Comparative proteomic profiling of human dental pulp stem cells and periodontal ligament stem cells under in vitro osteogenic induction

Salivary protein homology between humans and dogs: Mass spectrometry-based proteomics analysis

OBJECTIVE

This benchmark study aimed to investigate sex-related differences based on the identification and characterization of the salivary proteome of healthy male and female dogs using mass spectrometry (MS) technique and a homology-driven approach to analyze salivary proteins in both human and dog species utilizing protein sequence alignment technique.

METHODS

Unstimulated whole saliva was collected from 10 healthy Beagles. After processing the samples and determining the total protein content, in-solution protein digestion was performed involving denaturation, reduction of disulfide bonds, alkylation, and removal of interfering compounds. Samples were analyzed using LC-ESI-MS/MS.

RESULTS

LC-ESI-MS/MS analysis identified 327 and 341 unique proteins in male and female dog saliva, respectively, of which 318 (97.25 %) in male dogs and 326 (95.60 %) in female dogs were characterized. Abundant shared proteins included albumin, BPI fold-containing family A member 2, and VWFD domain-containing protein. A notable uncharacterized protein, VWFD domain-containing protein, was among the most abundant in both sexes. Comparative analysis of 69 abundant shared proteins indicated an upregulation of CES5A, EFHD, GC, IGHM, LOC100653049, KRT10, LCP1, PGD, TPI1 in male dogs, while LOC100855593 was upregulated in female dogs. In total, 84 % (n = 229/274) and 86 % (n = 235/275) salivary proteins identified in male and female dogs, respectively, were homologous to human proteins, with an overall homology of 86 % (n = 364/423), including 15 with 100 % homology.

CONCLUSION

The study revealed clear differences in the salivary proteomics profile of healthy male and female dogs. However, most of the salivary proteins in both male and female dogs showed homology with human salivary proteins.

CLINICAL RELEVANCE

The identification of unique salivary proteome profiles in male and female dogs, coupled with substantial homology to human proteins, provides promising biomarkers for health assessment, highlighting its clinical significance for diagnostics and therapeutic exploration not only in veterinary and human dentistry, but across mammalian species.

Comparison of Periodontal Ligament Stem Cells with Mesenchymal Stem Cells from Other Sources: A Scoping Systematic Review of In vitro and In vivo Studies

OBJECTIVE

The application of stem cells in regenerative medicine depends on their biological properties. This scoping review aimed to compare the features of periodontal ligament stem cells (PDLSSCs) with stem cells derived from other sources.

DESIGN

An electronic search in PubMed/Medline, Embase, Scopus, Google Scholar and Science Direct was conducted to identify in vitro and in vivo studies limited to English language.

RESULTS

Overall, 65 articles were included. Most comparisons were made between bone marrow stem cells (BMSCs) and PDLSCs. BMSCs were found to have lower proliferation and higher osteogenesis potential in vitro and in vivo than PDLSCs; on the contrary, dental follicle stem cells and umbilical cord mesenchymal stem cells (UCMSCs) had a higher proliferative ability and lower osteogenesis than PDLSCs. Moreover, UCMSCs exhibited a higher apoptotic rate, hTERT expression, and relative telomerase length. The immunomodulatory function of adipose-derived stem cells and BMSCs was comparable to PDLSCs. Gingival mesenchymal stem cells showed less sensitivity to long-term culture. Both pure and mixed gingival cells had lower osteogenic ability compared to PDLSCs. Comparison of dental pulp stem cells (DPSCs) with PDLSCs regarding proliferation rate, osteo/adipogenesis, and immunomodulatory properties was contradictory; however, in vivo bone formation of DPSCs seemed to be lower than PDLSCs.

CONCLUSION

In light of the performed comparative studies, PDLSCs showed comparable results to stem cells derived from other sources; however, further in vivo studies are needed to determine the actual pros and cons of stem cells in comparison to each other.

