Comparative proteomic analysis on acquired enamel pellicle at two time points in caries-susceptible and caries-free subjects

Mass spectrometry-based proteomic approaches for salivary protein biomarkers discovery and dental caries diagnosis: A critical review

Dental caries is a multifactorial chronic disease resulting from the intricate interplay among acid-generating bacteria, fermentable carbohydrates, and several host factors such as saliva. Saliva comprises several proteins which could be utilized as biomarkers for caries prevention, diagnosis, and prognosis. Mass spectrometry-based salivary proteomics approaches, owing to their sensitivity, provide the opportunity to investigate and unveil crucial cariogenic pathogen activity and host indicators and may demonstrate clinically relevant biomarkers to improve caries diagnosis and management. The present review outlines the published literature of human clinical proteomics investigations on caries and extensively elucidates frequently reported salivary proteins as biomarkers. This review also discusses important aspects while designing an experimental proteomics workflow. The protein-protein interactions and the clinical relevance of salivary proteins as biomarkers for caries, together with uninvestigated domains of the discipline are also discussed critically.

Proteomic analysis of meropenem-induced outer membrane vesicles released by carbapenem-resistant Klebsiella pneumoniae

Carbapenem-resistant Klebsiella pneumoniae (CRKP) is an important multidrug resistance (MDR) pathogen that threatens human health and is the main source of hospital-acquired infection. Outer membrane vesicles (OMVs) are extracellular vesicles derived from Gram-negative bacteria and contain materials involved in bacterial survival and pathogenesis. They also contribute to cellular communication to nearby or distant recipient cells and influence their functions and phenotypes. In this study, we sought to understand the mechanism of bacterial response to meropenem pressure and explore the relationship between pathogenic proteins and the high pathogenicity of bacteria. We performed whole-genome PacBio sequencing on a clinical CRKP strain, and its OMVs were characterized using nanoparticle tracking analysis, transmission electron microscopy, and proteomic analysis. Thousands of vesicle proteins have been identified in mass spectrometry-based high-throughput proteomics analyses of K. pneumoniae OMVs. Protein functionality analysis showed that the OMVs were predominantly involved in metabolic, intracellular compartments, nucleic acid binding, survival, defense, and antibiotic resistance, such as Chromosome partition protein MukB, 3-methyl-2-oxobutanoate hydroxymethyltransferase, methionine-tRNA ligase, Heat shock protein 60 family chaperone GroEL, and Gamma-glutamyl phosphate reductase. Additionally, a protein-protein interaction network demonstrated that OMVs from meropenem-treated K. pneumoniae showed the highest connectivity in DNA polymerase I, phenylalanine-tRNA ligase beta subunit, DNA-directed RNA polymerase subunit beta, methionine-tRNA ligase, DNA-directed RNA polymerase subunit beta, and DNA-directed RNA polymerase subunit alpha. The OMVs proteome expression profile indicates increased secretion of stress proteins released from meropenem-treated K. pneumoniae, which provides clues for revealing the biogenesis and pathophysiological functions of Gram-negative bacteria OMVs. The significant differentially expressed proteins identified in this study are of great significance for exploring effective control strategies for CRKP infection.IMPORTANCEMeropenem is one of the main antibiotics used in the clinical treatment of carbapenem-resistant Klebsiella pneumoniae (CRKP). This study demonstrated that some important metabolic changes occurred in meropenem-induced CRKP-outer membrane vesicles (OMVs), The OMVs proteome expression profile indicates increased secretion of stress proteins released from meropenem-induced Klebsiella pneumoniae. Furthermore, this is the first study to discuss the protein-protein interaction network of the OMVs released by CRKP, especially under antibiotic stress.

Application of omics technologies in cariology research: A critical review with bibliometric analysis

OBJECTIVES

To review the application of omics technologies in the field of cariology research and provide critical insights into the emerging opportunities and challenges.

DATA & SOURCES

Publications on the application of omics technologies in cariology research up to December 2022 were sourced from online databases, including PubMed, Web of Science and Scopus. Two independent reviewers assessed the relevance of the publications to the objective of this review.

STUDY SELECTION

Studies that employed omics technologies to investigate dental caries were selected from the initial pool of identified publications. A total of 922 publications with one or more omics technologies adopted were included for comprehensive bibliographic analysis. (Meta)genomics (676/922, 73 %) is the predominant omics technology applied for cariology research in the included studies. Other applied omics technologies are metabolomics (108/922, 12 %), proteomics (105/922, 11 %), and transcriptomics (76/922, 8 %).

