Precision dentistry: genes for smiles

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The long-term goal of Dr Kimon Divaris’ research is to further understand and thus to improve early childhood oral health, with a particular focus on early childhood caries (ECC). Based at the University of North Carolina at Chapel Hill, Dr Divaris and his team are continuing their quest to investigate the many different aspects that underlie the oral health of young children by assembling a paediatric precision medicine cohort. They are investigating genomics and other ‘omics’ aspects of oral health among a community-based sample of approximately 6,000 pre-school age children.
The enamel covering a tooth is the hardest substance in the human body, yet it is constantly exchanging minerals with the oral environment. This is due to the combined activity of the oral biofilm (i.e., the bacteria that constantly overlay our teeth and produce acidic metabolites, thus demineralising the enamel) and the saliva (that buffers the acid exposure and replenishes the mineral loss). Unfavourable changes in the composition or the transcriptional and metabolic activity of the oral biofilm, statuses described as dysbiotic, due to a sugar-rich diet or other factors create unfavourable shifts in this demineralisation-remineralisation balance. This imbalance is what constitutes a disease called ‘caries’. The disease process itself is not directly observable to a person; it becomes evident only once the effects of caries on tooth surfaces progress and manifest, so that clinical symptoms, such as white spot lesions or tooth structure loss (e.g., a cavity), are visible. It is thought that genetics explain around 40–70% of disease occurrence. Interestingly, this susceptibility seems to be independent of sweetness preference heritability, suggesting there are likely other mechanisms at play. Whilst caries is etiologically heterogeneous, meaning that different factors are responsible for disease initiation and progression among different people, it is mostly behaviourally-driven. Moreover, there are likely many interactions between genomic factors and common, modifiable risk factors, such as fluoride exposure and diet. However, the exact genetic components that contribute to caries etiology remain unknown.
Members of the ZOE 2.0 core team at UNC-Chapel Hill, from L to R: Dr Kimon Divaris, Ms Diane Baker, Mr Tom Pahel, Jr., Dr Jeannie Ginnis.
Early childhood caries (ECC) is the most common, chronic disease of childhood. Recent estimates suggest that around 30% of US children aged two to five are affected. ECC has substantial social and economic costs, beyond the obvious clinical-dental problems (e.g., pain and need for complex dental restorative treatment) that it confers. The disease prevalence shows marked differences between economic, social and racial/ethnic groups. In particular, ECC disproportionately affects minority and socioeconomically disadvantaged families – it is the same groups that are the least likely to be represented in biologically-informative (e.g., genetics and precision medicine) research, meaning that working with these and all population groups to conduct population health research is more important than ever in the battle against this disease and others. Children show varying susceptibility to caries. However, as with adult caries, the exact genetic basis for ECC remains unknown, as do the environmental interactions, which also remain elusive. These genetic influences-to-be-discovered are likely linked to dental anatomy, enamel quality, salivary properties, immunity, oral microbiome composition or function.
Currently in the oral health domain, there are few sizeable clinical investigations surveying diverse groups of participants in a detailed manner. This is a missed opportunity: the oral cavity provides easy access to potentially informative biomarkers via people’s saliva and the oral microbiome, and regular dental visits provide an ideal opportunity to monitor and promote oral health via these biological indicators. Looking forward, when precision dentistry materialises, we will likely be able to diagnose, and therefore treat, caries activity before the disease confers irreversible destruction to the enamel.
The wonderful world of ‘omics
We are well into the ‘big data’ era; with high throughput technologies becoming more accessible, the volume and depth of data available for analysis or ‘mining’ is booming. One of the advantages of these technologies is that they allow us to obtain a vast amount of data relatively quickly and these can subsequently be used to complement other metadata, such as geographical location, environment and behaviours.