Establishing protein expression profiles involved in tooth development using a proteomic approach

Various growth and transcription factors are involved in tooth development and developmental abnormalities; however, the protein dynamics do not always match the mRNA expression level. Using a proteomic approach, this study comprehensively analyzed protein expression in epithelial and mesenchymal tissues of the tooth germ during development. First molar tooth germs from embryonic day 14 and 16 Crlj:CD1 (ICR) mouse embryos were collected and separated into epithelial and mesenchymal tissues by laser microdissection. Mass spectrometry of the resulting proteins was carried out, and three types of highly expressed proteins [ATP synthase subunit beta (ATP5B), receptor of activated protein C kinase 1 (RACK1), and calreticulin (CALR)] were selected for immunohistochemical analysis. The expression profiles of these proteins were subsequently evaluated during all stages of amelogenesis using the continuously growing incisors of 3-week-old male ICR mice. Interestingly, these three proteins were specifically expressed depending on the stage of amelogenesis. RACK1 was highly expressed in dental epithelial and mesenchymal tissues during the proliferation and differentiation stages of odontogenesis, except for the pigmentation stage, whereas ATP5B and CALR immunoreactivity was weak in the enamel organ during the early stages, but became intense during the maturation and pigmentation stages, although the timing of the increased protein expression was different between the two. Overall, RACK1 plays an important role in maintaining the cell proliferation and differentiation in the apical end of incisors. In contrast, ATP5B and CALR are involved in the transport of minerals and the removal of organic materials as well as matrix deposition for CALR.

Integrative proteomics and phosphoproteomics profiling on osteogenic differentiation of periodontal ligament stem cell

This study aims to elucidate the phosphorylated profile of periodontal ligament stem cells (PDLSCs) osteogenic differentiation, which contributes to the promotion of periodontium regeneration. PDLSCs cultured in the osteogenic induction medium for 14 days were analyzed by proteomics and phosphoproteomics. Potential functions of phosphorylated differentially expressed proteins (DEPs) were annotated and enriched based on Gene Ontology (GO). Furtherly, overlapped DEPs were identified and conducted protein-protein interaction (PPI) network united with the top 20 up/downregulated phosphorylated DEPs. Hub phosphorylated DEPs were analyzed by Cytoscape, and the protein kinase phosphorylation network was predicted by iGPS. Proteomics identified 87 upregulated and 227 downregulated DEPs. Phosphoproteomics identified 460 upregulated and 393 downregulated phosphorylated DEPs, and they were primarily enriched in mitochondrial function and ion-channel related terms. Furthermore, 63 overlapped DEPs were recognized for more accurate predictions. Among the top 10 hub phosphorylated DEPs, only Integrin alpha-5 (ITGA5) expressed upregulated phosphorylation, and half of them belonged to extracellular matrix (ECM) proteins. In addition, numerous kinases corresponding to four interactive hub phosphorylated DEPs were predicted, including Collagen alpha-2(I) (COL1A2), Syndecan-1 (SDC1), Fibrillin-1 (FBN1), and ITGA5. Our findings established a basis for further elucidation of the phosphorylation of PDLSCs osteogenic differentiation, and COL1A2/SDC1/ITGA5/FBN1 phosphorylated network may dominate this process.

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.

Comparative Proteomic and Metabolomic Analysis of Human Osteoblasts, Differentiated from Dental Pulp Stem Cells, Hinted Crucial Signaling Pathways Promoting Osteogenesis

Population aging has been a global trend for the last decades, which increases the pressure to develop new cell-based or drug-based therapies, including those that may cure bone diseases. To understand molecular processes that underlie bone development and turnover, we followed osteogenic differentiation of human dental pulp stem cells (DPSCs) using a specific induction medium. The differentiation process imitating in vivo osteogenesis is triggered by various signaling pathways and is associated with massive proteome and metabolome changes. Proteome was profiled by ultrahigh-performance liquid chromatography and comprehensively quantified by ion mobility-enhanced mass spectrometry. From 2667 reproducibly quantified and identified proteins, 432 were differentially abundant by strict statistic criteria. Metabolome profiling was carried out by nuclear magnetic resonance. From 27 detected metabolites, 8 were differentially accumulated. KEGG and MetaboAnalyst hinted metabolic pathways that may be involved in the osteogenic process. Enrichment analysis of differentially abundant proteins highlighted PPAR, FoxO, JAK-STAT, IL-17 signaling pathways, biosynthesis of thyroid hormones and steroids, mineral absorption, and fatty acid metabolism as processes with prominent impact on osteoinduction. In parallel, metabolomic data showed that aminoacyl-tRNA biosynthesis, as well as specific amino acids, likely promote osteodifferentiation. Targeted immunoassays validated and complemented omic results. Our data underlined the complexity of the osteogenic mechanism. Finally, we proposed promising targets for future validation in patient samples, a step toward the treatment of bone defects.

