Transcriptome sequencing of gingival tissues from impacted third molars patients reveals the alterations of gene expression
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ABSTRACT:
PROVIDER: PRJNA683802 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR13224386_1.fastq.gz | Fastqsanger.gz | |||
| SRR13224386_2.fastq.gz | Fastqsanger.gz | |||
| SRR13224387_1.fastq.gz | Fastqsanger.gz | |||
| SRR13224387_2.fastq.gz | Fastqsanger.gz | |||
| SRR13224388_1.fastq.gz | Fastqsanger.gz |
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Project description:This first transcriptome analysis of gingival tissues from patients with surgical removal of impacted third molars provides new insights into postoperative genetic changes. The results may establish a basis for future research on minimizing the incidence of complications after flap-treated third molars.
2023-12-01 | GSE162912 | GEO
Project description:Impacted mandibular third molars (M3M) are associated with the occurrence of distal caries on the adjacent mandibular second molars (DCM2M). In this study, we aimed to develop and validate five machine learning (ML) models designed to predict the occurrence of DCM2Ms due to the proximity with M3Ms and determine the relative importance of predictive variables for DCM2Ms that are important for clinical decision making. A total of 2642 mandibular second molars adjacent to M3Ms were analyzed and DCM2Ms were identified in 322 cases (12.2%). The models were trained using logistic regression, random forest, support vector machine, artificial neural network, and extreme gradient boosting ML methods and were subsequently validated using testing datasets. The performance of the ML models was significantly superior to that of single predictors. The area under the receiver operating characteristic curve of the machine learning models ranged from 0.88 to 0.89. Six features (sex, age, contact point at the cementoenamel junction, angulation of M3Ms, Winter's classification, and Pell and Gregory classification) were identified as relevant predictors. These prediction models could be used to detect patients at a high risk of developing DCM2M and ultimately contribute to caries prevention and treatment decision-making for impacted M3Ms.
| S-EPMC8322059 | biostudies-literature
Project description:We examined gene expression signatures in healthy and diseased gingival tissues in 90 patients. Analysis of the gingival tissue transcriptome in states of periodontal health and disease may reveal novel insights of the pathobiology of periodontitis. Keywords: gingival tissue disease state analysis
2008-12-22 | GSE10334 | GEO
Project description:ObjectiveThe aim of this research was to evaluate the surgical complications and neurosensory deficits after coronectomy and the complete removal of mandibular third molars.MethodsThe study sample included patients requiring surgical removal of mandibular third molars. A coronectomy was conducted on 220 teeth showing signs of close proximity to the inferior alveolar canal. A complete extraction was performed on 218 teeth with no risk signs. The patients were evaluated at 1 week and 1, 3, 6, 12, and 24 months after surgery for pain, swelling, neurologic deficit, dry socket, postoperative bleeding, infection, root migration, and eruption.ResultsNo significant difference was noted in pain and swelling; however, bleeding and dry socket were significantly higher in the odontectomy group (P = .017). The inferior alveolar nerve deficit was higher in the odontectomy group (3.7%) than the coronectomy group (0.5%) (P = .017). The percentage and distance of root migration of coronectomised teeth at 3, 6, and 12 months were 60% (2.37 ± 0.96 mm), 66% (3.35 ± 0.86 mm), and 74% (3.85 ± 0.93 mm), respectively.ConclusionsCoronectomy is a safe procedure and should be performed when the roots are closely associated with the mandibular canal. Although root migration is common, the likelihood of root exposure is low and roots rarely need removal.
| S-EPMC10988245 | biostudies-literature
Project description:Fibroblasts are widely used cells for regenerative medicine in clinics, such as gingival or facial skin treatment. In fact, fibroblasts are considered as a mixture of various types of cells with "spindle shape" and there is no available clear marker. Gingival and dermal fibroblasts are similar in their morphology and function; however it is considered that the cultured cells retain their original characteristics depending on the origin, which may contribute to the differential therapeutic effects. For example, gingival wounds are known to heal relatively quickly with less scar formation compared with skin, which may imply their higher capability for regeneration as a therapeutic effect. The reason for this phenomenon may be partly due to characteristic differences between gingival and dermal fibroblasts including the expression of migration stimulating factor and matrix formation but these differences remain largely unknown. Recently, the characteristics of dermal fibroblasts have been reported to be different depending on body sites, such as face, trunk and plamoplantar skin. Although the expression of fibronectin and their splicing variants were known to be different between trunk and oral mucosal fibroblasts, there is still no detailed report on the functional differences between gingival and dermal fibroblasts. In this study, we investigated differential gene expression in normal gingival and dermal fibroblasts using DNA microarray to investigate the difference between the vague fibroblast-type cells from different tissue origin to achieve higher therapeutic effect in cell therapy.
