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Fries N, Haworth S, Shaffer J, Esberg A, Divaris K, Marazita M, Johansson I. A Polygenic Score Predicts Caries Experience in Elderly Swedish Adults. J Dent Res 2024; 103:502-508. [PMID: 38584306 PMCID: PMC11047011 DOI: 10.1177/00220345241232330] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/09/2024] Open
Abstract
Caries is a partially heritable disease, raising the possibility that a polygenic score (PS, a summary of an individual's genetic propensity for disease) might be a useful tool for risk assessment. To date, PS for some diseases have shown clinical utility, although no PS for caries has been evaluated. The objective of the study was to test whether a PS for caries is associated with disease experience or increment in a cohort of Swedish adults. A genome-wide PS for caries was trained using the results of a published genome-wide association meta-analysis and constructed in an independent cohort of 15,460 Swedish adults. Electronic dental records from the Swedish Quality Registry for Caries and Periodontitis (SKaPa) were used to compute the decayed, missing, and filled tooth surfaces (DMFS) index and the number of remaining teeth. The performance of the PS was evaluated by testing the association between the PS and DMFS at a single dental examination, as well as between the PS and the rate of change in DMFS. Participants in the highest and lowest deciles of PS had a mean DMFS of 63.5 and 46.3, respectively. A regression analysis confirmed this association where a 1 standard deviation increase in PS was associated with approximately 4-unit higher DMFS (P < 2 × 10-16). Participants with the highest decile of PS also had greater change in DMFS during follow-up. Results were robust to sensitivity analysis, which adjusted for age, age squared, sex, and the first 20 genetic principal components. Mediation analysis suggested that tooth loss was a strong mediating factor in the association between PS and DMFS but also supported a direct genetic effect on caries. In this cohort, there are clinically meaningful differences in DMFS between participants with high and low PS for caries. The results highlight the potential role of genomic data in improving caries risk assessment.
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Affiliation(s)
| | | | | | | | - K. Divaris
- University of North Carolina at Chapel Hill, Chapel Hill, NC, USA
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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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Fujihara C, Hafiyyah OA, Murakami S. Identification of disease-associate variants of aggressive periodontitis using genome-wide association studies. JAPANESE DENTAL SCIENCE REVIEW 2023; 59:357-364. [PMID: 37860752 PMCID: PMC10582758 DOI: 10.1016/j.jdsr.2023.09.001] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Revised: 09/20/2023] [Accepted: 09/24/2023] [Indexed: 10/21/2023] Open
Abstract
Aggressive periodontitis (AgP), Stage III or IV and Grade C according to the new periodontitis classification, is characterized by the rapid destruction of periodontal tissues in the systemically healthy population and often causes premature tooth loss. The presence of familial aggregation suggests the involvement of genetic factors in the pathogenesis. However, the genes associated with the onset and progression of the disease and details of its pathogenesis have not yet been fully identified. In recent years, the genome-wide approach (GWAS), a comprehensive genome analysis method using bioinformatics, has been used to search for disease-related genes, and the results have been applied in genomic medicine for various diseases, such as cancer. In this review, we discuss GWAS in the context of AgP. First, we introduce the relationship between single-nucleotide polymorphisms (SNPs) and susceptibility to diseases and how GWAS is useful for searching disease-related SNPs. Furthermore, we summarize the recent findings of disease-related genes using GWAS on AgP inside and outside Japan and a possible mechanism of the pathogenesis of AgP based on available literature and our research findings. These findings will lead to advancements in the prevention, prognosis, and treatment of AgP.
