Identifying cell-type-specific marker genes of dental epithelial cells using single-cell RNA sequence: A review

Single-cell RNA sequencing (scRNA-seq) has transformed our understanding of dental epithelial heterogeneity, revealing that dental cell types have distinct gene expression profiles. Ameloblasts differentiate from the inner enamel epithelium into the pre-ameloblast, secretory, and maturation phases, and their molecular functions have been extensively described. In contrast, the molecular markers and functional roles of non-ameloblast populations such as the outer enamel epithelium, stellate reticulum, and stratum intermedium, remain unexplored.

We systematically compiled the canonical and newly proposed marker genes from published scRNA-seq tooth development studies. We integrated these datasets with experimental validations from the literature using immunostaining or in situ hybridization of mouse tooth tissues. We examined the dental phenotypes reported in mouse knockout models using the Mouse Genome Informatics and Online Mendelian Inheritance in Man databases to determine the functional relevance of each gene. Genes specifically expressed within each cluster validated by histological experiments, were further assessed using cap analysis of the gene expression sequencing (CAGE-seq) database in the mouse tooth germ and whole body to identify genes that were preferentially enriched in the teeth.

We established an updated molecular map for each dental epithelial cell type through integrating scRNA-seq, histological validation, phenotypic databases, and CAGE-seq. This framework describes the molecular identities of ameloblast and nonameloblast lineages, emphasizes key marker genes across dental epithelial populations, and provides a comprehensive basis for interpreting enamel phenotypes, guiding future tooth development research.