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Zhang JS, Huang S, Chen Z, Chu CH, Takahashi N, Yu OY. Application of omics technologies in cariology research: A critical review with bibliometric analysis. J Dent 2024; 141:104801. [PMID: 38097035 DOI: 10.1016/j.jdent.2023.104801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 12/06/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023] Open
Abstract
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.
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Affiliation(s)
| | - Shi Huang
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, PR China
| | - Zigui Chen
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, PR China; Department of Microbiology, Faculty of Medicine, The Chinese University of Hong Kong, Hong Kong SAR, PR China
| | - Chun-Hung Chu
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, PR China
| | - Nobuhiro Takahashi
- Division of Oral Ecology and Biochemistry, Tohoku University Graduate School of Dentistry, Sendai, Japan
| | - Ollie Yiru Yu
- Faculty of Dentistry, The University of Hong Kong, Hong Kong SAR, PR China.
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Alqahtani AA, Alhalabi F, Alam MK. Salivary elemental signature of dental caries: a systematic review and meta-analysis of ionomics studies. Odontology 2024; 112:27-50. [PMID: 37526792 DOI: 10.1007/s10266-023-00839-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2022] [Accepted: 07/14/2023] [Indexed: 08/02/2023]
Abstract
Trace- and macro-chemical elements are crucial for cellular physiological functioning, and their alterations in biological fluids might be associated with an underlying pathological state. Hence, this study aimed to examine and summarize the published literature concerning the application of salivary ionomics for caries diagnosis. An extensive search of studies was conducted using PubMed, EMBASE, Web of Science, and Scopus, without any language and year restriction for answering the following PECO question: "In subjects (i.e., children, adolescents, or adults) with good systematic health, are there any variations in the salivary concentrations of trace- or macro-elements between caries-free (CF) individuals and caries-active (CA) subjects?" A modified version of the QUADOMICS tool was used to assess the quality of the included studies. The Review Manager Version 5.4.1. was used for data analyses. The analysis of salivary chemical elements that significantly differed between CF and CA subjects was also performed. Thirty-four studies were included, involving 2299 CA and 1669 CF subjects, having an age range from 3 to 64 years in over 16 countries. The meta-analysis revealed a statistically significant difference (p < 0.05) in the salivary levels of calcium, phosphorus, chloride, magnesium, potassium, sodium, and zinc between CA and CF subjects, suggesting higher levels of calcium, phosphorus, potassium, and sodium in CF subjects while higher levels of chloride, magnesium, and zinc in CA patients. Half of the included studies (17/34) were considered high quality, while the remaining half were considered medium quality. Only zinc and chloride ions were found to be higher significantly and consistent in CF and CA subjects, respectively. Conflicting outcomes were observed for all other salivary chemical elements including aluminum, bromine, calcium, copper, fluoride, iron, potassium, magnesium, manganese, sodium, ammonia, nitrite, nitrate, phosphorus, lead, selenium, and sulfate ions.
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Affiliation(s)
- Abdullah Ali Alqahtani
- Department of Conservative Dental Sciences, College of Dentistry, Prince Sattam Bin Abdulaziz University, 11942, Alkharj, Saudi Arabia.
| | - Feras Alhalabi
- Department of Conservative Dental Sciences, College of Dentistry, Prince Sattam Bin Abdulaziz University, 11942, Alkharj, Saudi Arabia
| | - Mohammad Khursheed Alam
- Orthodontics, Department of Preventive Dental Science, College of Dentistry, Jouf University, Sakaka, Saudi Arabia
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Adeoye J, Su YX. Artificial intelligence in salivary biomarker discovery and validation for oral diseases. Oral Dis 2024; 30:23-37. [PMID: 37335832 DOI: 10.1111/odi.14641] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Revised: 05/19/2023] [Accepted: 05/28/2023] [Indexed: 06/21/2023]
Abstract
Salivary biomarkers can improve the efficacy, efficiency, and timeliness of oral and maxillofacial disease diagnosis and monitoring. Oral and maxillofacial conditions in which salivary biomarkers have been utilized for disease-related outcomes include periodontal diseases, dental caries, oral cancer, temporomandibular joint dysfunction, and salivary gland diseases. However, given the equivocal accuracy of salivary biomarkers during validation, incorporating contemporary analytical techniques for biomarker selection and operationalization from the abundant multi-omics data available may help improve biomarker performance. Artificial intelligence represents one such advanced approach that may optimize the potential of salivary biomarkers to diagnose and manage oral and maxillofacial diseases. Therefore, this review summarized the role and current application of techniques based on artificial intelligence for salivary biomarker discovery and validation in oral and maxillofacial diseases.
