Dentistry proteomics: From laboratory development to clinical practice

Evaluation of method parameters for sound undecalcified dental enamel proteomics using liquid chromatography-mass spectrometry

OBJECTIVE

This study aims to validate a methodology for analyzing undecalcified, sound dental enamel proteomics using Liquid Chromatography-Mass Spectrometry (LC-MS). The study evaluates various parameters, including the impact of dental root coverage on protein contamination, the efficacy of protease inhibitors during enamel sample preparation, repeatability of LC-MS measurements on dental enamel, and statistical analysis. The study also assesses the effectiveness of combined trypsin and semi-trypsin searches in Mascot for obtaining additional protein identification data.

DESIGN

Sound dental enamel was removed using a wet grinding technique, then digested with trypsin and labeled with TMT prior to LC-MS analysis. The resulting proteomes were matched against the Homo sapiens Swissprot Database, with searches in Mascot performed using both trypsin and semitrypsin. Statistical methods were employed to analyze the data.

RESULTS

The study found that covering dental roots with composite during dental enamel microdissection is advisable, while using protease inhibition during microdissection may not be fully supported. The proteomic analyses demonstrated statistical repeatability and reliability, with consistent and reproducible proteomic data obtained from healthy dental enamel. Furthermore, employing both trypsin and semitrypsin searches in Mascot provided additional proteomic information.

CONCLUSIONS

Overall, this study validates a methodology for analyzing undecalcified, sound dental enamel proteomics using LC-MS, and provides insights into various factors that can affect the quality and reliability of proteomic data. These findings have implications for future studies pursuant to understanding the proteomic mechanisms underlying dental enamel formation and other associated processes.

Genomic Medicine in Canine Periodontal Disease: A Systematic Review

Genomic medicine has become a growing reality; however, it is still taking its first steps in veterinary medicine. Through this approach, it will be possible to trace the genetic profile of a given individual and thus know their susceptibility to certain diseases, namely periodontal disease. This condition is one of the most frequently diagnosed in companion animal clinics, especially in dogs. Due to the limited existing information and the lack of comprehensive studies, the objective of the present study was to systematically review the existing scientific literature regarding genomic medicine in canine periodontal disease and determine which genes have already been studied and their probable potential. This study followed the recommendations of the PRISMA 2020 methodology. Canine periodontal disease allied to genomic medicine were the subjects of this systematic review. Only six articles met all of the inclusion criteria, and these were analyzed in detail. These studies described genetic variations in the following genes: interleukin-6, interleukin-10, interleukin-1, lactotransferrin, toll-like receptor 9, and receptor activator of nuclear factor-kappa B. Only in two of them, namely interleukin-1 and toll-like receptor 9 genes, may the identified genetic variations explain the susceptibility that certain individuals have to the development of periodontal disease. It is necessary to expand the studies on the existing polymorphic variations in genes and their relationship with the development of periodontal disease. Only then will it be possible to fully understand the biological mechanisms that are involved in this disease and that determine the susceptibility to its development.

Quantitative proteomic analysis in symptomatic and asymptomatic apical periodontitis

AIM

To quantitatively and qualitatively compare the host proteomic profile in samples of symptomatic and asymptomatic apical periodontitis (AP) using nano-liquid chromatography-electron spray tandem mass spectrometry.

METHODOLOGY

Samples were obtained from 18 patients with radiographically evident AP, divided into symptomatic and asymptomatic groups (nine per group) according to clinical characteristics. After sample collection, protein extraction, purification and quantification of the samples were performed, which were analysed by reverse-phase liquid chromatography coupled to mass spectrometry. Label-free quantitative proteomic analysis was performed by Protein Lynx Global Service software. Differences in expression of proteins between the groups were calculated using the Monte Carlo algorithm, considering P < 0.05 for down-regulated proteins and 1 - P > 0.95 for up-regulated proteins. Proteins were identified with the embedded ion accounting algorithm in the software and a search of the Homo sapiens UniProt database.