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Affiliation(s)
- Chiharu Fujihara
- Department of Periodontology and Regenerative Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan
| | - Osa Amila Hafiyyah
- Department of Periodontology and Regenerative Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan
- Department of Periodontics, Faculty of Dentistry, Universitas Gadjah Mada, Yogyakarta, Indonesia
| | - Shinya Murakami
- Department of Periodontology and Regenerative Dentistry, Osaka University Graduate School of Dentistry, Osaka, Japan
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Petty LE, Silva R, de Souza LC, Vieira AR, Shaw DM, Below JE, Letra A. Genome-wide Association Study Identifies Novel Risk Loci for Apical Periodontitis. J Endod 2023; 49:1276-1288. [PMID: 37499862 PMCID: PMC10543637 DOI: 10.1016/j.joen.2023.07.018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Revised: 07/07/2023] [Accepted: 07/16/2023] [Indexed: 07/29/2023]
Abstract
INTRODUCTION Apical periodontitis (AP) is a common consequence of root canal infection leading to periapical bone resorption. Microbial and host genetic factors and their interactions have been shown to play a role in AP development and progression. Variations in a few genes have been reported in association with AP; however, the lack of genome-wide studies has hindered progress in understanding the molecular mechanisms involved. Here, we report the first genome-wide association study of AP in a large and well-characterized population. METHODS Male and female adults (n = 932) presenting with deep caries and AP (cases), or deep caries without AP (controls) were included. Genotyping was performed using the Illumina Expanded Multi-Ethnic Genotyping Array (MEGA). Single-variant association testing was performed adjusting for sex and 5 principal components. Subphenotype association testing, analyses of genetically regulated gene expression, polygenic risk score, and phenome-wide association (PheWAS) analyses were also conducted. RESULTS Eight loci reached near genome-wide significant association with AP (P < 5 × 10-6); gene-focused analyses replicated 3 previously reported associations (P < 8.9 × 10-5). Sex-specific and subphenotype-specific analyses revealed additional significant associations with variants genome-wide. Functionally oriented gene-based analyses revealed 8 genes significantly associated with AP (P < 5 × 10-5), and PheWAS analysis revealed 33 phecodes associated with AP risk score (P < 3.08 × 10-5). CONCLUSIONS This study identified novel genes/loci contributing to AP and specific contributions to AP risk in men and women. Importantly, we identified additional systemic conditions significantly associated with AP risk. Our findings provide strong evidence for host-mediated effects on AP susceptibility.
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Affiliation(s)
- Lauren E Petty
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Renato Silva
- Department of Endodontics, University of Pittsburgh School of Dental Medicine, Pittsburgh, Pennsylvania
| | | | - Alexandre R Vieira
- Department of Oral and Craniofacial Sciences, University of Pittsburgh School of Dental Medicine, Pittsburgh, Pennsylvania
| | - Douglas M Shaw
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Jennifer E Below
- Vanderbilt Genetics Institute, Vanderbilt University Medical Center, Nashville, Tennessee
| | - Ariadne Letra
- Department of Endodontics, University of Pittsburgh School of Dental Medicine, Pittsburgh, Pennsylvania; Department of Endodontics, UTHealth School of Dentistry at Houston, Houston, Texas; Department of Diagnostic and Biomedical Sciences, UTHealth School of Dentistry at Houston, Houston, Texas; Center for Craniofacial Research, UTHealth School of Dentistry at Houston, Houston, Texas.
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5
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van Meijeren-van Lunteren AW, Liu X, Veenman FCH, Grgic O, Dhamo B, van der Tas JT, Prijatelj V, Roshchupkin GV, Rivadeneira F, Wolvius EB, Kragt L. Oral and craniofacial research in the Generation R study: an executive summary. Clin Oral Investig 2023:10.1007/s00784-023-05076-1. [PMID: 37301790 DOI: 10.1007/s00784-023-05076-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2022] [Accepted: 05/04/2023] [Indexed: 06/12/2023]
Abstract
OBJECTIVES Oral conditions are of high prevalence and chronic character within the general population. Identifying the risk factors and determinants of oral disease is important, not only to reduce the burden of oral diseases, but also to improve (equal access to) oral health care systems, and to develop effective oral health promotion programs. Longitudinal population-based (birth-)cohort studies are very suitable to study risk factors on common oral diseases and have the potential to emphasize the importance of a healthy start for oral health. In this paper, we provide an overview of the comprehensive oral and craniofacial dataset that has been collected in the Generation R study: a population-based prospective birth cohort in the Netherlands that was designed to identify causes of health from fetal life until adulthood. METHODS Within the multidisciplinary context of the Generation R study, oral and craniofacial data has been collected from the age of 3 years onwards, and continued at the age of six, nine, and thirteen. Data collection is continuing in 17-year-old participants. RESEARCH OUTCOMES In total, the cohort population comprised 9749 children at birth, and 7405 eligible participants at the age of seventeen. Based on questionnaires, the dataset contains information on oral hygiene, dental visits, oral habits, oral health-related quality of life, orthodontic treatment, and obstructive sleep apnea. Based on direct measurements, the dataset contains information on dental caries, developmental defects of enamel, objective orthodontic treatment need, dental development, craniofacial characteristics, mandibular cortical thickness, and 3D facial measurements. CONCLUSIONS Several research lines have been set up using the oral and craniofacial data linked with the extensive data collection that exists within the Generation R study. CLINICAL RELEVANCE Being embedded in a multidisciplinary and longitudinal birth cohort study allows researchers to study several determinants of oral and craniofacial health, and to provide answers and insight into unknown etiologies and oral health problems in the general population.
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Affiliation(s)
- Agatha W van Meijeren-van Lunteren
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- The Generation R Study Group, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
| | - Xianjing Liu
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- The Generation R Study Group, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
| | - Francien C H Veenman
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- The Generation R Study Group, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
| | - Olja Grgic
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- The Generation R Study Group, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
| | - Brunilda Dhamo
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- The Generation R Study Group, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
| | - Justin T van der Tas
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- The Generation R Study Group, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
| | - Vid Prijatelj
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- The Generation R Study Group, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
| | - Gennady V Roshchupkin
- The Generation R Study Group, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- Department of Radiology and Nuclear Medicine, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- Department of Epidemiology, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
| | - Fernando Rivadeneira
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- The Generation R Study Group, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
| | - Eppo B Wolvius
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
- The Generation R Study Group, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands
| | - Lea Kragt
- Department of Oral & Maxillofacial Surgery, Special Dental Care and Orthodontics, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands.
- The Generation R Study Group, Erasmus University Medical Centre, PO Box 2040, 3000 CA, Rotterdam, the Netherlands.
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Zhu Y, Wang Y, Zhang S, Li J, Li X, Ying Y, Yuan J, Chen K, Deng S, Wang Q. Association of polymicrobial interactions with dental caries development and prevention. Front Microbiol 2023; 14:1162380. [PMID: 37275173 PMCID: PMC10232826 DOI: 10.3389/fmicb.2023.1162380] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Accepted: 05/02/2023] [Indexed: 06/07/2023] Open
Abstract
Dental caries is a common oral disease. In many cases, disruption of the ecological balance of the oral cavity can result in the occurrence of dental caries. There are many cariogenic microbiota and factors, and their identification allows us to take corresponding prevention and control measures. With the development of microbiology, the caries-causing bacteria have evolved from the traditional single Streptococcus mutans to the discovery of oral symbiotic bacteria. Thus it is necessary to systematically organized the association of polymicrobial interactions with dental caries development. In terms of ecology, caries occurs due to an ecological imbalance of the microbiota, caused by the growth and reproduction of cariogenic microbiota due to external factors or the disruption of homeostasis by one's own factors. To reduce the occurrence of dental caries effectively, and considering the latest scientific viewpoints, caries may be viewed from the perspective of ecology, and preventive measures can be taken; hence, this article systematically summarizes the prevention and treatment of dental caries from the aspects of ecological perspectives, in particular the ecological biofilm formation, bacterial quorum sensing, the main cariogenic microbiota, and preventive measures.
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Affiliation(s)
- Yimei Zhu
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Ying Wang
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Shuyang Zhang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Jiaxuan Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Xin Li
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Yuanyuan Ying
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Jinna Yuan
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Keda Chen
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
| | - Shuli Deng
- Stomatology Hospital, School of Stomatology, Zhejiang University School of Medicine, Zhejiang Provincial Clinical Research Center for Oral Diseases, Key Laboratory of Oral Biomedical Research of Zhejiang Province, Cancer Center of Zhejiang University, Hangzhou, China
| | - Qingjing Wang
- Shulan International Medical College, Zhejiang Shuren University, Hangzhou, Zhejiang, China
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Chisini L, Costa F, Horta B, Tovo-Rodrigues L, Demarco F, Correa M. Sweet Taste Receptor Gene and Caries Trajectory in the Life Course. J Dent Res 2023; 102:422-430. [PMID: 36609159 PMCID: PMC10041601 DOI: 10.1177/00220345221138569] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
This study aims to investigate whether the trajectory of dental caries in the life course is associated with rs307355 (TAS1R3) and rs35874116 (TAS1R2) and if there is an epistatic association between rs307355 (TAS1R3) and rs35874116 (TAS1R2). A representative sample of all 5,914 births from the 1982 Pelotas birth cohort was prospectively investigated, and the decayed, missing, and filled teeth (DMF-T) components were assessed at ages 15 (n = 888), 24 (n = 720), and 31 (n = 539) y. Group-based trajectory modeling was used to identify groups with similar trajectories of DMF-T components in the life course. Genetic material was collected, and rs307355 (TAS1R3) and rs35874116 (TAS1R2) were genotyped. Ethnicity was evaluated using ADMIXTURE. Generalized multifactor dimensionality reduction software was used to investigate epistatic interactions. Considering rs307355 (TAS1R3) in the additive effect, the genotype TT was associated with the high decayed trajectory group (odds ratio [OR] = 4.52; 95% confidence interval [CI], 1.15-17.74) and the high missing trajectory group (OR = 3.35; 95% CI, 1.09-10.26). In the dominant effect, the genotype CT/TT was associated with the high decayed trajectory group (OR = 1.64; 95% CI, 1.14-2.35). Allele T was associated with an increased odds of 64% (OR = 1.64; 95% CI, 1.20-2.25) for the decayed component and 41% (OR = 1.41; 95% CI, 1.04-1.92) for the missing component. No associations were observed between rs307355 (TAS1R3) and the filled component. rs35874116 (TAS1R2) was not associated with DMF-T components. Positive epistatic interactions were observed involving rs307355 (TAS1R3) and rs35874116 (TAS1R2) with the decayed component (OR = 1.72; 95% CI, 1.04-2.84). Thus, rs307355 (TAS1R3) genotypes and alleles seem positively associated with the trajectory of decayed and missing components in the life course. Epistatic interaction between rs307355 and rs35874116 may increase the decayed caries trajectory.