With the rise of multi-omics information, the face of healthcare will certainly be transformed in the coming years Quote_brain

Dr Divaris’ current project, ZOE-G4S, or Zero-Out Early childhood caries – Genes for Smiles (frequently referred to as the ZOE 2.0 study), is a valiant five-year undertaking, now in its third year. The project entails a community-based, genetic epidemiological study of early childhood oral health among 6,000 children aged three to four, who are part of multi-ethnic communities enrolled in Head Start programmes across the state of North Carolina.
The study comprises several stages and has many moving parts. In the first stage, the team develops partnerships with community organisations, specifically public preschool programmes and centres. In the context of these partnerships and with support from the state’s dental public health workforce, the team offers oral health education and other health promotion activities. Trained and calibrated clinical examiners conduct research oral examinations involving biospecimen (saliva and dental plaque/biofilm) collection, while providing a positive dental examination experience for this young population. Saliva samples are collected for genomics analysis and visual (ICDAS) diagnostic criteria are used to determine the prevalence and severity of caries experience and other clinical-dental conditions. Dental plaque samples are collected and stored for feasibility studies and future comprehensive microbiome analyses including metagenomics, metatranscriptomics and metabolomics. The team is also collecting water samples from participants’ home water sources to measure fluoride content via the state’s laboratory of public health. Anthropometric, behavioural and other information is also collected as part of a comprehensive data collection process. In a second stage, a trans-ethnic genome-wide association analysis (GWAS) will interrogate the human genome for areas (loci) and markers that are associated with ECC and other clinical-dental characteristics of interest (e.g., enamel defects). This will then allow the GWAS data to be annotated and further interrogated against other biological data layers that are already available, and to determine their transferability and generalisation to other population groups. The main benefits of projects incorporating GWAS is their agnostic scan of the human genome (i.e., analysing millions of data points across the genome) versus single or small numbers of candidate genes.
Hopefully, large-scale cohort studies such as these will allow the biological, behavioural and contextual determinants of early childhood oral health to be better understood. Generating this type of combined clinical, epidemiologic, behavioural, contextual and multi-omics information is necessary for the realisation of precision medicine in the oral health domain.

Large-scale cohort studies such as ZOE 2.0 will allow the biological, behavioural and contextual determinants of early childhood oral health to be better understood Quote_brain

Up close and personal
Medicine, public health and many other disciplines are moving towards a precision approach, meaning that every case of health or disease is examined and treated on an individual basis, taking into account a large number of individual factors, such as genetic background, other ‘omics data, lifestyle and environment. This would allow clinicians to make accurate diagnoses and to provide specifically designed treatment plans to each individual patient in a precise manner. The dream isn’t that far from reality, with the rise and increasing affordability of generating ‘omics data, including genomics, metagenomics, transcriptomics, proteomics, metabolomics and epigenomics, the face of healthcare will certainly be transformed in the coming years.
And this is the goal of Dr Divaris’ project.
This project is the first to look at genomic influences on ECC and will include often under-represented populations. Leading on from this work, Dr Divaris hopes that the results will provide target genes and pathways that will go on to influence future work, and will also provide information that can be used to inform risk estimation and enable the efficient allocation of caries prevention measures to those children who are deemed to be at highest risk. Geographic location and other area-level characteristics are also important aspects in this process.
Unpacking the complexity of pathways involved in oral dysbiosis and dental caries development and the upstream challenges faced by young children and their families, will add a major step towards personalised, precision dental care. In reality, this must translate into socially responsible practices, precision public health, interventions and policies that will bring about sustainable population-level oral health improvements.

