Proteomic analysis of human dental pulp in different clinical diagnosis

Proteomic analysis of dental pulp from deciduous teeth in comparison to permanent teeth: an in-vitro study

PURPOSE

The aims of this study were to identify proteomic profiles of dental pulp from deciduous teeth and compare the profiles of the two dentitions.

METHODS

Teeth that were caries-free and had normal pulp conditions were collected from twelve healthy individuals. The obtained teeth consisted of deciduous teeth (n = 6) and permanent teeth (n = 6). Proteins were extracted from pulp tissue and then analysed using liquid chromatography-tandem mass spectrometry. MaxQuant was used to identify and quantify proteins from raw mass spectrometry data of the collected deciduous and previously analysed permanent dental pulp. Differentially expressed proteins (DEPs) between the dental pulp of the two dentitions were identified by a statistical analysis conducted using Metaboanalyst with criteria P-value < 0.05 and fold change > 2.

RESULTS

A total of 3,636 proteins were identified in the dental pulp of deciduous teeth. The biological process functional classifications of these proteins were primarily concerned with cellular process, biological regulation, metabolic process and response to stimulus. Dental pulp protein profiles differed significantly between deciduous and permanent teeth, with 736 proteins being differentially expressed, the majority of which were highly expressed in the pulp of deciduous teeth. Pathway analysis indicated DEPs to be involved in tumour necrosis factor (TNF) signalling, nuclear factor kappa B signalling, and odontoclast/osteoclast differentiation.

CONCLUSION

While the dental pulp of deciduous and permanent teeth shares some characteristics, there are also significant differences in protein expression, with the TNF signalling pathway and odontoclast/osteoclast differentiation being promoted in the dental pulp of deciduous teeth.

Preparation and characterization of bovine dental pulp-derived extracellular matrix hydrogel for regenerative endodontic applications: an in vitro study

BACKGROUND

The use of biological scaffolds in regenerative endodontics has gained much attention in recent years. The search for a new biomimetic scaffold that contains tissue-specific cell homing factors could lead to more predictable tissue regeneration. The aim of this study was to prepare and characterize decellularized bovine dental pulp-derived extracellular matrix (P-ECM) hydrogels for regenerative endodontic applications.

METHODS

Freshly extracted bovine molar teeth were collected. Bovine dental pulp tissues were harvested, and stored at -40º C. For decellularization, a 5-day protocol was implemented incorporating trypsin/EDTA, deionized water and DNase treatment. Decellularization was evaluated by DNA quantification and histological examination to assess collagen and glycosaminoglycans (GAGs) content. This was followed by the preparation of P-ECM hydrogel alone or combined with hyaluronic acid gel (P-ECM + HA). The fabricated scaffolds were then characterized using protein quantification, hydrogel topology and porosity, biodegradability, and growth factor content using Enzyme-linked immunosorbent assay (ELISA): transforming growth factor beta-1(TGF-β1), basic fibroblast growth factor (bFGF), bone morphogenetic protein 2 (BMP-2) and vascular endothelial growth factor (VEGF).

RESULTS

Decellularization was histologically confirmed, and DNA content was below (50 ng/mg tissue). P-ECM hydrogel was prepared with a final ECM concentration of 3.00 mg/ml while P-ECM + HA hydrogel was prepared with a final ECM concentration of 1.5 mg/ml. Total protein content in P-ECM hydrogel was found to be (439.0 ± 123.4 µg/µl). P-ECM + HA showed sustained protein release while the P-ECM group showed gradual decreasing release. Degradation was higher in P-ECM + HA which had a significantly larger fiber diameter, while P-ECM had a larger pore area percentage. ELISA confirmed the retention and release of growth factors where P-ECM hydrogel had higher BMP-2 release, while P-ECM + HA had higher release of TGF-β1, bFGF, and VEGF.

CONCLUSIONS

Both P-ECM and P-ECM + HA retained their bioactive properties demonstrating a potential role as functionalized scaffolds for regenerative endodontic procedures.

Comparative proteomic analysis of dental pulp from supernumerary and normal permanent teeth

OBJECTIVES

To obtain and compare the protein profiles of supernumerary and normal permanent dental pulp tissues.

