Homo sapiens
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1121421 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Periodontitis is a chronic inflammatory disease resulting from a dysbiosis of the dental biofilm and a dysregulated host response in susceptible individuals. It is characterized by periodontal attachment destruction, bone resorption, and eventual tooth loss. Salivary biomarkers have been sought to predict and prevent periodontitis. This comparative study analyzed the salivary proteome of 30 individuals with chronic periodontitis (CP) and 10 with periodontal health (PH), and correlated specific proteins with clinical parameters of disease by using mass spectrometry. Stimulated whole saliva was obtained and pooled for 5 healthy controls and 15 CP patients, precipitated with TCA, digested enzymatically with trypsin and analyzed by an LTQ Orbitrap Velos equipped with a nanoelectrospray ion source. A wide range of salivary proteins of various functions was significantly reduced in CP individuals, whereas salivary acidic proline-rich phosphoprotein, submaxillary gland androgen-regulated protein, histatin, fatty acid-binding protein, thioredoxin, and cystatin were predominant in diseased patients and correlated significantly with signs of periodontal attachment loss and inflammation. Specific salivary proteins were associated with PH and CP. These differences in salivary proteome profiles may contribute to the identification of disease indicators or signatures and the improvement of periodontal diagnosis.
2020-05-20 | PXD015024 | Pride
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: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:This study profiles single-cell transcriptomes derived from human periodontal granulation tissue collected during routine periodontal surgery at Guy’s Hospital, King’s College London. Tissue was harvested following step 1 and step 2 periodontal treatment. Following dissociation and quality control, libraries were prepared using the 10x Genomics Chromium Single Cell 3’ kit and sequenced on an Nextseq 2000. The study aimed to elucidate cellular heterogeneity in periodontal lesions in otherwise healthy individuals.
2025-10-23 | GSE294615 | GEO
Project description:To gain insights into the in vivo function of miRNAs in the context of periodontitis, we examined the occurrence of miRNAs in healthy and diseased gingival tissues and validated their in silico-predicted targets through mRNA profiling using whole-genome microarrays in the same specimens. Eighty-six individuals with periodontitis contributed 198 gingival papillae: 158 'diseased' (bleeding-on-probing, PD > 4 mm, and AL ≥ 3 mm) and 40 'healthy' (no bleeding, PD ≤ 4 mm, and AL ≤ 2 mm). Expression of 1,205 miRNAs was assessed by microarrays, followed by selected confirmation by quantitative RT-PCR. Predicted miRNA targets were identified and tested for enrichment by Gene Set Enrichment Analysis (GSEA). Enriched gene sets were grouped in functional categories by DAVID and Ingenuity Pathway Analysis. One hundred fifty-nine miRNAs were significantly differentially expressed between healthy and diseased gingiva. Four miRNAs (hsa-miR-451, hsa-miR-223, hsa-miR-486-5p, hsa-miR-3917) were significantly overexpressed, and 7 (hsa-miR-1246, hsa-miR-1260, hsa-miR-141, hsa-miR-1260b, hsa-miR-203, hsa-miR-210, hsa-miR-205*) were underexpressed by > 2-fold in diseased vs. healthy gingiva. GSEA and additional filtering identified 60 enriched miRNA gene sets with target genes involved in immune/inflammatory responses and tissue homeostasis. This is the first study that concurrently examined miRNA and mRNA expression in gingival tissues and will inform mechanistic experimentation to dissect the role of miRNAs in periodontal tissue homeostasis and pathology.
2014-02-05 | GSE54710 | GEO
Project description:<h4><strong>BACKGROUND AND HYPOTHESIS: </strong>It is presently unclear why there is a high prevalence of periodontal disease in individuals living with chronic kidney disease. Whilst some have argued that periodontal disease causes chronic kidney disease, we hypothesized that alterations in saliva and the oral microenvironment in organisms with kidney disease may initiate periodontal disease by causing dysbiosis of the oral microbiota.</h4><h4><strong>METHODS: </strong>Experimental kidney disease was created using adenine feeding and subtotal nephrectomy in rats, and by adenine feeding in mice. Loss of periodontal bone height was assessed using a dissecting microscope supported by micro-CT, light, confocal and electron microscopy, and immunohistochemistry. Salivary biochemistry was assessed using NMR spectroscopy. The oral microbiome was evaluated using culture-based and molecular methods, and the transmissibility of dysbiosis was assessed using co-caging and microbial transfer experiments into previously germ-free recipient mice.</h4><h4><strong>RESULTS: </strong>We demonstrate that experimental kidney disease causes a reproducible reduction of alveolar bone height, without gingival inflammation or overt hyperparathyroidism but with evidence of failure of bone formation at the periodontal crest. We show that kidney disease alters the biochemical composition of saliva and induces progressive dysbiosis of the oral microbiota, with microbial samples from animals with kidney disease displaying reduced overall bacterial growth, increased alpha diversity, reduced abundance of key components of the healthy oral microbiota such as Streptococcus and Rothia, and an increase in minor taxa including those from gram-negative phyla Proteobacteria and Bacteroidetes. Co-housing diseased rats with healthy ones ameliorates the periodontal disease phenotype, whilst transfer of oral microbiota from mice with kidney disease causes periodontal disease in germ-free animals with normal kidney function.</h4><h4><strong>CONCLUSIONS: </strong>We advocate that periodontal disease should be regarded as a complication of kidney disease, initiated by oral dysbiosis through mechanisms independent of overt inflammation or hyperparathyroidism.</h4>