RESULTS

A total of 853 individual human proteins were identified. In the quantitative analysis, common proteins to both groups accounted for 143 proteins. Differences in expression between groups resulted in 51 up-regulated proteins (1 - P > 0.95) in the symptomatic group, including alpha-1-antitrypsin, protein S100-A8, myeloperoxidase, peroxiredoxin and lactotransferrin. This group also had 43 down-regulated proteins (P < 0.05), comprising immunoglobulin, neutrophil defensin, pyruvate kinase and alpha-enolase. The qualitative analysis considered only the exclusive proteins of each group. For the symptomatic group, 318 complete proteins and 29 fragments were identified, such as dedicator of cytokinesis protein, intersectin, prostaglandin, phospholipase DDHD2 and superoxide dismutase. For the asymptomatic group, 326 complete proteins and 37 fragments were identified, including azurocidin, C-reactive protein, collagen alpha, cathepsin, heat shock and laminin.

CONCLUSIONS

Quantitative differences in the expression of common proteins in cases of symptomatic and asymptomatic AP were found, which were mostly related to host immune response in both groups. Exclusive proteins in the symptomatic group were mainly related to the host response to the presence of viruses in endodontic infections, oxidative stress and proteolytic enzymes. The results provide a basis for a better understanding of cellular and molecular pathways involved in AP, establishing specific proteomic profiles for symptomatic and asymptomatic conditions.

Characterization of Odontogenic Differentiation from Human Dental Pulp Stem Cells Using TMT-Based Proteomic Analysis

Background

The repair of dental pulp injury relies on the odontogenic differentiation of dental pulp stem cells (DPSCs). To better understand the odontogenic differentiation of DPSCs and identify proteins involved in this process, tandem mass tags (TMTs) coupled with liquid chromatography-tandem mass spectrometry (LC-MS/MS) were applied to compare the proteomic profiles of induced and control DPSCs.

Methods

The proteins expressed during osteogenic differentiation of human DPSCs were profiled using the TMT method combined with LC-MS/MS analysis. The identified proteins were subjected to Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses. Then, a protein-protein interaction (PPI) network was constructed. Two selected proteins were confirmed by western blotting (WB) analysis.

Results

A total of 223 proteins that were differentially expressed were identified. Among them, 152 proteins were significantly upregulated and 71 were downregulated in the odontogenic differentiation group compared with the control group. On the basis of biological processes in GO, the identified proteins were mainly involved in cellular processes, metabolic processes, and biological regulation, which are connected with the signaling pathways highlighted by KEGG pathway analysis. PPI networks showed that most of the differentially expressed proteins were implicated in physical or functional interaction. The protein expression levels of FBN1 and TGF-β2 validated by WB were consistent with the proteomic analysis.

Conclusions

This is the first proteomic analysis of human DPSC odontogenesis using a TMT method. We identified many new differentially expressed proteins that are potential targets for pulp-dentin complex regeneration and repair.

Proteomic analysis of human dental pulp in different clinical diagnosis

OBJECTIVES

The present study aimed to identify proteins obtained from pulp tissue and correlate with each clinical diagnosis (healthy pulp, inflamed pulp, and necrotic pulp).

MATERIALS AND METHODS

A total of forty-five molars were used. Three biological replicas were evaluated. Lysis and sonication were used for protein extraction. Protein quantification was assessed by using the Bradford technique, and shotgun proteome analysis was performed by nanoUPLC-MS^E using a Synapt G2 mass spectrometer. Mass spectra data were processed using the Waters PLGS software, and protein identification was done using the human Uniprot database appended to the PLGS search engine.

RESULTS

A total of 123 different proteins were identified in all evaluated pulp conditions. Among these, 66 proteins were observed for healthy pulp, 66 for inflamed pulp, and 91 for necrotic pulp. Most protein identification was related to immune response, multi-organism process, platelet activation, and stress in inflamed pulp samples compared to healthy pulp. Proteins related to cellular component organization or biogenesis, developmental process, growth, immune response, multi-organism process, response to stimulus, signaling, stress, and transport were identified in cases of apical periodontitis compared to inflamed pulp.