CONCLUSION

This study identified an emerging trend in the application of multiple omics technologies in cariology research. Omics technologies possess significant potential in developing strategies for the detection, staging evaluation, risk assessment, prevention, and management of dental caries. Despite the numerous challenges that lie ahead, the integration of multi-omics data obtained from individual biological samples, in conjunction with artificial intelligence technology, may offer potential avenues for further exploration in caries research.

CLINICAL SIGNIFICANCE

This review presented a comprehensive overview of the application of omics technologies in cariology research and discussed the advantages and challenges of using these methods to detect, assess, predict, prevent, and treat dental caries. It contributes to steering research for improved understanding of dental caries and advancing clinical translation of cariology research outcomes.

Salivary Pellicle Formed on Dental Composites Evaluated by Mass Spectrometry-An In Situ Study

(1) Background: In the oral environment, sound enamel and dental restorative materials are immediately covered by a pellicle layer, which enables bacteria to attach. For the development of new materials with repellent surface functions, information on the formation and maturation of salivary pellicles is crucial. Therefore, the present in situ study aimed to investigate the proteomic profile of salivary pellicles formed on different dental composites. (2) Methods: Light-cured composite and bovine enamel samples (controls) were exposed to the oral cavity for 30, 90, and 120 min. All samples were subjected to optical and mechanical profilometry, as well as SEM surface evaluation. Acquired pellicles and unstimulated whole saliva samples were analyzed by SELDI-TOF-MS. The significance was determined by the generalized estimation equation and the post-hoc bonferroni adjustment. (3) Results: SEM revealed the formation of homogeneous pellicles on all test and control surfaces. Profilometry showed that composite surfaces tend to be of higher roughness compared to enamel. SELDI-TOF-MS detected up to 102 different proteins in the saliva samples and up to 46 proteins in the pellicle. Significant differences among 14 pellicle proteins were found between the composite materials and the controls. (4) Conclusions: Pellicle formation was material- and time-dependent. Proteins differed among the composites and to the control.

Proteomic profile of the acquired enamel pellicle of children with early childhood caries and caries-free children

Acquired enamel pellicle plays an important role in the pathogenesis of early childhood caries (ECC), working as a protective interface between the tooth and the oral cavity. The aim of this cross-sectional in vivo proteomic study was to compare the acquired enamel pellicle protein profile of 3-5-year-old children with ECC (n = 10) and caries-free children (n = 10). Acquired enamel pellicle samples were collected and processed for proteomic analysis (nLC-ESI-MS/MS). In total, 241 proteins were identified. Basic salivary proline-rich protein 1 and 2, Cystatin-B, and SA were found only in the caries free group. When comparing caries free and ECC groups, lower protein levels were found in the caries free group for hemoglobin subunit beta, delta, epsilon, gamma-2, globin domain-containing protein and gamma-1, neutrophil defensin 3, serum albumin, protein S100-A8, and S100-A9. The proteins histatin-1, statherin, salivary acidic proline-rich phosphoprotein ½, proline-rich protein 4, submaxillary gland androgen-regulated protein 3B, alpha-amylase 1 and 2B were found at higher levels in the caries free group. The exclusive and the proteins found at higher levels in the caries free group might have protective functions that play a role in the prevention of caries, besides providing important insights to be evaluated in future studies for the possible development of new therapeutic strategies for ECC.

Caries Management-The Role of Surface Interactions in De- and Remineralization-Processes

BACKGROUND

Bioadhesion and surface interactions on enamel are of essential relevance for initiation, progression and prevention of caries and erosions. Salivary proteins on and within initial carious and erosive lesions can facilitate or aggravate de- and remineralization. This applies for the pellicle layer, the subsurface pellicle and for proteins within initial carious lesions. Little is known about these proteinaceous structures related to initial caries and erosion. Accordingly, there is a considerable demand for an understanding of the underlying processes occurring at the interface between the tooth surface and the oral cavity in order to develop novel agents that limit and modulate caries and erosion. Objectives and findings: The present paper depicts the current knowledge of the processes occurring at the interface of the tooth surface and the oral fluids. Proteinaceous layers on dental hard tissues can prevent or aggravate demineralization processes, whereas proteins within initial erosive or carious lesions might hinder remineralization considerably and restrict the entry of ions into lesions.

CONCLUSIONS

Despite the fact that organic-inorganic surface interactions are of essential relevance for de- and remineralization processes at the tooth surface, there is limited knowledge on these clinically relevant phenomena. Accordingly, intensive research is necessary to develop new approaches in preventive dentistry.

