Inferring RBP-mediated regulation in lung squamous cell carcinoma

RNA-binding proteins (RBPs) play key roles in post-transcriptional regulation of mRNAs. Dysregulations in RBP-mediated mechanisms have been found to be associated with many steps of cancer initiation and progression. Despite this, previous studies of gene expression in cancer have ignored the effect of RBPs. To this end, we developed a lasso regression model that predicts gene expression in cancer by incorporating RBP-mediated regulation as well as the effects of other well-studied factors such as copy-number variation, DNA methylation, TFs and miRNAs. As a case study, we applied our model to Lung squamous cell carcinoma (LUSC) data as we found that there are several RBPs differentially expressed in LUSC. Including RBP-mediated regulatory effects in addition to the other features significantly increased the Spearman rank correlation between predicted and measured expression of held-out genes. Using a feature selection procedure that accounts for the adaptive search employed by lasso regularization, we identified the candidate regulators in LUSC. Remarkably, several of these candidate regulators are RBPs. Furthermore, majority of the candidate regulators have been previously found to be associated with lung cancer. To investigate the mechanisms that are controlled by these regulators, we predicted their target gene sets based on our model. We validated the target gene sets by comparing against experimentally verified targets. Our results suggest that the future studies of gene expression in cancer must consider the effect of RBP-mediated regulation.No sponso

Detection of Helicobacter pylori using PCR in dental plaque of patients with and without gastritis

Objectives: Helicobacter pylori (H. pylori) accounts for gastritis, peptic ulcer and is a probable cause of gastric cancer. Since its detection in the oral cavity, concerns have been raised about dental plaque as a reservoir for reinfection. The aim of this study was to detect the organism in the dental plaque and to determine the association, if any, between H. pylori gastritis and dental plaque contamination causing H. pylori. Study design: A polymerase chain reaction-based method was used for detection of H. pylori in clinical specimens. Supra and subgingival samples were collected from 67 patients with chronic periodontitis, 23 of whom were also suffering from gastritis. The data were analyzed with Chi square and Fisher exact test and the statistical significance was set to 0.05. Results: H. pylori was scarce in patients with periodontitis(5.9%). There was a significant association between the presence of H. pylori in the dental plaque and gastritis (p=0.012). Conclusions: Although rarely seen, H. pylori infected dental plaque may be a source for reinfection. It is therefore suggested that professional plaque removal and oral hygiene procedures be performed, along with the antibiotic treatment of H. pylori

A comparative study of the long term results of root coverage with connective tissue graft or enamel matrix protein: 24-month results

Background: The objective of this study was to compare the 24 month results of coronally advanced fl ap + enamel matrix derivates (EMD+CAF) and CAF+ connective tissue graft (CTG+CAF) in the treatment of Miller Class I recession defects.Methods: Twelve patients with bilateral gingival recessions were treated with EMD+CAF or CTG+CAF. Vertical recession depth (VRD), keratinized tissue width (KTW), clinical attachment level (CAL), and clinical probing depth (CPD) were measured preoperatively, 1 and 2 years post surgery. A paired t-test and independent t-test were used to compare differences for the measured characters within and between groups, respectively.Results: After 24 months a signifi cant decrease in VRD was observed in CAF + EMD (3.33±0.30 mm) and CAF + CTG (4.5 ± 0.28 mm) treated sites. There was also a signifi cant increase in KTW (0.83±0.23 mm versus 2.08±0.14 mm in EMD+CAF and CTG+CAF sites, respectively). The gain in CAL was 3.54 ± 0.38 mm and 4.45±0.30 mm in EMD+CAF and CTG+CAF group, respectively. There were signifi cant differences between the treatments for VRD, CAL, and KTW at the end of study.Conclusions: The CTG+CAF procedure seems to provide better long-term results than the EMD+CAF in obtaining root coverage, increasing the KTW and CAL gain

Enamel matrix derivative Emdogain® as an adjuvant for a laterally-positioned flap in the treatment of gingival recession: an electron microscopic appraisal

Enamel matrix derivative (EMD), such as Emdogain®, has been suggested for the improvement of wound healing in periodontal surgical therapy. The present qualitative study seeks to illustrate the ultrastructural changes associated with a human gingival wound at 10 days after the application of EMD as an adjunct to a laterally-positioned flap in a patient with gingival recession. An otherwise healthy patient, who had been suffering from bilateral gingival recession defects on teeth #23 and #26, was studied. One defect was treated with a laterally-positioned flap, while the other was treated with a combination of EMD and a laterally-positioned flap. Ten days after the operation gingival biopsy specimens were obtained from the dentogingival region and examined using a transmission electron microscope. A considerable difference was found in both the cellular and extracellular phases of EMD and non-EMD sites. The fibroblasts of EMD site were more rounded with plump cytoplasms and euchromatic nuclei. A well-developed rough endoplasmic reticulum and numerous mitochondria could be detected. In contrast, the fibroblasts of non-EMD site were of flattened spindle-like morphology. While the signs of apoptosis could rarely be detected at EMD site, apoptotic bodies and ultra-structural evidence of apoptosis (crescent-like heterochromatic nuclei and dilated nuclear envelopes) were consistent features at non-EMD site. The extracellular matrix at EMD site mainly consisted of well-organised collagen fibres, while non-EMD site contained sparse and incompletely-formed collagen fibres. Coccoid bacteria were noted within the extracellular matrix and neutrophils at non-EMD site. It seems that EMD may enhance certain features of gingival wound healing, which may be attributable to its anti-apoptotic, anti-bacterial or anti-inflammatory properties