CONCLUSIONS

The progression of the disease to inflamed pulp promoted a high abundance of proteins related to the immune system and stress. Comparing the necrotic pulp with inflamed pulp conditions, a high abundance of proteins was noticed related to metabolism, transport, and response between organisms.

CLINICAL RELEVANCE

This finding may assist in future studies of new markers, understanding of tissue engineering, and development of future products.

Advances of Proteomic Sciences in Dentistry

Applications of proteomics tools revolutionized various biomedical disciplines such as genetics, molecular biology, medicine, and dentistry. The aim of this review is to highlight the major milestones in proteomics in dentistry during the last fifteen years. Human oral cavity contains hard and soft tissues and various biofluids including saliva and crevicular fluid. Proteomics has brought revolution in dentistry by helping in the early diagnosis of various diseases identified by the detection of numerous biomarkers present in the oral fluids. This paper covers the role of proteomics tools for the analysis of oral tissues. In addition, dental materials proteomics and their future directions are discussed.

Cytoskeletal binding proteins distinguish cultured dental follicle cells and periodontal ligament cells

Human dental follicle cells (DFCs) and periodontal ligament cells (PDLCs) derived from the ectomesenchymal tissue, have been shown to exhibit stem/progenitor cell properties and the ability to induce tissue regeneration. Stem cells in dental follicle differentiate into cementoblasts, periodontal ligament fibroblasts and osteoblasts, these cells form cementum, periodontal ligament and alveolar bone, respectively. While stem cells in dental follicle are a precursor to periodontal ligament fibroblasts, the molecular changes that distinguish cultured DFCs from PDLCs are still unknown. In this study, we have compared the immunophenotypic features and cell cycle status of the two cell lines. The results suggest that DFCs and PDLCs displayed similar features related to immunophenotype and cell cycle. Then we employed an isobaric tag for relative and absolute quantitation (iTRAQ) proteomics strategy to reveal the molecular differences between the two cell types. A total of 2138 proteins were identified and 39 of these proteins were consistently differentially expressed between DFCs and PDLCs. Gene ontology analyses revealed that the protein subsets expressed higher in PDLCs were related to actin binding, cytoskeletal protein binding, and structural constituent of muscle. Upon validation by real-time PCR, western blotting, and immunofluorescence staining. Tropomyosin 1 (TPM1) and caldesmon 1 (CALD1) were expressed higher in PDLCs than in DFCs. Our results suggested that PDLCs display enhanced actin cytoskeletal dynamics relative to DFCs while DFCs may exhibit a more robust antioxidant defense ability relative to PDLCs. This study expands our knowledge of the cultured DFCs and PDLCs proteome and provides new insights into possible mechanisms responsible for the different biological features observed in each cell type.

Role of proteomics in physiologic and pathologic conditions of dentistry: Overview

Proteomics is the study of structure and function of proteins in a large scale. For any living organism, preteins are considered to be the vital part because of its role in metabolic pathways of cells. These proteins not only play a role in physiological condition of the cell but also in altered manner during pathologic conditions. These altered proteins in diseased conditions are called as biomarkers. Several such biomarkers were identified in oral diseaes. This review is a brief note on proteins involved in odontogenesis and list of altered proteins proteins identified in various dental and oral diseases. The knowledge about the role of proteomics in dentistry and the importance of proteomic studies in early diagnosis and prognostic part of oral diseases helps in appliction of precised and sucessful treatment.

Proteomics of Human Teeth and Saliva

Teeth have been a focus of interest for many centuries – due to medical problems with them. They are the hardest part of the human body and are composed of three mineralized parts – enamel, dentin and cementum, together with the soft pulp. However, saliva also has a significant impact on tooth quality. Proteomic research of human teeth is now accelerating, and it includes all parts of the tooth. Some methodological problems still need to be overcome in this research field – mainly connected with calcified tissues. This review will provide an overview of the current state of research with focus on the individual parts of the tooth and pellicle layer as well as saliva. These proteomic results can help not only stomatology in terms of early diagnosis, identifying risk factors, and systematic control.