Revisiting “‐omics” in Oral Health and Disease

Bostancı, Nagihan

doi:10.1002/prca.201900022

Cited by 3 publications

(4 citation statements)

References 21 publications

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“…Next to the search for such individual marker molecules, high‐throughput ‘omics’ technologies could hold a greater promise for the development of ‘intelligent’ diagnostic utilities. In addition, the molecular derivatives of technologies should be supplemented with data regarding enzymatic activities, radiological imaging, as well as behavioural and environmental attributes, in order to reach fully integrated diagnostic utilities (Bostanci, 2020 ; Nonaka & Wong, 2018 ). In other terms, at least in the context of systemic health monitoring, we should be leaning towards multi‐dimensional personalized data and biosignatures.…”

Section: Systemic Biomarkersmentioning

confidence: 99%

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A critical analysis of research methods to study clinical molecular biomarkers in Endodontic research

Zehnder

Belibasakis

2021

Int Endodontic J

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The term biomarker has been defined as a characteristic that is objectively measured and evaluated as an indicator of normal biological and pathogenic processes, or pharmacologic responses to a therapeutic intervention (Atkinson & Colburn, 2001). The term is mainly used to describe a molecule collected from a biological fluid that is correlated to a specific condition, development of a condition or identification of the same. Hence, any type of study that identifies and correlates molecules from endodontic samples, such as biofilm components in symptomatic versus non-symptomatic cases (Loureiro et al., 2021) could be seen as biomarker research. Moreover, the term 'biomarker' is also used in the context of imaging, and describes a biological feature or set of features in a diagnostic image, that can then be analysed using specific algorithms (Smith et al., 2003). This is also beyond the scope of this text, but represents an interesting and timely

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Section: Systemic Biomarkersmentioning

confidence: 99%

“…radiographic) data. Combination of diverse databases via artificial intelligence and machine learning tools are supposed to improve diagnosis, prognosis and treatment planning, whilst minimizing human error (Bostanci, 2020 ; Hung et al, 2020 ).…”

Section: Data Presentation and Analysismentioning

confidence: 99%

A critical analysis of research methods to study clinical molecular biomarkers in Endodontic research

Zehnder

Belibasakis

2021

Int Endodontic J

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“…In systemically healthy individuals, the salivary protein composition and levels are relatively stable over longer periods of time [ 36 ] and may well reflect serum composition [ 37 ], whereas the fraction of proteins showing inter-individual variability makes salivary proteome a useful medium for biomarker identification [ 38 ]. The evolution from gel electrophoresis assays that enabled separation of proteins by size/charge, to the mass spectrometry sequencing platforms, able to sequence multiple proteins in a single run, has led to a giant quantitative leap in salivary protein discovery in saliva from less than 20 [ 39 ] to more 1000 in any given sample [ 40 ].…”

Section: Salivary Proteomics Discovery For Personalized Periodontal H...mentioning

confidence: 99%

Precision periodontal care: from omics discoveries to chairside diagnostics

Bostancı

Belibasakis

2023

Clin Oral Invest

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The interface of molecular science and technology is guiding the transformation of personalized to precision healthcare. The application of proteomics, genomics, transcriptomics, and metabolomics is shaping the suitability of biomarkers for disease. Prior validation of such biomarkers in large and diverse patient cohorts helps verify their clinical usability. Incorporation of molecular discoveries into routine clinical practice relies on the development of customized assays and devices that enable the rapid delivery of analytical data to the clinician, while the patient is still in session. The present perspective review addresses this topic under the prism of precision periodontal care. Selected promising research attempts to innovate technological platforms for oral diagnostics are brought forward. Focus is placed on (a) the suitability of saliva as a conveniently sampled biological specimen for assessing periodontal health, (b) proteomics as a high-throughput approach for periodontal disease biomarker identification, and (c) chairside molecular diagnostic assays as a technological funnel for transitioning from the laboratory benchtop to the clinical point-of-care.

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“…Recently, researchers have employed new techniques and methods to help obtain more information on tissues and cells. Biomedical “omics” approaches rely on collecting large amounts of omics data, combined with bioinformatics and biostatistics, to drive new and deeper insights into complex biology ( 4 ). In previous studies, single-cell RNA-seq analysis was successfully applied to analyze the cellular heterogeneity of cells in the periodontium and their developmental relationship with early precursor cells, such as identifying PTHrP+ cells in the dental follicle as important precursor cells that may give birth to osteoblasts, periodontal ligament cells, and cementoblasts to provide a cell source for later periodontal tissue formation ( 5 ).…”

Section: Introductionmentioning

confidence: 99%

Transcriptome landscape comparison of periodontium in developmental and renewal stages

Deng

Luo²,

Xie³

et al. 2023

Front. Endocrinol.

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ObjectivesPeriodontium regeneration remains a significant challenge in clinics and research, and it is essential to understand the stage-specific biological process in situ. However, differing findings have been reported, and the mechanism has yet to be elucidated. The periodontium of adult mice molars is considered to be stable remodeling tissue. At the same time, the continuously growing incisors and the developing dental follicle (DF) of postnatal mice highly represent fast remodeling tissue. In this study, we attempted to explore different clues of temporal and spatial comparisons to provide improved references for periodontal regeneration.MethodsPeriodontal tissues from the developing periodontium (DeP) of postnatal mice, and continuously growing periodontium (CgP) and stable remodeling periodontium (ReP) of adult mice were isolated and compared using RNA sequencing. Based on the Dep and CgP separately compared with the ReP, differentially expressed genes and signaling pathways were analyzed using GO, KEGG databases, and Ingenuity Pathway Analysis (IPA). The results and validation were obtained by immunofluorescence staining and RT-PCR assays. Data were expressed as means ± standard deviation (SD) and analyzed by GraphPad Prism 8 software package, and one-way ANOVA was used to test multiple groups.ResultsPrincipal component analysis showed that the three groups of periodontal tissue were successfully isolated and had distinct expression profiles. A total of 792 and 612 DEGs were identified in the DeP and CgP groups compared with the ReP. Upregulated DEGs in the DeP were closely related to developmental processes, while the CgP showed significantly enhanced cellular energy metabolism. The DeP and CgP showed a common downregulation of the immune response, with activation, migration, and recruitment of immune cells. IPA and further validation jointly suggested that the MyD88/p38 MAPK pathway played an essential regulatory role in periodontium remodeling.ConclusionTissue development, energy metabolism, and immune response were critical regulatory processes during periodontal remodeling. Developmental and adult stages of periodontal remodeling showed different expression patterns. These results contribute to a deeper understanding of periodontal development and remodeling and may provide references for periodontal regeneration.

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Revisiting “‐omics” in Oral Health and Disease

Cited by 3 publications

References 21 publications

A critical analysis of research methods to study clinical molecular biomarkers in Endodontic research

A critical analysis of research methods to study clinical molecular biomarkers in Endodontic research

Precision periodontal care: from omics discoveries to chairside diagnostics

Transcriptome landscape comparison of periodontium in developmental and renewal stages

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