TMT proteomic analysis for molecular mechanism of Staphylococcus aureus in response to freezing stress

The foodborne pathogen Staphylococcus aureus continues to challenge the food industry due to the pathogenicity and tolerance of the bacterium. As a common storage condition for frozen food during transportation, distribution, and storage, freezing does not seem to be entirely safe due to the cold tolerance of S. aureus. In addition, our study indicated that the biofilm formation ability of S. aureus was significantly increased in response to freezing stress. To explore the molecular mechanism regulating the response to freezing stress, the proteomics signature of S. aureus after freezing stress based on tandem mass tag (TMT) labeling and liquid chromatography tandem mass spectrometry (LC-MS/MS) was analyzed. Gene Ontology and pathway analysis revealed that ribosome function, metabolism, RNA repair, and stress response proteins were differentially regulated (P < 0.05). Furthermore, transpeptidase sortase A, biofilm operon icaADBC HTH-type negative transcriptional regulator IcaR, and HTH-type transcriptional regulator MgrA were involved in the modulation of increased biofilm formation in response to freezing stress (P < 0.05). Moreover, significant lysine acetylation and malonylation signals in the S. aureus response to freezing stress were observed. Collectively, the current work provides additional insight for comprehending the molecular mechanism of S. aureus in response to freezing stress and presents potential targets for developing strategies to control S. aureus. KEY POINTS: • TMT proteomic analysis was first used on S. aureus in response to freezing stress. • Ribosome-, metabolism-, and biofilm-related proteins change after freezing stress. • Increased biofilm formation in S. aureus responded to freezing stress.

Mucins 5b and 7 and secretory IgA in the oral acquired pellicle of children with caries and caries-free children

OBJECTIVE

The objective of this study was to determine whether differences in the abundance of mucins 5b and 7 as well as secretory IgA exist in the oral acquired pellicle between children with active caries and caries-free children.

DESIGN

Pellicle formation was performed for 10 min in-situ on ceramic slabs in the oral cavity of children (5-7 years of age) with caries (n = 15) and without signs of caries (n = 13). Furthermore, unstimulated saliva was collected. Concentrations of Muc5b, Muc7 and sIgA were measured in desorbed pellicle eluates and in saliva.

RESULTS

Significantly larger concentrations of Muc5b, Muc7 and sIgA were detected in the pellicle obtained from children with caries compared to caries-free children. However, in the salivary samples concentrations of mucins Muc5b and Muc7 as well as sIgA did not differ significantly between the two groups.

CONCLUSIONS

All three pellicle components Muc5b, Muc7 as well as sIgA could be identified as potential biomarkers for early childhood caries with high sensitivity and specificity. This could contribute to a better understanding of the different caries susceptibility in children.

Analysis of salivary proteomic biomarkers for the surveillance of changes in high-risk status of early childhood caries

Background

Early childhood caries is an urgent public health concern. The aim of this study was to investigate salivary proteomic biomarkers for the surveillance of changes in the high-risk status of early childhood caries. The process involves the screening of specific salivary peptides that were differentially expressed only under dynamic changes in individual caries status.

Methods

Stimulated whole saliva samples were collected from 28 kindergarten children aged 3–4 years in Beijing at baseline and 3 months and 6 months after baseline. A total of 68 samples were collected. In terms of their caries status and progress during the observation period, participants were divided into 3 groups; 7 in the non-caries recurrence group, 6 in the caries recurrence group, and 15 in the healthy control group. Salivary peptides that exhibited no significant differences in cross-sectional comparisons between different groups of caries status but only expressed differentially along with dynamic changes of individual caries were screened using the technique of magnetic beads combined with matrix-assisted laser desorption-ionization time-of-flight mass spectrometry (MALDI-TOF MS). The technique of liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS/MS) was employed to identify the proteins from which these peptides were derived.

Results

We found two salivary peptides differentially expressed only under dynamic changes in individual caries status in the above comparisons; mass-to-charge ratio (m/z) values of the two peptides were 1045.9 and 2517.6, respectively (P < 0.05). Principal component analysis (PCA) and the decision tree model based on these two peptides showed an acceptable distinguishing ability for changes in the high-risk status of early childhood caries. The source proteins of the two peptides with m/z values of 1045.9 and 2517.6 were identified as submandibular gland androgen regulatory protein 3B (SMR-3B) and mucin-7, respectively.

Conclusions

Two proteins in children’s saliva, namely SMR-3B and mucin-7, have the potentiality to serve as candidate biomarkers for dynamic surveillance of changes in high-risk status of early childhood caries.