MATERIALS AND METHODS

Dental pulp tissues were obtained from supernumerary and normal permanent teeth. Proteins were extracted and analyzed by liquid chromatography-tandem mass spectrometry (LC/MS-MS). Protein identification and quantification from MS data was performed with MaxQuant. Statistical analysis was conducted using Metaboanalyst to identify differentially expressed proteins (DEPs) (P-value < 0.05, fold-change > 2). Gene Ontology enrichment analyses were performed with gProfiler.

RESULTS

A total of 3,534 proteins were found in normal dental pulp tissue and 1,093 in supernumerary dental pulp tissue, with 174 DEPs between the two groups. This analysis revealed similar functional characteristics in terms of cellular component organization, cell differentiation, developmental process, and response to stimulus, alongside exclusive functions unique to normal permanent dental pulp tissues such as healing, vascular development and cell death. Upon examination of DEPs, these proteins were associated with the processes of wound healing and apoptosis.

CONCLUSIONS

This study provides a comprehensive understanding of the protein profile of dental pulp tissue, including the first such profiling of supernumerary permanent dental pulp. There are functional differences between the proteomic profiles of supernumerary and normal permanent dental pulp tissue, despite certain biological similarities between the two groups. Differences in protein expression were identified, and the identified DEPs were linked to the healing and apoptosis processes.

CLINICAL RELEVANCE

This discovery enhances our knowledge of supernumerary and normal permanent pulp tissue, and serves as a valuable reference for future studies on supernumerary teeth.

Evaluation of oxidative stress cycle in healthy and inflamed dental pulp tissue: a laboratory investigation

OBJECTIVES

The purpose of this study was to investigate the oxidative stress cycle consisting of reactive oxygen molecules (ROS), glutathione (GSH) and glutathione S-transferase (GST) in caries-related pulp inflammation.

METHODOLOGY

Fifty-four pulp tissue samples were collected from healthy donors with the diagnosis of reversible pulpitis, symptomatic irreversible pulpitis, and healthy pulp. Twelve pulp samples from each group were homogenized and total protein, ROS, GSH, and GST were measured by spectrophotometer. The remaining 6 samples from each group were prepared for paraffin block and used for the histopathologic and immunohistochemical evaluation of oxidative stress parameters and TUNEL labeling. Data were analyzed statistically.

RESULTS

The results revealed that total protein levels significantly decreased; however, ROS levels increased in both reversible and irreversible pulpitis compared to the healthy pulp (p < 0.01). Also, as inflammation increases, GST enzyme levels decrease while GSH levels increase significantly (p < 0.05). It was found that the number of TUNEL (+) cells was increased in irreversible pulpitis samples compared to healthy and reversible pulpitis groups (p < 0.05). GSTP1 and GSH immunoreactivity were also observed in irreversible pulpitis samples.

CONCLUSIONS

It has been revealed that caries-related inflammation alters the oxidative stress cycle in dental pulp tissue. The increase in GSH levels in the inflamed dental pulp due to the increase in ROS levels may improve the defensive ability of the dental pulp.

CLINICAL RELEVANCE

There is a relationship between oxidative stress and inflammation. Control of excessive oxidative stress in pulpitis can stimulate reparative and regenerative processes. The present findings may provide an overview of the management of oxidative stress in cases with pulpitis during regenerative treatments.

Teeth with acute apical abscess vs. teeth with chronic apical periodontitis: a quantitative and qualitative proteomic analysis

OBJECTIVE

To quantitatively and qualitatively analyze the proteomic profile of teeth with acute apical abscesses (AAA) compared with teeth with chronic apical periodontitis (CAP) and to correlate the expression of detected human proteins with their main biological functions.

MATERIALS AND METHODS

Samples were obtained from root canals of 9 patients diagnosed with AAA and 9 with CAP. Samples were analyzed by reversed-phase liquid chromatography coupled to mass spectrometry. Label-free quantitative proteomic analysis was performed by Protein Lynx Global Service software. Differences in protein expression were calculated using the t-test (p < 0.05).