2010-05-28 | GSE22029 | GEO
Project description:This study aimed to compare a flapless surgical approach (FSA) with a traditional envelope flap (traditional approach (TA)). Every patient was treated with two approaches: TA and FSA. The primary outcome variables were both the discomfort during the post-operative convalescence and the correct final recovery of the impacted area. The secondary outcome variable was the average duration of the surgery. Post-operative pain and oedema were recorded. The measurements of soft tissue interface toward the distobuccal edge of the second molar were taken by periodontal probe before surgery (baseline) and 8 weeks after surgery. Statistical software was used to evaluate the data; a p-value < 0.05 was considered statistically significant. Twenty-four teeth of 12 patients (six Caucasian males and six Caucasian females, aged 23 ± 4 (17-30) years) with both lower impacted third molars (Ms3) were analysed. Considering an alpha error 0.05 that sample size allows power from 0.80 to 0.90, depending on the variable evaluated. Concerning attached gingiva, oedema and pain, the linear mixed model resulted in a statistically significant difference between the TA and FSA (p = 0.003; p < 0.01; and p = 0.018, respectively). Conversely, the model did not show a difference (p = 0.322) if pocket probing depth was considered. The FSA procedure was faster (p < 0.05) than the TA procedure (17 min and 8 s (±6 s) vs. 28 min and 6 s (±4 s), respectively). The results suggest that the FSA could be a suitable option for improving the surgical removal of lower Ms3. However, additional randomized controlled trial studies are necessary to confirm the reliability of our procedure and to verify its suitability in more complex Ms3 classifications.
| S-EPMC7914559 | biostudies-literature
Project description:We examined gene expression signatures in healthy and diseased gingival tissues in 90 patients. Analysis of the gingival tissue transcriptome in states of periodontal health and disease may reveal novel insights of the pathobiology of periodontitis. Keywords: gingival tissue disease state analysis Ninety non-smokers, 63 with chronic and 27 with aggressive periodontitis, each contributing with >=2 “diseased” interproximal papillae (with bleeding on probing, probing pocket depth >=4mm, and clinical attachment loss >=3mm) and a “healthy” papilla, if available (no BoP, PPD<=4mm and CAL<=2mm). RNA was extracted, amplified, reverse transcribed, labeled, and hybridized with AffymetrixU133Plus2.0 arrays. Transcriptome analysis was conducted on a total of 247 samples (from 183 diseased and 64 healthy sites).
2008-12-22 | E-GEOD-10334 | biostudies-arrayexpress
Project description:Background:The prophylactic extraction of third molars is a common practice in dental offices, but divergent opinions are found in the literature regarding the indication of this procedure. The aim of the present study was to determine the prevalence of pathological changes associated with the pericoronal tissue of asymptomatic impacted third molars that could justify prophylactic extraction. Materials and Methods:A cross-sectional observational study was conducted in which 109 pericoronal tissues with no radiographic evidence of pathology were histopathologically analyzed. The specimens were fixed in 10% formalin, embedded in paraffin, stained with hematoxylin and eosin and analyzed individually by two pathologists. Result:The frequency of inflammatory infiltrate in the dental follicle of patients older than 20 years of age was significantly higher than that of younger patients (p?=?0.004), demonstrating an association between inflammation in the dental follicle and patient age. The occurrence of squamous metaplasia was also greater in patients older than 20 years (p?=?0.042), demonstrating that the prevalence of squamous metaplasia increases with age. A significant association was also found between inflammation and squamous metaplasia (p?<?0.001). Conclusion:Pathological changes may be present in the dental follicle of impacted third molars even in the absence of clinical or radiographic signs of disease.