Systems biology analysis of osteogenic differentiation behavior by canine mesenchymal stem cells derived from bone marrow and dental pulp

Utilization of canine mesenchymal stem cells (cMSCs) for regenerating incorrigible bone diseases has been introduced. However, cMSCs harvested from different sources showed distinct osteogenicity. To clarify this, comparative proteomics-based systems biology analysis was used to analyze osteogenic differentiation behavior by cMSCs harvested from bone marrow and dental pulp. The results illustrated that canine dental pulp stem cells (cDPSCs) contained superior osteogenicity comparing with canine bone marrow-derived MSCs (cBM-MSCs) regarding alkaline phosphatase activity, matrix mineralization, and osteogenic marker expression. Global analyses by proteomics platform showed distinct protein clustering and expression pattern upon an in vitro osteogenic induction between them. Database annotation using Reactome and DAVID revealed contrast and unique expression profile of osteogenesis-related proteins, particularly on signaling pathways, cellular components and processes, and cellular metabolisms. Functional assay and hierarchical clustering for tracking protein dynamic change confirmed that cBM-MSCs required the presences of Wnt, transforming growth factor (TGF)-beta, and bone-morphogenetic protein (BMP) signaling, while cDPSCs mainly relied on BMP signaling presentation during osteogenic differentiation in vitro. Therefore, these findings illustrated the comprehensive data regarding an in vitro osteogenic differentiation behavior by cBM-MSCs and cDPSCs which is crucial for further mechanism study and the establishment of cMSC-based bone tissue engineering (BTE) for veterinary practice.

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.

Proteomic profiling of various human dental stem cells - a systematic review

BACKGROUND

The proteomic signature or profile best describes the functional component of a cell during its routine metabolic and survival activities. Additional complexity in differentiation and maturation is observed in stem/progenitor cells. The role of functional proteins at the cellular level has long been attributed to anatomical niches, and stem cells do not deflect from this attribution. Human dental stem cells (hDSCs), on the whole, are a combination of mesenchymal and epithelial coordinates observed throughout craniofacial bones to pulp.

AIM

To specify the proteomic profile and compare each type of hDSC with other mesenchymal stem cells (MSCs) of various niches. Furthermore, we analyzed the characteristics of the microenvironment and preconditioning changes associated with the proteomic profile of hDSCs and their influence on committed lineage differentiation.

METHODS

Literature searches were performed in PubMed, EMBASE, Scopus, and Web of Science databases, from January 1990 to December 2018. An extra inquiry of the grey literature was completed on Google Scholar, ProQuest, and OpenGrey. Relevant MeSH terms (PubMed) and keywords related to dental stem cells were used independently and in combination.

RESULTS

The initial search resulted in 134 articles. Of the 134 full-texts assessed, 96 articles were excluded and 38 articles that met the eligibility criteria were reviewed. The overall assessment of hDSCs and other MSCs suggests that differences in the proteomic profile can be due to stem cellular complexity acquired from varied tissue sources during embryonic development. However, our comparison of the proteomic profile suffered inconsistencies due to the heterogeneity of various hDSCs. We believe that the existence of a heterogeneous population of stem cells at a given niche determines the modalities of regeneration or tissue repair. Added prominences to the differences present between various hDSCs have been reasoned out.

CONCLUSION

Systematic review on proteomic studies of various hDSCs are promising as an eye-opener for revisiting the proteomic profile and in-depth analysis to elucidate more refined mechanisms of hDSC functionalities.

Proteomic analysis of human periodontal ligament cells under hypoxia

BACKGROUND

The periodontal ligament is essential for homeostasis of periodontal tissue. A hypoxic milieu of the periodontal tissue is generated under periodontitis or during orthodontic treatment, which affects the periodontal and bone remodelling process. Here, we provide a comprehensive proteomic characterization of periodontal ligament cells under hypoxic conditions, aiming to reveal previously unappreciated biological changes and to help advance hypoxia-based therapeutic strategies for periodontal diseases.