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Affiliation(s)
- L.A. Chisini
- Graduate Program in Dentistry, Federal University of Juiz de Fora, Governador Valadares, MG, Brazil
| | - F.D.S. Costa
- International Center for Equity in Health, Postgraduate Program of Epidemiology, Federal University of Pelotas, Pelotas, Brazil
| | - B.L. Horta
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, RS, Brazil
| | - L. Tovo-Rodrigues
- Postgraduate Program in Epidemiology, Federal University of Pelotas, Pelotas, RS, Brazil
| | - F.F. Demarco
- Graduate Program in Dentistry, Federal University of Pelotas, Pelotas, RS, Brazil
| | - M.B. Correa
- Graduate Program in Dentistry, Federal University of Juiz de Fora, Governador Valadares, MG, Brazil
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8
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Chisini LA, Varella de Carvalho R, Dos Santos Costa F, Salvi LC, Demarco FF, Britto Correa M. Genes and single nucleotide polymorphisms in the pathway of saliva and dental caries: a systematic review and meta-analysis. BIOFOULING 2023; 39:8-23. [PMID: 36644905 DOI: 10.1080/08927014.2022.2162891] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Revised: 12/01/2022] [Accepted: 12/21/2022] [Indexed: 06/17/2023]
Abstract
The aim of this systematic review and meta-analysis was to investigate the influence of single nucleotide polymorphisms (SNPs), related to genes in salivary composition and flow, on dental caries experience. Sixteen studies were included in the systematic review and ten in the meta-analysis. Forty-four SNPS, covering four genes (CA6, AQP2, AQP5, and MUC5B) were identified. Most of the SNPs were not associated with caries in meta-analysis. Homozygous TT genotype of the SNP CA6 rs17032907(C/T) was associated with caries [OR = 3.23(1.39-7.49)]. The pool effect of the SNPs assessed in AQP5 was associated with a reduction in the likelihood of caries [OR = 0.75(0.59-0.95)]. Considering all SNPs of salivary composition and flow, the effect allele was associated with a 75% increase in the likelihood of caries [OR = 1.75(1.06-2.89)] in the homozygous genotype. The present findings showed that the genes in salivary composition and flow can play an important role in dental caries experience.
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Affiliation(s)
- Luiz Alexandre Chisini
- Graduate Program in Dentistry, Federal University of Juiz de Fora, Governador Valadares, Minas Gerais, Brazil
| | - Rodrigo Varella de Carvalho
- Graduate Program in Dentistry, Federal University of Juiz de Fora, Governador Valadares, Minas Gerais, Brazil
| | | | - Luana Carla Salvi
- Graduate Program in Biology, University of Vale do Taquari, Rio Grande do Sul, Brazil
| | - Flávio Fernando Demarco
- Graduate Program in Dentistry, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Marcos Britto Correa
- Graduate Program in Dentistry, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
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9
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Biedziak B, Dąbrowska J, Szponar-Żurowska A, Bukowska-Olech E, Jamsheer A, Mojs E, Mulle J, Płoski R, Mostowska A. Identification of a new familial case of 3q29 deletion syndrome associated with cleft lip and palate via whole-exome sequencing. Am J Med Genet A 2023; 191:205-219. [PMID: 36317839 DOI: 10.1002/ajmg.a.63015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2022] [Revised: 08/22/2022] [Accepted: 09/24/2022] [Indexed: 11/06/2022]
Abstract
Many unbalanced large copy number variants reviewed in the paper are associated with syndromic orofacial clefts, including a 1.6 Mb deletion on chromosome 3q29. The current report presents a new family with this recurrent deletion identified via whole-exome sequencing and confirmed by array comparative genomic hybridization. The proband exhibited a more severe clinical phenotype than his affected mother, comprising right-sided cleft lip/alveolus and cleft palate, advanced dental caries, heart defect, hypospadias, psychomotor, and speech delay, and an intellectual disability. Data analysis from the 3q29 registry revealed that the 3q29 deletion increases the risk of clefting by nearly 30-fold. No additional rare and pathogenic nucleotide variants were identified that could explain the clefting phenotype and observed intrafamilial phenotypic heterogeneity. These data suggest that the 3q29 deletion may be the primary risk factor for clefting, with additional genomic variants located outside the coding sequences, methylation changes, or environmental exposure serving as modifiers of this risk. Additional studies, including whole-genome sequencing or methylation analyses, should be performed to identify genetic factors underlying the phenotypic variation associated with the recurrent 3q29 deletion.