Effect of resveratrol on the biofilm formation and physiological properties of avian pathogenic Escherichia coli

Avian pathogenic Escherichia coli (APEC) is widely distributed, causing great economic losses to the poultry industry. The formation of APEC biofilms causes chronic, persistent, and repeated infections in the clinic, making treatment difficult. Resveratrol is a natural product, which has good health benefits including antimicrobial, anti-inflammatory, and cardiovascular activities. Resveratrol shows efficient inhibition of bacterial biofilm formation. However, a comprehensive understanding of the proteomic properties of APEC treated resveratrol is still lacking. In this study, APEC cells treated by resveratrol were investigated using a label-free differential proteomic method. Several proteins, including those related to a two-component system and chemotaxis, were found to be implicated in APEC biofilm formation. In addition, the physiological properties were significantly changed in terms of purine, pyruvate, and glyoxylate and dicarboxylate metabolism in APEC. Data are available via ProteomeXchange with the identifier PXD025706. We speculated that pyruvate dehydrogenase might be a potential target to inhibit Escherichia coli biofilm formation. Overall, our results indicated that resveratrol inhibits APEC biofilm formation by regulating the levels of proteins in two-component systems, especially chemotaxis proteins. The results showed that resveratrol had a potential application in inhibiting the biofilm formation of APEC. SIGNIFICANCE: This study elucidated the mechanism of resveratrol inhibiting biofilm formation of avian pathogenic Escherichia coli (APEC) based on a label-free differential proteomics. It was indicated that resveratrol inhibits APEC biofilm formation by regulating the levels of proteins in two component systems, especially chemotaxis proteins. Meanwhile, we speculated that pyruvate dehydrogenase might be a potential target to inhibit Escherichia coli biofilm formation. It shows that resveratrol has a potential application prospect in inhibiting the biofilm formation of APEC.

Functional biomedical materials derived from proteins in the acquired salivary pellicle

In the oral environment, the acquired salivary pellicle (ASP) on the tooth surface comprises proteins, glycoproteins, carbohydrates, and lipids. The ASP can specifically and rapidly adsorb on the enamel surface to provide effective lubrication, protection, hydration, and remineralisation, as well as be recognised by various bacteria to form a microbial biofilm (plaque). The involved proteins, particularly various phosphoproteins such as statherins, histatins, and proline-rich proteins, are vital to their specific functions. This review first describes the relationship between the biological functions of these proteins and their structures. Subsequently, recent advances in functional biomedical materials derived from these proteins are reviewed in terms of dental/bone therapeutic materials, antibacterial materials, tissue engineering materials, and coatings for medical devices. Finally, perspectives and challenges regarding the rational design and biomedical applications of ASP-derived materials are discussed.

Novel lactotransferrin-derived synthetic peptides suppress cariogenic bacteria in vitro and arrest dental caries in vivo: [Novel lactotransferrin-derived anticaries peptides]

Objectives: The aim of the study was to design and synthesise novel lactotransferrin-derived antimicrobial peptides (AMPs) with enhanced antibacterial activity against cariogenic bacteria. Methods: We obtained the LF-1 (WKLLRKAWKLLRKA) and LF-2 (GKLIWKLLRKAWKLLRKA) AMPs, based on the N-terminal functional sequence of lactotransferrin, and characterised their physicochemical properties and secondary structure. Their antibacterial activity against caries-associated bacteria was evaluated using bacterial susceptibility and time-killing assays, as well as transmission electron microscopy (TEM). The antibiofilm activity against Streptococcus mutans biofilms was determined using biofilm susceptibility assays and confocal laser scanning microscopy (CLSM). A rodent model of dental caries was adopted to evaluate their anticaries effectiveness in vivo. Results: Both peptides possessed an α-helical structure with excellent amphipathicity. LF-1 was effective against S. mutans and Actinomyces species, whereas LF-2 showed more potent antibacterial activity than LF-1 against a broader spectrum of tested strains. Both peptides inhibited the formation of S. mutans biofilm starting at 8 μmol/L and exerted effective eradication of S. mutans in preformed biofilms. Both peptides exhibited satisfactory biocompatibility and exerted significant anticaries effects in a rodent model. Conclusion s: Both lactotransferrin-derived peptides displayed strong antimicrobial activity against cariogenic bacteria and S. mutans biofilm in vitro and effectively inhibited dental caries in vivo.

The salivary pellicle on dental biomaterials

The salivary pellicle, an adlayer formed by adsorption of salivary components on teeth and dental biomaterials, has direct consequences on basic outcomes of dentistry. Here, we provide an overview of salivary pellicle formation processes with a critical focus on dental biomaterials. We describe and critique the array of salivary pellicle measurement techniques. We also discuss factors that may affect salivary pellicle formation and the heterogeneity of the published literature describing salivary pellicle formation on dental biomaterials. Finally, we survey the many effects salivary pellicles have on dental biomaterials and highlight its implications on design criteria for dental biomaterials. Future investigations may lead to rationally designed dental biomaterials to control the salivary pellicle and enhance material function and patient outcomes.