dental pulp cells. Cluster 0 were mature pulp cells, which located at the upper portion of crown. The main functions of cluster 0 were osteogenesis and extracellular structure organization. Cluster 1 were apical papilla cells, which located at the apical part of roots, whose main functions were extracellular structure organization and organ development. Cluster 2 were cycling cells, which were actively proliferated, resided in the lower portion of the crown. Cluster 3 and 4 were preodontoblasts and odontoblasts, respectively. Their functions were closely related to biomineralization. The proportion of mature pulp cells increased with the development process, while the proportion of cycling cells and odontoblast lineage decreased. According to the expression pattern of marker genes of each cluster, we constructed a cell atlas of dental pulp. Pseudotime trajectory analysis found there were two development trajectories within dental pulp. They both started from SPARC related modular calcium binding 2 (Smoc2)+ dental papilla cells, then went through DNA topoisomerase Ⅱ alpha (Top2a)+ cycling cells, and finally divided into coxsackie virus and adenovirus receptor (Cxadr)+ mature pulp cells or dentin sialophosphoprotein (Dspp)+ odontoblasts two lineages. Conclusions: scRNA-seq could fully discover the intercellular heterogeneity of cells on transcriptome level, which provides a powerful tool to study the process and regulatory mechanism of organ development.目的： 通过在单细胞水平分析小鼠磨牙细胞间异质性，构建牙髓细胞发育的时空图谱，进一步揭示牙齿发育的过程和调控机制。 方法： 分别收集出生后0、3 d的C57BL/6小鼠下颌第一磨牙各10颗，制备单细胞悬液，采用单细胞转录组测序（single-cell RNA sequencing，scRNA-seq）技术进行测序。从本课题组前期研究中提取7 d小鼠磨牙scRNA-seq数据，与0、3 d数据进行合并分析。使用Seurat程序对测序数据进行质控、标准化、降维和聚类分析；Monocle程序进行拟时序分析，预测发育轨迹；Scillus程序进行基因本体分析，对细胞功能进行注释。使用原位杂交技术对标记基因进行体内定位，明确不同亚群细胞的体内分布和时空变化。 结果： Seurat分析显示小鼠磨牙细胞具有26个细胞亚群，可分为牙髓细胞、牙囊细胞、上皮细胞、免疫细胞、内皮细胞、管周细胞、胶质细胞和红细胞等八大类细胞，其中牙髓细胞包含5个亚群：成熟牙髓细胞，标记基因为柯萨奇病毒腺病毒受体（coxsackie virus and adenovirus receptor，Cxadr）；牙乳头细胞，标记基因为SPARC相关模块化钙结合蛋白2（SPARC related modular calcium binding 2，Smoc2）；周期细胞，标记基因为Ⅱ型DNA拓扑异构酶（DNA topoisomerase Ⅱ alpha，Top2a）；前成牙本质细胞，标记基因为棕榈酰蛋白羧酸酯酶（notum palmitoleoyl-protein carboxylesterase，Notum）；成牙本质细胞，标记基因为牙本质涎磷蛋白（dentin sialophosphoprotein，Dspp）。随着牙胚发育，成熟牙髓细胞的比例逐渐增加，周期细胞和成牙本质细胞比例逐渐降低。原位杂交染色和基因本体分析结果显示，Cxadr+成熟牙髓细胞定位于牙冠上部，主要功能为成骨和“细胞外结构组织”；Smoc2+牙乳头细胞位于根尖，主要功能与“细胞外结构组织”和器官发育相关；Top2a+周期细胞位于牙冠下部，进行有丝分裂；Notum+前成牙本质细胞邻近上皮根鞘，和Dspp+成牙本质细胞的主要功能同为生物矿化。Monocle分析显示牙髓细胞有2条发育轨迹，从Smoc2+牙乳头细胞起始，经过Top2a+周期细胞，再分化为Cxadr+成熟牙髓细胞或成牙本质细胞。 结论： scRNA-seq技术能在转录组水平充分揭示细胞间的异质性，为研究器官发育过程和调控机制提供了有力工具。.