RESULTS

In total, 246 human proteins were identified from all samples. Proteins exclusively found in the AAA group were mainly associated with the immunoinflammatory response and oxidative stress response. In the quantitative analysis, 17 proteins were upregulated (p < 0.05) in the AAA group, including alpha-1-acid glycoprotein, hemopexin, fibrinogen gamma chain, and immunoglobulin. Additionally, 61 proteins were downregulated (p < 0.05), comprising cathepsin G, moesin, gelsolin, and transketolase. Most of the proteins were from the extracellular matrix, cytoplasm, and nucleus.

CONCLUSIONS

The common proteins between the groups were mainly associated with the immune response at both expression levels. Upregulated proteins mostly belonged to the acute-phase proteins, while the downregulated proteins were associated with DNA/RNA regulation and repair, and structural function.

CLINICAL RELEVANCE

The host response is directly related to the development of apical abscesses. Thus, understanding the behavior of human proteins against the endodontic pathogens involved in this condition might contribute to the study of new approaches related to the treatment of this disease.

Proteomic analysis of infected root canals with apical periodontitis in patients with type 2 diabetes mellitus: A cross-sectional study

AIM

This study aimed to quantitatively and qualitatively determine the proteomic profile of apical periodontitis (AP) in type 2 diabetes mellitus (T2DM) patients in comparison with systemically noncompromised patients and to correlate the protein expression of both groups with their biological functions.

METHODOLOGY

The sample consisted of 18 patients with asymptomatic AP divided into two groups according to the presence of T2DM: diabetic group-patients with T2DM (n = 9) and control group-systemically healthy patients (n = 9). After sample collection, the root canal samples were prepared for proteomic analysis using reverse-phase liquid chromatography-mass spectrometry. Label-free quantitative proteomic analysis was performed by Protein Lynx Global Service software. Differences in protein expression between groups were calculated using t-test (p < .05). Biological functions were analysed using the Homo sapiens UniProt database.

RESULTS

A total of 727 human proteins were identified in all samples. Among them, 124 proteins common to both groups were quantified, out of which 65 proteins from the diabetic group showed significant differences compared with the control: 43 upregulated (p < .05) and 22 downregulated (p < .05) proteins. No significant differences in protein expression were seen for the remaining 59 proteins (p > .05). Most proteins with differences in expression were related to immune/inflammatory response. Neutrophil gelatinase-associated lipocalin, Plastin-2, Lactotransferrin and 13 isoforms of immunoglobulins were upregulated. In contrast, Protein S100-A8, Protein S100-A9, Histone H2B, Neutrophil defensin 1, Neutrophil defensin 3 and Prolactin-inducible protein were downregulated.

CONCLUSIONS

Quantitative differences were demonstrated in the expression of proteins common to diabetic and control groups, mainly related to immune response, oxidative stress, apoptosis and proteolysis. These findings revealed biological pathways that provide the basis to support clinical findings on the relationship between AP and T2DM.

Application of Proteomics in Apical Periodontitis

Apical periodontitis is an inflammatory reaction of the periradicular tissues as a consequence of multispecies microbial communities organized as biofilms within the root canal system. Periradicular tissue changes at the molecular level initiate and orchestrate the inflammatory process and precede the presentation of clinical symptoms. Inflammatory mediators have been studied at either the proteomic, metabolomic, or transcriptomic levels. Analysis at the protein level is the most common approach used to identify and quantify analytes from diseased periradicular tissues during root canal treatment, since it is more representative of definitive and active periradicular inflammatory mediator than its transcript expression level. In disease, proteins expressed in an altered manner could be utilized as biomarkers. Biomarker proteins in periradicular tissues have been qualitatively and quantitatively assessed using antibodies (immunoassays and immunostaining) or mass spectrometry-based approaches. Herein, we aim to provide a comprehensive understanding of biomarker proteins identified in clinical studies investigating periradicular lesions and pulp tissue associated with apical periodontitis using proteomics. The high throughput mass spectrometry-based proteomics has the potential to improve the current methods of monitoring inflammation while distinguishing between progressive, stable, and healing lesions for the identification of new diagnostic and therapeutic targets. This method would provide more objective tools to (a) discover biomarkers related to biological processes for better clinical case selection, and (b) determine tissue response to novel therapeutic interventions for more predictable outcomes in endodontic treatment.