Single-Cell Transcriptomic Profiling of Human Dental Pulp in Sound and Carious Teeth: A Pilot Study

Abstract

A comprehensive understanding of dental pulp cellular compositions and their molecular responses to infection are crucial for the advancement of regenerative dentistry. Here, we presented a pilot study of single-cell transcriptomic profiles of 6,810 pulpal cells isolated from a sound human maxillary third molar and three carious teeth with enamel and deep dental caries. We observed altered immune cell compositions of the dental pulp in deep, but not enamel ones. Differential expression analysis revealed up-regulation of several pro-inflammatory, anti-inflammatory, and mineralization-related genes in the immune and stromal cells of the deep dental caries. Making use of an algorithm for predicting cell-to-cell interactions from single-cell transcriptomic profiles, we showed an increase in cell-cell interactions between B cells, plasma cells and macrophages, and other cell types in deep dental caries, including those between TIMP1 (odontoblasts)—CD63 (myeloid cells), and CCL2 (macrophages)—ACKR1 (endothelial cells). Collectively, our work highlighted the single-cell level gene regulations and intercellular interactions in the dental pulps in health and disease.

Establishment of inclusive single-cell transcriptome atlases from mouse and human tooth as powerful resource for dental research

“…To complement the mouse tooth sc atlas, we also set out to establish an inclusive sc transcriptomic atlas of healthy human teeth (molars) by combining the at present six publicly available datasets ( Figure 3A ; Table 4 ) ( Krivanek et al, 2020 ; Pagella et al, 2021b ; Shi et al, 2021 ; Yin et al, 2021 ; Hemeryck et al, 2022 ; Opasawatchai et al, 2022 ). Following stringent quality control, 57,906 cells were found suitable for further bioinformatic analysis, with the datasets contributing between 524 and 21,453 cells to the total set, and cells sampled from various dental tissue types (e.g., 24,412 cells from DP and 7,119 from DF) ( Supplementary Figures S3A,B , Table 5 ).…”

“…In parallel to composing the healthy tooth atlas, we established a sc transcriptome atlas of diseased human tooth, integrating the at present publicly available datasets from patients with deep caries, enamel caries, chronic apical periodontitis (CAP) and periapical granuloma ( Table 4 ) ( Lin et al, 2022 ; Opasawatchai et al, 2022 ). Following strict quality control, 17,016 cells were retained of which 3,562 and 13,454 cells were derived from dental pulp and periapical diseases (corresponding to the individual datasets), respectively ( Supplementary Figures S3F,G , Table 5 ).…”

“…Regarding mouse, single-cell RNA-sequencing (scRNA-seq) datasets were generated from the constantly (re-)growing incisor and the more static, human-resembling molar at different timepoints, either of whole tooth or specific tissue components ( Sharir et al, 2019 ; Takahashi et al, 2019 ; Chen et al, 2020 ; Chiba et al, 2020 , 2021 ; Krivanek et al, 2020 ; Wen et al, 2020 ; Nagata et al, 2021 ; Zhao et al, 2021 ). Human sc transcriptomic data were predominantly generated from dental pulp and periodontal tissues of molars in both healthy and diseased states ( Krivanek et al, 2020 ; Pagella et al, 2021b ; Shi et al, 2021 ; Yin et al, 2021 ; Hemeryck et al, 2022 ; Lin et al, 2022 ; Opasawatchai et al, 2022 ). All these sc analyses generated deeper insight into the tooth molecular and cellular landscape, furthering the understanding of dental cell type heterogeneity and tooth biology.…”

Intercellular crosstalk in adult dental pulp is mediated by heparin-binding growth factors Pleiotrophin and Midkine

“…FASTQ files of single-cell RNA sequencing (scRNA-seq) data were retrieved from published studies (2,(9)(10)(11)(12)(13). The data were selected based on healthy human tissue.…”

“…Researchers have used this technology to generate transcriptomes of developing teeth in mice (7,8). Recent studies of human DP have identified cells involved in tissue development (2), delineated major cellular components of adult DP (9), and described enriched cell types under carious lesion conditions (10).…”