Amlodipine-induced gingival hyperplasia

Drug-induced gingival hyperplasia is a serious concern both for the patient and the clinician. A 45 year-old Caucasian male patient with hypertension, who received amlodipine (10 mg/day, single dose orally) for two months, sought medical attention because of the new-onset gingival enlargement. On clinical examination a generalized and firm overgrowth of the gingival throughout the maxilla and the mandible were evident. The lack of gingival inflammation and purulent discharge were other features of the clinical scenario. Histological assessment of the biopsy specimen revealed the hyperplasia of connective tissue, epithelial acanthosis, and elongated rete ridges along with few inflammatory cells. The histological and the clinical evidences were consistent with amlodipine-induced gingival hyperplasia. We believe that the present report indicates the most rapidly developed case of amlodipine-induced gingival hyperplasia reported to date. The related literature is reviewed and the underlying pathogenic mechanisms of this rare side-effect are discussed here

Comparison of salivary level of leptin in chronic periodontitis patients and healthy controls

Objectives Periodontal disease is an inflammatory condition of the tooth-supporting structures. Leptin is a hormone produced by the human body under different circumstances such as infection. It affects the production of cytokines, phagocytosis and the inflammation process. This study aimed to compare the salivary level of leptin in chronic periodontitis (CP) patients and healthy controls.Methods In this case-control study, saliva samples were collected from 43 subjects including 22 CP patients and 21 healthy controls. The salivary level of leptin was determined using the ELISA. Data were analyzed by the independent t-test.Results Despite the presence of leptin in the saliva of CP patients and healthy controls, no significant difference was noted in its salivary concentration between the two groups (p>0.05).Conclusion The salivary level of leptin in CP patients was not significantly different from that in healthy controls. Further studies with larger sample size are required to confirm the results of this stud

The Clinical Evaluation of the Effects of Low-Level Laser Therapy on the Donor and Recipient Sites of the Free Gingival Graft: A Case Series

Introduction: Free gingival grafting is among the most foreseeing procedures for increasing the zone of keratinized attached gingiva and enhancing soft tissue around the teeth and dental implants. Nowadays low-level laser therapy (LLLT) is a promising approach in providing patients with more pleasing results in terms of esthetics and comfort. This study aims to investigate the effects of LLLT on gingival recessions treated with free gingival graft (FGG).Methods: This case series was conducted on 12 individuals requiring a bilateral gingival graft in the mandibular region. There was a 30-day interval between the two operations. The test side was selected randomly and irradiated by a low-level laser (LLL) just before surgery. The patients did not know which side was irradiated. LLLT was applied to the donors’ as well as recipients’ site immediately after the operation and 48 hours later. The patients were instructed to record their post-operative pain in a visual analogue scale (VAS) 3 and 24 hours and 7 days after the surgical procedure. The clinical photographs were taken immediately and 30 days after surgical treatment were graded by three experienced periodontists for color matching to adjacent tissues.Results: Ten individuals could finish the study. The test group presented significantly better shade matching and wound healing at the palatal donor site on days 7, 14 and 21. There was a significant reduction in postoperative pain after 24 hours (P = 0.007). No statistically significant difference was found between both groups in terms of clinical periodontal indices.Conclusion: LLLT could reduce post-operative pain 24 hours after surgical treatment. Furthermore, the application of LLLT could improve the donors’ site healing and the recipients’ site color matching

Assessment of Sterility and Residual Solvents Agents in Antler-derived and Bovine Xenograft Bone Substitutes: An In-vitro Study

Objectives This study aimed to assess and compare the results of sterility and residual solvent testing in a newly developed antler-derived xenograft versus a bovine-derived xenograft. Methods First, test and control samples were prepared using thermal and chemical procedures, involving immersion in deionized water for 24 hours, drying, boiling in sterile water, chemical treatment with chloroform and methanol, and heating at 650°C in a furnace. Next, they were sterilized via gamma radiation at 25 kGy. The sterility test was then performed based on the ISO 11737-2:2019 standard, using the direct inoculation method. Finally, residual solvent testing was carried out via gas chromatography-mass spectrometry. