Single-cell sequencing, spatial transcriptome ad periodontitis: Rethink pathogenesis and classification.

OBJECTIVE: This narrative review illuminates on the application of single-cell RNA sequencing (scRNA-seq) and spatial transcriptomics (ST) in periodontitis and highlights the probability of relating cell population and gene signatures to the pathogenesis of the disease for a better diagnosis. METHODS: An electronic search of the literature in the PubMed database for the keywords, "single cell sequencing" OR "spatial transcriptomics" and "periodontitis" OR "gingiva" OR "oral mucosa" yielded 486 research articles and reviews. After filtering duplicates and careful curation, 22 papers conducted in humans were retained. RESULTS: The molecular mechanisms underlying periodontitis are complex and involve the interaction of multiple cells and various gene expressions. Most residing cells in periodontal tissues participate in maintaining homeostasis and health, while in addition to infiltrating immune cells contribute to the fight against the bacterial insult. CONCLUSION: scRNA-seq and ST have provided new insights into the cellular and molecular changes associated with periodontitis for a better diagnosis and clinical outcome. New functions of cells and genes are revealed with these techniques; however, no cells or gene signatures are attributed to periodontitis so far.

CRISPR-Cas9: A cornerstone for the evolution of precision medicine.

Modern genetic therapy incorporates genomic testing and genome editing. It is the finest approach for precision medicine. Genome editing is a state-of-the-art technology to manipulate gene expression thus generating a particular genotype. It encompasses multiple programmable nuclease-based approaches leading to genetic changes. Not surprisingly, this method triggered internationally a wide array of controversies in the scientific community and in the public since it transforms the human genome. Given its importance, the pace of this technology is exceptionally fast. In this report, we introduce one aspect of genome editing, the CRISPR/Cas9 system, highlight its potential to correct genetic mutations and explore its utility in clinical setting. Our goal is to enlighten health care providers about genome editing and incite them to take part of this vital debate.

Regulatory elements and genetic variations in periodontal diseases.

OBJECTIVE: Current evidence suggests that many GWAS and IL1 SNPs are associated with periodontal diseases but their functional role remains ambiguous. Therefore, it is imperative to elucidate the molecular pathways through which these SNPs might act on the development of the disease. The purpose of this review was to highlight the regulatory elements of noncoding regions of the genome and provide insights on the functional role of periodontitis-associated GWAS and IL1 SNPs. DESIGN: A search was performed using ENCODE data available on different browsers. RESULTS: GWAS and IL1 SNPs overlap DNase I hypersensitivity sites, histone modifications and transcription binding sites. Some of these noncoding variants influenced the transcription activity of inflammatory genes. CONCLUSION: SNPs associated with periodontal diseases may contribute to the development of the disorder through their functional roles. Unraveling the character of genetic components might explain the diversity of clinical phenotypes among population groups as well as disease susceptibility.

Smoking and diabetes. Epigenetics involvement in osseointegration.

Bone quality is a poorly defined parameter for successful implant placement, which largely depends upon many environmental and genetic factors unique to every individual. Smoking and diabetes are among the environmental factors that most impact osseointegration. However, there is an inter-individual variability of bone response in smokers and diabetic patients. Recent data on gene-environment interactions highlight the major role of epigenetic changes to induce a specific phenotype. Histone acetylation and DNA methylation are the main events that occur and modulate the gene expression. In this paper, we emphasize the impact of epigenetics on diabetes and smoking and describe their significance in bone healing. Also, we underscore the importance of adopting a new approach in clinical management for implant placement by customizing the treatment according to the patient's specific characteristics.

Host genome, epigenome, and oral microbiome interactions: toward personalized periodontal therapy.

Periodontal diseases are multidimensional and complex. Bacterial content is the initiator, but disease progression depends on genetic and environmental parameters related to the host. Although bone loss magnitude is the common resulting outcome, the biologic process likely represents a unique inflammatory response characteristic to every individual. Therefore, it is obvious that practitioners must take into account the influence of these parameters and tailor a treatment accordingly. New, emerging deoxyribonucleotide-based technologies allow integration of the biologic impact of the environment, and periodontists should be prepared to incorporate these technologies into their practice to advance personalized medicine. This commentary provides updated insights on the distinctiveness of inflammation per individual in terms of microbiome and genome specificity and cites some educational resources helpful for implementing individualized therapy.

BMP-2: biological challenges to its clinical use.

Protein therapy using osteogenic factors is an exciting technique for bone regeneration and implant placement. BMPs are known to stimulate bone formation in ectopic sites; BMP-2 is the most commonly used. In 2007, the FDA approved BMP-2 delivered with an absorbable collagen sponge (ACS) carrier for clinical use in craniofacial deformities. Almost all the publications on BMP-2 showed relatively significant results in augmenting bone at the site of implantation for a period of up to 16 weeks; however, the long-term clinical outcome of BMP-2 application is lacking and yet to be proven reproducible. Many biological obstacles prevent the maintenance and prolonged existence of high bone volume initially formed, thus compromising the long-term implant survival. In this paper, we review these obstacles and highlight their importance in the oral environment. We underscore the ambiguity that has emerged about the safety of BMP-2 in clinical application. Since biology dictates success, we believe at present that any protein therapy for bone regeneration is likely to be ineffective over a long period of time.