2025-09-04 | MTBLS1833 | MetaboLights
Project description:To gain insights into the in vivo function of miRNAs in the context of periodontitis, we examined the occurrence of miRNAs in healthy and diseased gingival tissues and validated their in silico-predicted targets through mRNA profiling using whole-genome microarrays in the same specimens. Eighty-six individuals with periodontitis contributed 198 gingival papillae: 158 'diseased' (bleeding-on-probing, PD > 4 mm, and AL M-bM-^IM-% 3 mm) and 40 'healthy' (no bleeding, PD M-bM-^IM-$ 4 mm, and AL M-bM-^IM-$ 2 mm). Expression of 1,205 miRNAs was assessed by microarrays, followed by selected confirmation by quantitative RT-PCR. Predicted miRNA targets were identified and tested for enrichment by Gene Set Enrichment Analysis (GSEA). Enriched gene sets were grouped in functional categories by DAVID and Ingenuity Pathway Analysis. One hundred fifty-nine miRNAs were significantly differentially expressed between healthy and diseased gingiva. Four miRNAs (hsa-miR-451, hsa-miR-223, hsa-miR-486-5p, hsa-miR-3917) were significantly overexpressed, and 7 (hsa-miR-1246, hsa-miR-1260, hsa-miR-141, hsa-miR-1260b, hsa-miR-203, hsa-miR-210, hsa-miR-205*) were underexpressed by > 2-fold in diseased vs. healthy gingiva. GSEA and additional filtering identified 60 enriched miRNA gene sets with target genes involved in immune/inflammatory responses and tissue homeostasis. This is the first study that concurrently examined miRNA and mRNA expression in gingival tissues and will inform mechanistic experimentation to dissect the role of miRNAs in periodontal tissue homeostasis and pathology. The dataset comprise 200 gingival tissue samples from 86 patients with periodontitis. All samples are included in this series, but 2 where not included in the study, as they did not pass our QC. Each patient has one or more healthy and disease sample and samples can be of chronic or aggressive periodontitis type.
2014-02-05 | E-GEOD-54710 | biostudies-arrayexpress
Project description:Over the last years, proteomic techniques have been demonstrated to be valuable tools for analysing the periodontal proteome in saliva samples, contributing to identifying extensive and comprehensive protein profiles associated with periodontitis. However, the periodontal proteome has not yet been studied using sequential window acquisition of all theoretical mass spectra (SWATH-MS). Consequently, the objective of the present longitudinal research was to study the periodontal proteome in saliva in three clinical conditions (periodontal health, untreated periodontitis, and treated periodontitis), applying SWATH-MS to 1) analyse the periodontal proteome structure in the three clinical groups, 2) compare the differential protein expression between the three clinical groups, and 3) evaluate the diagnostic accuracy of the proteins quantified to identify new biomarkers with a high capacity to discriminate the three clinical conditions. A total of 85 subjects, 44 periodontally healthy and 41 with generalised untreated periodontitis in stages III-IV, were included, and saliva samples were collected. The diagnosis of periodontal status was conducted by two experienced dentists using clinical and radiographic criteria. The definition of periodontal status was established following the Classification of Periodontal Diseases and Conditions published in 2018. In the untreated periodontitis group, 38 underwent conventional non-surgical treatment and were evaluated clinically after two months (treated periodontitis group). In the revaluation, 36 individuals showed significant clinical improvement in the mean full-mouth probing pocket depth (PPD) value, and saliva samples were collected from them.
2025-04-23 | PXD043491 | Pride
Project description:Over the last years, proteomic techniques have been demonstrated to be valuable tools for analysing the periodontal proteome in gingival crevicular fluid (GCF) samples contributing to identifying extensive and comprehensive protein profiles associated with periodontitis. However, the periodontal proteome has not yet been studied using sequential window acquisition of all theoretical mass spectra (SWATH-MS). Consequently, the objective of the present longitudinal research was to investigate the periodontal proteome in GCF in three clinical conditions (periodontal health, untreated periodontitis, and treated periodontitis), applying SWATH-MS to 1) analyse the periodontal proteome structure in the three clinical groups, 2) compare the differential protein expression between the three clinical groups, and 3) evaluate the diagnostic accuracy of the proteins quantified to identify new biomarkers with a high capacity to discriminate the three clinical conditions. A total of 84 subjects, 44 periodontally healthy and 40 with generalised untreated periodontitis in stages III-IV, were included, and GCF samples were collected. The diagnosis of periodontal status was conducted by two experienced dentists using clinical and radiographic criteria. The definition of periodontal status was established following the Classification of Periodontal Diseases and Conditions published in 2018. In the untreated periodontitis group, 38 underwent conventional non-surgical treatment and were evaluated clinically after two months (treated periodontitis group). In the revaluation, 25 individuals showed significant clinical improvement in probing pocket depth (PPD) at the selected sites, and GCF samples were collected from them.
2024-10-17 | PXD043474 | Pride