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Affiliation(s)
- John Adeoye
- Division of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Hong Kong, Hong Kong SAR, China
| | - Yu-Xiong Su
- Division of Oral and Maxillofacial Surgery, Faculty of Dentistry, University of Hong Kong, Hong Kong SAR, China
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Niu Y, Zhang C, Sun Y, Dong L, Si Y, Yang J, Zhu P, Yang F. Symbiotic relationship between Prevotella denticola and Streptococcus mutans enhances virulence of plaque biofilms. Arch Oral Biol 2023; 151:105714. [PMID: 37141746 DOI: 10.1016/j.archoralbio.2023.105714] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2023] [Revised: 04/25/2023] [Accepted: 04/26/2023] [Indexed: 05/06/2023]
Abstract
OBJECTIVES This study aimed to explore that whether interactions between Prevotella denticola and Streptococcus mutans could promote the establishment of hypervirulent biofilms on teeth surface and eventually influence the occurrence and development of caries. DESIGN Based on single-species biofilms of either P. denticola or S. mutans, and dual-species biofilms of both bacteria, we compared the virulence properties associated with cariogenicity in vitro, including carbohydrate metabolism and acid productivity, synthesis of extracellular polysaccharides, biomass and architecture of biofilms, level of enamel demineralization and expression of virulence genes associated with carbohydrate metabolism and adhesion in S. mutans. RESULTS The data demonstrated that, compared to single-species of above two taxa, dual-species produced lactate by metabolizing carbohydrates at a higher level during the observation period. Moreover, dual-species biofilms accrued more biomass and exhibited more dense microcolonies and abundant extracellular matrix. And it's noticeable that the level of enamel demineralization in dual-species biofilms was more augmented than that of single-species. In addition, the presence of P. denticola induced the expression of virulence genes gtfs and gbpB in S. mutans. CONCLUSIONS Symbiotic relationship between P. denticola and S. mutans enhances caries-associated virulence of plaque biofilms, which might provide new strategies for effective prevention and treatment of caries.
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Affiliation(s)
- Yufen Niu
- Stomatology Center, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, China; School of Stomatology, Dalian Medical University, Dalian, China
| | - Chunyan Zhang
- Stomatology Center, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, China
| | - Yanfei Sun
- Stomatology Center, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, China
| | - Lei Dong
- Stomatology Center, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, China; School of Stomatology, Dalian Medical University, Dalian, China
| | - Yuan Si
- Stomatology Center, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, China
| | - Jiazhen Yang
- Department of Pediatric Dentistry, Qingdao Stomatological Hospital, Qingdao, China
| | - Pengfei Zhu
- Single-Cell Center, CAS Key Laboratory of Biofuels, Shandong Key Laboratory of Energy Genetics, Shandong Energy Institute, Qingdao New Energy Shandong Laboratory, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences, Qingdao, China
| | - Fang Yang
- Stomatology Center, Qingdao Hospital, University of Health and Rehabilitation Sciences (Qingdao Municipal Hospital), Qingdao, China.
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Huang Z, Yang X, Huang Y, Tang Z, Chen Y, Liu H, Huang M, Qing L, Li L, Wang Q, Jie Z, Jin X, Jia B. Saliva - a new opportunity for fluid biopsy. Clin Chem Lab Med 2023; 61:4-32. [PMID: 36285724 DOI: 10.1515/cclm-2022-0793] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 09/29/2022] [Indexed: 12/15/2022]
Abstract
Saliva is a complex biological fluid with a variety of biomolecules, such as DNA, RNA, proteins, metabolites and microbiota, which can be used for the screening and diagnosis of many diseases. In addition, saliva has the characteristics of simple collection, non-invasive and convenient storage, which gives it the potential to replace blood as a new main body of fluid biopsy, and it is an excellent biological diagnostic fluid. This review integrates recent studies and summarizes the research contents of salivaomics and the research progress of saliva in early diagnosis of oral and systemic diseases. This review aims to explore the value and prospect of saliva diagnosis in clinical application.
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Affiliation(s)
- Zhijie Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Xiaoxia Yang
- Department of Endodontics, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Yisheng Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Zhengming Tang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Yuanxin Chen
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Hongyu Liu
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Mingshu Huang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Ling Qing
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Li Li
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Qin Wang
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
| | - Zhuye Jie
- BGI Genomics, BGI-Shenzhen, Shenzhen, P.R. China
- Shenzhen Key Laboratory of Human Commensal Microorganisms and Health Research, BGI-Shenzhen, Shenzhen, P.R. China
- Laboratory of Genomics and Molecular Biomedicine, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Xin Jin
- BGI Genomics, BGI-Shenzhen, Shenzhen, P.R. China
- School of Medicine, South China University of Technology, Guangzhou, P.R. China
| | - Bo Jia
- Department of Oral Surgery, Stomatological Hospital, Southern Medical University, Guangzhou, P.R. China
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Biofilm accumulation and sucrose rinse modulate calcium and fluoride bioavailability in the saliva of children with early childhood caries. Sci Rep 2022; 12:10283. [PMID: 35717506 PMCID: PMC9206641 DOI: 10.1038/s41598-022-14583-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 04/27/2022] [Indexed: 11/08/2022] Open
Abstract
This study aimed at investigating the combined effect of biofilm accumulation and 20% sucrose rinse on the modulation of calcium (Ca2+), phosphate (Pi), and fluoride (F-) bioavailability in the saliva of children with early childhood caries (ECC). Fifty-six preschoolers of both genders were evaluated according to caries experience and activity: caries-free (CF, n = 28) and with ECC (n = 28) and then, submitted to biofilm intervention (biofilm accumulation). In each situation, saliva samples were collected before and five minutes after a 20% sucrose rinse to determine the concentrations of Ca2+, Pi, and F-. Calcium concentration was significantly lower in the biofilm accumulation situation compared to the situation of biofilm mechanical control (p ≤ 0.01), except for CF children after sucrose rinse. Biofilm accumulation increased salivary calcium concentration in children with ECC after sucrose rinse (p = 0.04), whereas mechanical biofilm control reduced it in both groups (p = 0.000). Phosphate concentration was influenced by mechanical control of biofilm in CF children (p = 0.03). The fluoride bioavailability was reduced by sucrose rinse and biofilm accumulation in CF and ECC children (p ≤ 0.002). In conclusion, the combined effect of biofilm accumulation and sucrose rinse modifies the bioavailability of calcium and fluoride in the saliva of children with early childhood caries.
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Zhou X, Li H, Zhu C, Yuan C, Meng C, Feng S, Sun X, Zheng S. Analysis of salivary proteomic biomarkers for the surveillance of changes in high-risk status of early childhood caries. BMC Oral Health 2021; 21:572. [PMID: 34749719 PMCID: PMC8573911 DOI: 10.1186/s12903-021-01930-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Accepted: 10/25/2021] [Indexed: 11/10/2022] Open
Abstract
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.
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Affiliation(s)
- Xinzhu Zhou
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, 100081, PR China
| | - Haozhe Li
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, 100081, PR China
| | - Ce Zhu
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, 100081, PR China.,Department of Preventive Dentistry, Shanghai Jiao Tong University School of Dentistry, Shanghai Ninth People's Hospital, Shanghai, 200011, PR China
| | - Chao Yuan
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, 100081, PR China
| | - Chunhua Meng
- Second Kindergarten in Asian Games Village, Chaoyang Disctrict, Beijing, Beijing, 100101, PR China
| | - Shulan Feng
- Second Kindergarten in Asian Games Village, Chaoyang Disctrict, Beijing, Beijing, 100101, PR China
| | - Xiangyu Sun
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, 100081, PR China.
| | - Shuguo Zheng
- Department of Preventive Dentistry, Peking University School and Hospital of Stomatology, National Center of Stomatology, National Clinical Research Center for Oral Diseases, National Engineering Laboratory for Digital and Material Technology of Stomatology, Beijing, 100081, PR China.
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