Do you think we’ll ever see a world where ECC in some communities will be completely absent?
I consider myself an optimist, yet I think it will be very hard to eradicate dental caries or specifically, ECC. A background level of disease is likely going to persist despite all our scientific and clinical advances; however, I am convinced that we could achieve a very low caries rate at the population level. Frankly, I think that social and upstream approaches such as decisively taxing (or finding a good alternative to) sugar, amplifying school-based health promotion activities and in general empowering healthy communities, will be most effective in tackling ECC.
What do you see as the biggest limitation to ‘omics studies, currently?
We still don’t have very good methods to make sense of these data, especially when we are dealing with multiple data layers or types – in ZOE 2.0, we can generate four levels of omics data: human genomics, microbial taxonomy (whole genome sequencing shotgun), microbial activity/gene expression (RNA-seq.) and biofilm activity (metabolomics). Putting all this information together to tell one story is something that we cannot efficiently do without ignoring some information (e.g., low frequency variants or microbes) that could be important or informative – our collaborators and other teams around the world are working hard to achieve integrative omics analysis methods.
Dreaming big, would there be the potential for intervention if we know the genetic markers responsible for ECC i.e., could gene therapy be a viable treatment option one day?
Certainly. Developing a vaccine against dental caries has been the long-standing goal of many investigators and groups round the world but this has been elusive to date. It is conceivable that a gene therapy could be developed resulting in protective innate immunity against caries-associated bacteria, less soluble enamel, more favourable tooth anatomy or salivary properties, or something else. In my opinion, the most likely mechanism of a future groundbreaking intervention would be something that effectively and selectively disrupts the oral biofilm in a way that the commensal health-associated microbiome remains intact while the ‘bad’ players are evicted, reduced or deactivated.
To what extent does the oral microbiome contribute to caries, and is this something that could be manipulated, for example by diet?
The oral microbiome plays a major, causative role – the way I see it, dental caries is a predominantly dysbiotic disease (i.e., a microbial imbalance) that results in a biochemical, mineral imbalance on the tooth surface. So, the disease is the dysbiotic shift and not the resulting tooth cavity. Unfortunately, in most aspects of dentistry, even today, the cavity (the result of the disease) is considered the disease. Understanding the disease as a microbial imbalance that can be modulated, influenced and treated by behavioural (e.g., diet modifications) or chemotherapeutic (e.g., fluorides) interventions will be a catalytic, favourable paradigm shift for dentistry.
Who will benefit most from this research? Will it be the children themselves, policy makers, future generations or all of the aforementioned?
Advances in the sciences and clinical practice ultimately benefit everyone, even if the benefits are not immediately evident. The participating children benefit from having a positive introduction to oral health care by experiencing a fun clinical-dental examination, as well as from the oral health education component. We believe that participating programmes and centres also benefit from their participation via a heightened awareness and attention we bring to oral health. Ultimately, large segments of the population, both children and their families, as well as the health system, will benefit from the development of precision oral health care in early childhood.
Research Objectives
Dr Divaris’ work aims to understand, and therefore improve, early childhood oral health via a precision dentistry approach. He is currently working on a large-scale research study that is collecting and investigating genomics and other ‘omics data from approximately 6,000 children.
NIH/NIDCR U01-DE025046

  • Kari North, PhD, Professor of Epidemiology, Gillings School of Global Public Health, University of North Carolina at Chapel Hill
  • Gary Slade, BDS, PhD, Distinguished Professor of Dental Ecology, School of Dentistry, University of North Carolina at Chapel Hill.

Kimon Divaris is a board-certified Paediatric Dentist and Epidemiologist. He is Associate Professor and Research Director in the Department of Pediatric Dentistry, School of Dentistry and adjunct Associate Professor of Epidemiology, Gillings School of Global Public Health, both at UNC-Chapel Hill. He has had substantial scholarly activity and is recipient of numerous awards. His research interests are diverse and include both proximal (biological) and distal (social) determinants of health, with focus on oral health promotion among preschool-age child populations and understanding the genetic, biological and microbial basis of dental caries and periodontal diseases. He is active in clinical care, mentoring and teaching, and research.
Dr Kimon Divaris
Associate Professor, Departments of Pediatric Dentistry & Epidemiology
UNC School of Dentistry, CB#7450
University of North Carolina at Chapel Hill
Chapel Hill, N.C. 27599-7450
T: +1 919 537 3556

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