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Spatial Transcriptomics Analysis of inflamed versus healthy Dental Pulps

ABSTRACT: Diagnostic protocols in endodontics rely heavily on subjective pain assessments and sensibility testing, which often fail to reflect the true histopathological and molecular state of the pulp. This limitation can result in misdiagnosis of reversible pulpitis as irreversible, leading to unnecessary devitalization of teeth that might otherwise respond to vital pulp therapy (VPT). Improved understanding of pulp biology is essential to refine case selection and enhance VPT outcomes. We aim to investigate the transcriptomic profiles of pulpitis, identify inflammation subtypes, and improve classification beyond the traditional reversible/irreversible framework. Methods: Spatial transcriptomics (Visium-CytAssist-V2) was used to analyze four dental pulp tissues. Cell deconvolution and differential gene expression analyses were performed to characterize transcriptomic signatures of healthy pulp (HL), reversible pulpitis (RP), and irreversible pulpitis (IP), with specific attention to coronal regions adjacent to carious lesions.

ORGANISM(S): Homo sapiens

PROVIDER: GSE322883 | GEO | 2026/05/01

REPOSITORIES: GEO

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Project description:Purpose: To compare the transcriptional changes of genes in dental pulp tissues with different degrees of inflammatory severity and investigate the role of RAD54B in inflamed human dental pulp cells (hDPCs) Methods: Normal, carious, and pulpitis human dental pulp tissues were collected. Total RNA extracted were subjected to RNA-sequencing and gene expression profiles were further studied by Gene Ontology (GO) and KEGG pathway analysis. DEGs (differentially expressed genes) in homologous recombination repair (HRR) were validated with qRT-PCR. The expression of RAD54B and TNF-α in human dental pulp tissues was detected by immunohistochemistry. HDPCs were cultured and RAD54B level in hDPCs was detected after LPS stimulation using western blot. CCK-8 was applied to investigate the cell proliferation of hDPCs transfected with negative control (Nc) small interfering RNA (siRNA), RAD54B siRNA, P53 siRNA or both siRNAs with or without LPS stimulation. Flow cytometry was applied to detect the cell cycle distribution, and western blot and immunofluorescence were utilized to analyze the expression of RAD54B, P53 and P21 under the above treatments. One-way and two-way ANOVA followed by LSD posttest were used for statistical analysis. Results: RNA-sequencing results identified DEGs among three groups. KEGG pathway analysis revealed enrichment of DEGs in Replication and Repair pathway. HRR and non-homologous end joining (NHEJ) components were further verified and qRT-PCR results were basically consistent with the sequencing data. RAD54B, a HRR accessory factor highly expressed in carious and pulpitis tissues compared to normal pulp, was chosen as our gene of interest. High RAD54B expression was confirmed in inflamed human dental pulp tissues and LPS-stimulated hDPCs. Upon RAD54B knockdown, P53 and P21 expressions in hDPCs were upregulated whereas the cell proliferation was significantly downregulated, accompanied with increased G2/M phase arrest. After inhibiting P53 expression in RAD54B-knockdown hDPCs, P21 expression and cell proliferation were reversed. Conclusions: Gene expression profiles of normal, carious and pulpitis human dental pulp tissues were revealed. HRR components was elucidated to function in dental pulp inflammation. Among HRR DEGs, RAD54B could regulate the cell proliferation of inflamed hDPCs via P53/P21 signaling. This research not only deepens our understanding of dental pulp inflammation but also provides a new insight to clarify the underlying mechanisms.

Project description:Tooth decay, also known as dental caries, is a prevalent oral health problem that significantly reduces an individual's quality of life; however, it can be effectively managed through restorative treatments. The condition primarily affects the enamel and dentin structures and can be treated before it progresses to the pulp chamber. Even in cases where the caries does not reach the pulp, microbial products from the lesion can still penetrate the pulp chamber, potentially inducing stress on pulp cells, including dental pulp stem cells (DPSCs). Even in the absence of direct pulpal exposure, microbial by-products originating from carious lesions may diffuse through dentinal tubules, potentially exerting stress on pulpal cells, including dental pulp stem cells (DPSCs). In this study, we performed a comparative analysis of the biological and proteomic profiles of DPSCs isolated from carious teeth that had not reached the pulp and those isolated from healthy teeth. In this study, we conducted a comparative analysis of the biological and proteomic profiles of dental pulp stem cells (DPSCs) isolated from clinically asymptomatic teeth with deep dentinal caries that had not reached the pulp and those isolated from healthy teeth. After evaluation of biological mechanisms such as senescence and apoptosis, we examined both the whole-cell proteome and secretome of these DPSCs by conducting a shotgun proteomics approach. Our findings indicate that the DPSC population isolated from decayed teeth exhibited a significantly higher proportion of senescent cells compared to the control group. Proteomic analysis further revealed that DPSCs from decayed teeth activated specific signaling pathways in response to microbial products, manifesting an inflammatory profile. Additionally, we observed an upregulation in the expression of proteins associated with extracellular matrix (ECM) remodeling and components of the senescence-associated secretory phenotype (SASP), both of which are hallmarks of the senescence process. This study highlights that even in the absence of direct pulp involvement, microbial stress resulting from caries can impact DPSCs within the pulp. The study reveals that DPSCs can be affected by microbial signals from carious lesions, even when the pulp appears clinically intact. The activation of senescence and inflammatory mechanisms in these affected cells may have deleterious effects on other critical tissues within the organism. Consequently, restorative treatments should consider targeting not only the decayed tissue but also the senescent cells within the pulp that may have been affected by the microbial stress induced by caries.

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Spatial Transcriptomics Analysis of inflamed versus healthy Dental Pulps

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