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Affiliation(s)
- Barbara Biedziak
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | - Justyna Dąbrowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poznan, Poland
| | - Anna Szponar-Żurowska
- Department of Orthodontics and Craniofacial Anomalies, Poznan University of Medical Sciences, Poznan, Poland
| | | | - Aleksander Jamsheer
- Department of Medical Genetics, Poznan University of Medical Sciences, Poznan, Poland
| | - Ewa Mojs
- Department of Clinical Psychology, Poznan University of Medical Sciences, Poznan, Poland
| | - Jennifer Mulle
- Psychiatry, Robert Wood Johnson Medical School, Rutgers University, New Brunswick, New Jersey, USA
| | - Rafał Płoski
- Department of Medical Genetics, Warsaw Medical University, Warsaw, Poland
| | - Adrianna Mostowska
- Department of Biochemistry and Molecular Biology, Poznan University of Medical Sciences, Poznan, Poland
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10
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Orlova E, Dudding T, Chernus JM, Alotaibi RN, Haworth S, Crout RJ, Lee MK, Mukhopadhyay N, Feingold E, Levy SM, McNeil DW, Foxman B, Weyant RJ, Timpson NJ, Marazita ML, Shaffer JR. Association of Early Childhood Caries with Bitter Taste Receptors: A Meta-Analysis of Genome-Wide Association Studies and Transcriptome-Wide Association Study. Genes (Basel) 2022; 14:59. [PMID: 36672800 PMCID: PMC9858612 DOI: 10.3390/genes14010059] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/14/2022] [Accepted: 12/17/2022] [Indexed: 12/28/2022] Open
Abstract
Although genetics affects early childhood caries (ECC) risk, few studies have focused on finding its specific genetic determinants. Here, we performed genome-wide association studies (GWAS) in five cohorts of children (aged up to 5 years, total N = 2974, cohorts: Center for Oral Health Research in Appalachia cohorts one and two [COHRA1, COHRA2], Iowa Fluoride Study, Iowa Head Start, Avon Longitudinal Study of Parents and Children [ALSPAC]) aiming to identify genes with potential roles in ECC biology. We meta-analyzed the GWASs testing ~3.9 million genetic variants and found suggestive evidence for association at genetic regions previously associated with caries in primary and permanent dentition, including the β-defensin anti-microbial proteins. We then integrated the meta-analysis results with gene expression data in a transcriptome-wide association study (TWAS). This approach identified four genes whose genetically predicted expression was associated with ECC (p-values < 3.09 × 10−6; CDH17, TAS2R43, SMIM10L1, TAS2R14). Some of the strongest associations were with genes encoding members of the bitter taste receptor family (TAS2R); other members of this family have previously been associated with caries. Of note, we identified the receptor encoded by TAS2R14, which stimulates innate immunity and anti-microbial defense in response to molecules released by the cariogenic bacteria, Streptococcus mutans and Staphylococcus aureus. These findings provide insight into ECC genetic architecture, underscore the importance of host-microbial interaction in caries risk, and identify novel risk genes.
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Affiliation(s)
- Ekaterina Orlova
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Tom Dudding
- Bristol Dental School, University of Bristol, Bristol BS1 2LY, UK
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, University of Bristol, Bristol BS8 1QU, UK
| | - Jonathan M. Chernus
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
| | - Rasha N. Alotaibi
- Dental Health Department, College of Applied Medical Sciences, King Saud University, Riyadh 12372, Saudi Arabia
| | - Simon Haworth
- Bristol Dental School, University of Bristol, Bristol BS1 2LY, UK
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, University of Bristol, Bristol BS8 1QU, UK
| | - Richard J. Crout
- Department of Periodontics, School of Dentistry, West Virginia University, Morgantown, WV 26505, USA
| | - Myoung Keun Lee
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Nandita Mukhopadhyay
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Eleanor Feingold
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - Steven M. Levy
- Department of Preventive & Community Dentistry, University of Iowa College of Dentistry, Iowa City, IA 52242, USA
| | - Daniel W. McNeil
- Department of Psychology & Department of Dental Public Health and Professional Practice, West Virginia University, Morgantown, WV 26505, USA
| | - Betsy Foxman
- Center for Molecular and Clinical Epidemiology of Infectious Diseases, Department of Epidemiology, School of Public Health, University of Michigan, Ann Arbor, MI 48109, USA