| S-EPMC6181856 | biostudies-literature
Project description:The aim of this systematic review is to evaluate and compare the risks and benefits of germectomy and delayed removal of third molars and develop a patient management algorithm for second molar eruption in syndrome/incompliant patients. A literature search was performed in the following databases; the Cochrane Central Register of Controlled Trials (CENTRAL), PubMed, Scopus, and Web of Science. Last search was done on July 2nd, 2018 including articles published from the last 18 years. The search aimed to identify all relevant studies written in English language. Gray literature was excluded. Risk of bias was evaluated with specific predetermined criteria. This systematic literature review was reported according to the PRISMA-P statement and was registered in the PROSPERO database with the following protocol ID: 104261. Literature search war performed on July 2018 and updated on February 2019. A total of 1610 articles were screened. After abstract screening and discarding duplicates, 86 full-text articles were obtained and subjected to additional evaluation. Four articles were included in the review. Three studies were considered as having a medium risk of bias and one was assessed as at high risk. Due to the heterogeneity of presenting results and a very low number of included studies a quantitative analysis was not possible. Only qualitative analysis was made. Considering the limited number of studies included and the level of risk of bias there is no sufficient evidence to state the benefits of preventive removal of impacted third molars, especially in patients with poor oral hygiene due to intellectual disability. Early germectomy represents an elective approach of pathologic alteration of tooth germ; orthodontic issues meet appropriate indication for a delayed removal. Given the best evidence-based information regarding patients' medical condition, we highlight the need to provide an ethical-based comprehensive approach in the diagnostic workflow and the assessment of treatment outcome.
| S-EPMC6473914 | biostudies-literature
Project description:Fibroblasts are widely used cells for regenerative medicine in clinics, such as gingival or facial skin treatment. In fact, fibroblasts are considered as a mixture of various types of cells with "spindle shape" and there is no available clear marker. Gingival and dermal fibroblasts are similar in their morphology and function; however it is considered that the cultured cells retain their original characteristics depending on the origin, which may contribute to the differential therapeutic effects. For example, gingival wounds are known to heal relatively quickly with less scar formation compared with skin, which may imply their higher capability for regeneration as a therapeutic effect. The reason for this phenomenon may be partly due to characteristic differences between gingival and dermal fibroblasts including the expression of migration stimulating factor and matrix formation but these differences remain largely unknown. Recently, the characteristics of dermal fibroblasts have been reported to be different depending on body sites, such as face, trunk and plamoplantar skin. Although the expression of fibronectin and their splicing variants were known to be different between trunk and oral mucosal fibroblasts, there is still no detailed report on the functional differences between gingival and dermal fibroblasts. In this study, we investigated differential gene expression in normal gingival and dermal fibroblasts using DNA microarray to investigate the difference between the vague fibroblast-type cells from different tissue origin to achieve higher therapeutic effect in cell therapy. Gingival and dermal tissues were collected from healthy patients. After successive stages primary culture and RNA extraction and hybridization on Affymetrix microarrays (Genome Focus Array). Dermal and gingival tissues were obtained from healthy volunteers (8 cases for dermal tissue; 6 females, 2 males , average age 48 and 8 cases for buccal gingival tissue; 6 females, 2 males, average age 43) whose informed consent was obtained according to a protocol approved by the ethics committee of Nagoya University Hospital. After enzymatic digestion, tissues were cultured in Dulbecco's modified Eagle's medium (DMEM) containing 10% fetal bovine serum at 37°C in the presence of 5% CO2 for about 4 weeks as reported previously. Total mRNAs were extracted from cells between passages 4-5 by Trizol reagent (Invitrogen, Carlsbad, CA, USA) and were applied to Human Focus Arrays (Affymetrix, Santa Clara, CA, USA) for microarray analysis according to the manufacturer's protocol (http://www.affymetrix.com/support/technical/manuals.affx). The gene expression data were analyzed by Arrayassist (Stratagene, La Jolla, CA, USA). Briefly, 8,500 probes on the array, normalization and scaling (MAS5), flag-positive gene selection, unpaired t-test, and CV selection (<20) resulted in 5,284 genes to analyze. GO (Gene ontology) analysis was performed using the software default settings to find the gene group related to the same category of biological function by searching common key terms that were reported for each gene.
2010-06-08 | E-GEOD-22029 | biostudies-arrayexpress