Mesenchymal stem cells and their challenges for bone regeneration and osseointegration.

Bone regeneration is an indispensable procedure for implant placement. Original techniques based on mesenchymal stromal cell (MSC) therapy are emerging with the goal of speeding up biology, thereby reducing the osseointegration period. Many products found their way in clinical application, yet their reliability remains uncertain because many in vitro culture-related challenges are facing these cells once they are out of their biologic environment. In this commentary, these limitations are discussed with the emphasis of their impact on the performance of MSCs. Clinicians should be aware of these issues before implementing this cell-based regenerative technique.

Activating transcription factor-2 in survival mechanisms in head and neck carcinoma cells.

BACKGROUND: Activating transcription factor-2 (ATF2) is associated with tumor progression but is not well studied in head and neck squamous cell carcinoma (HNSCC). Its effects in stress and its importance in other survival mechanisms were studied. METHODS: ATF2 expression and nuclear activation were confirmed in HNSCC. After modulation of ATF2, in vitro effects on proliferation and chemosensitivity were studied. Effects on in vivo tumor growth and interleukin 8 (IL-8) expression were determined. Tumor necrosis factor-alpha (TNF-α) treatment was used to further evaluate cytokine production and chemosensitivity. RESULTS: Reductions of ATF2 resulted in significant nuclear p-ATF2 activation, cisplatin resistance, and augmented IL-8 expression without affecting in vivo tumor growth. In this setting, TNF increases p-p38 phosphorylation and chemosensitivity while further enhancing IL-8 production. CONCLUSION: Our data suggest regulatory roles for ATF2 in TNF-related mechanisms of HNSCC. Its perturbation and nuclear activation are associated with significant effects on survival and cytokine production.

Personalized implant therapy: new perspectives in bone remodeling assessment.

Current approaches for immediately loading dental implants rely upon clinical trials and evidence-based practice. Despite their wide utility, these studies have limited predictability because they ignore a whole set of parameters, mainly the environmental parameters that have increasingly influenced the bone biological response. Bone is a very dynamic tissue and its reaction to surgical and functional implant procedures is variable; therefore, bone remodeling must be a key factor in any clinical decision, and a need for reliable tests to evaluate this process is an eventual challenge to implant success. New advances in medicine based upon individual genomic, proteomic and metabolomic studies incorporate the impact of environmental elements, permitting a better targeting of implant therapy. Previously, we proposed a new clinical concept of implant therapy based on personalized bone turnover. Here, we elaborate on current tests and future "omics" biotechnologies to assess the turnover process, hence, providing a realistic approach to individual evaluations of bone remodeling.

Bone remodeling and individual-based implant therapy.

There has been a strong movement in implant dentistry to immediately load implants at time of placement. This movement has been generated by implant manufacturers, who have acceded to patient wishes for faster function and fewer surgeries. Immediate function has been a therapy for tooth extraction and implant replacement and for implant loading at the time of implant placement in edentulous sites. Bone is a dynamic connective tissue and its reaction to surgery is in response to modeling and remodeling. In this paper, the literature of bone remodeling is reviewed, with emphasis on various parameters that modulate this process and have an impact on the healing period of osseointegration and the prognosis for immediate or delayed loading of dental implants. These parameters define a bone phenotype characteristic of each individual. I suggest a new therapeutic concept for implant dentistry that I call "individualized implant therapy".

Detection of apoptotic gene expression in human osteoblast-like cells by cDNA microarrays.

Global gene expression during the induction of ion pair-mediated apoptosis was evaluated by an apoptosis microarray system. Human bone marrow stromal cells were cultured in the presence of 10(-6) M dexamethasone to promote osteogenesis. After 28 days, these cells expressed elevated alkaline phosphatase activity and maintained Cbfa1 expression even when challenged with an apoptogen. Apoptosis was initiated by treating cells with 3 mM Ca(2+) and 5 mM Pi for 4 h. 32P-Labeled mRNA was hybridized to a human apoptosis microarray containing 205 cDNA fragments. We found that apoptosis influenced the expression of 15 genes mainly involved in cell cycle and cell signaling. These genes included IGFBPs and ERK1, known to play a role in cell survival; GST and GST mu, required for maintenance of thiol redox; TNFR1, a gene product that initiates cell death; and finally, BAD, a gene that encodes a proapoptotic protein. Real-time PCR analysis showed that the expression of ERK1, TNFR1, and GST was modulated by 1.89-, 2.66-, and 1.6 fold after 4 h and by 1-, 1.91-, and 1.5 fold, respectively, after 8 h treatment with the ion pair. In addition, we also measured the expression of Bcl-2 and Bax by quantitative RT-PCR. We noted that these two genes were increased 3.07 and 2.99 fold, respectively, after 8 h treatment with the apoptogen. Results of this study suggest that the ion pair influenced ERK1 and TNFR1 signaling pathways and affected thiol metabolism, whereas Bcl-2 and Bax were expressed at late stages of the death process.