| | - Robert J. Weyant
- Dental Public Health, School of Dental Medicine, University of Pittsburgh, Pittsburgh, PA 15213, USA
| | - Nicholas J. Timpson
- Medical Research Council Integrative Epidemiology Unit, Department of Population Health Sciences, University of Bristol, Bristol BS8 1QU, UK
- Avon Longitudinal Study of Parents and Children, University of Bristol, Bristol BS8 1QU, UK
| | - Mary L. Marazita
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
| | - John R. Shaffer
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA 15260, USA
- Center for Craniofacial and Dental Genetics, Department of Oral and Craniofacial Sciences, University of Pittsburgh, Pittsburgh, PA 15261, USA
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Cogulu D, Saglam C. Genetic aspects of dental caries. FRONTIERS IN DENTAL MEDICINE 2022. [DOI: 10.3389/fdmed.2022.1060177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022] Open
Abstract
Dental caries is a common chronic disease affecting humans in all age groups. Various factors can affect the formation of caries including demineralization and remineralization processes with oral flora; dietary and oral hygiene habits; salivary composition, flow rate, pH and buffering capacity; morphological features of the teeth; fluoride exposures, environmental and socioeconomic factors. One of the most important factors causing inter-individual variations in caries susceptibility is the host genetics. Several genes affect individual caries susceptibility. Genes play a role in immune response, development of saliva and tooth enamel. The present review aims to overview the literature focusing on the genetic features of dental caries.
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12
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Winchester EW, Hardy A, Cotney J. Integration of multimodal data in the developing tooth reveals candidate regulatory loci driving human odontogenic phenotypes. FRONTIERS IN DENTAL MEDICINE 2022; 3:1009264. [PMID: 37034481 PMCID: PMC10078798 DOI: 10.3389/fdmed.2022.1009264] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Human odontogenic aberrations such as abnormal tooth number and delayed tooth eruption can occur as a symptom of rare syndromes or, more commonly, as nonsyndromic phenotypes. These phenotypes can require extensive and expensive dental treatment, posing a significant burden. While many dental phenotypes are heritable, most nonsyndromic cases have not been linked to causal genes. We demonstrate the novel finding that common sequence variants associated with human odontogenic phenotypes are enriched in developmental craniofacial enhancers conserved between human and mouse. However, the bulk nature of these samples obscures if this finding is due to the tooth itself or the surrounding tissues. We therefore sought to identify enhancers specifically active in the tooth anlagen and quantify their contribution to the observed genetic enrichments. We systematically identified 22,001 conserved enhancers active in E13.5 mouse incisors using ChIP-seq and machine learning pipelines and demonstrated biologically relevant enrichments in putative target genes, transcription factor binding motifs, and in vivo activity. Multi-tissue comparisons of human and mouse enhancers revealed that these putative tooth enhancers had the strongest enrichment of odontogenic phenotype-associated variants, suggesting a role for dysregulation of tooth developmental enhancers in human dental phenotypes. The large number of these regions genome-wide necessitated prioritization of enhancer loci for future investigations. As enhancers modulate gene expression, we prioritized regions based on enhancers' putative target genes. We predicted these target genes and prioritized loci by integrating chromatin state, bulk gene expression and coexpression, GWAS variants, and cell type resolved gene expression to generate a prioritized list of putative odontogenic phenotype-driving loci active in the developing tooth. These genomic regions are of particular interest for downstream experiments determining the role of specific dental enhancer:gene pairs in odontogenesis.
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Affiliation(s)
| | - Alexis Hardy
- Master of Genetics Program, Paris Diderot University,
Paris, France
| | - Justin Cotney
- Department of Genetics and Genome Sciences, University of
Connecticut School of Medicine, Farmington, CT, United States
- Institute for Systems Genomics, University of Connecticut,
Storrs, CT, United States
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