METHODS

Human periodontal ligament cells (hPDLCs) were characterized using immunohistochemistry (IHC) and flow cytometry (FACS). Successful hypoxia treatment of hPDLCs with 1% O2 was confirmed by qRT-PCR. Proliferation was evaluated using an MTT assay. The proteomic expression profile under hypoxia was studied with the isobaric tags for relative and absolute quantification (iTRAQ) approach followed by protein identification and bioinformatic analysis, and western blot verification was performed.

RESULTS

The hPDLCs were positive for vimentin, CD73 and CD105 and negative for keratin, CD34 and CD45. After hypoxia treatment, the mRNA expression of hypoxia-inducible factor 1a (HIF1a) was upregulated. The proliferation rate was elevated during the first 6 h but decreased from 6 h to 72 h. A total of 220 differentially expressed proteins were quantified in hPDLCs under hypoxia (1% O2, 24 h), including 153 upregulated and 67 downregulated proteins, five of which were verified by western blot analysis. The Gene Ontology enriched terms included the energy metabolic process, membrane-bound organelle and vesicle, and protein binding terms. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis indicated several involved pathways, including glycolysis/gluconeogenesis, biosynthesis of amino acids, the HIF-1 signalling pathway, and focal adhesion. A protein-protein interaction (PPI) network demonstrated the dominant role of autophagy over apoptosis under hypoxia.

CONCLUSION

The proteomic profile of hPDLCs under hypoxia was mainly related to energy metabolism, autophagy, and responses to stimuli such as adhesion and inflammation. Previously unrecognized proteins including solute carrier family proteins, heat shock proteins, ubiquitination-related enzymes, collagen and S100 family proteins are involved in adaptive response to hypoxia in hPDLCs and are thus of great research interest in future work.

Stathmin regulates the proliferation and odontoblastic/osteogenic differentiation of human dental pulp stem cells through Wnt/β-catenin signaling pathway

Odontoblastic/osteogenic differentiation of human dental pulp stem cells (hDPSCs) is a key factor in tooth and pulp regeneration, but its mechanism still remains unknown. The purpose of this research is to look into the mechanism by which Stathmin affects the proliferation and odontoblastic/osteogenic differentiation of hDPSCs, and whether the Wnt/β- catenin is related to this regulation. First, the Stathmin expression was inhibited by lentiviral vector, after that the transcriptome sequencing technology was used to screen the differentially expressed genes, then we found Wnt5a which related to the regulation of Wnt/β-catenin was regulated. Comparing with hDPSC in the control group, the shRNA-Stathmin group inhibited proliferation and odontoblastic/osteogenic differentiation. The result of molecular analysis indicated that the Wnt/β-catenin was inhibited when Stathmin was silenced. After that, the shRNA-Stathmin group were added with LiCl (activator of Wnt/β-catenin), and the Wnt/β-catenin was significantly activated in β-catenin. After activation of the Wnt/β-catenin, the proliferation of hDPSCs was significantly increased and the expression of genes related to odontoblastic/osteogenic differentiation was also significantly increased. Taken together, these findings reveal for the first time that the Stathmin-Wnt/β-catenin plays a positive regulatory role in hDPSC proliferation and odontoblastic/osteogenic differentiation. SIGNIFICANCE: Transcriptome sequencing revealed that Stathmin interacts with Wnt/β-catenin signaling pathway-related proteins such as Wnt5a. At the same time, experiments have confirmed that Stathmin protein can affect the proliferation and odontogenetic differentiation of hDPSCs.The innovation of this paper is to link the Stathmin and Wnt/β-catenin signaling pathways for the first time, to explore the interaction of Stathmin and Wnt/β-catenin signaling pathways and the mechanism of this regulation on human dental pulp stem cells (hDPSCs) of odontoblastic/osteogenic differentiation and proliferation function. Especially for the regulation of odontoblastic/osteogenic differentiation, we have verified this mechanism at the molecular level and characterization leveland this regulation also provides new ideas for dental pulp tissue engineering. At the same time, more than 3000 proteins related to the change of Stathmin level were screened by transcriptome sequencing technology, which provided a possibility to further exploration of the regulation mechanism of Stathmin on various aspects of cell biological characteristics.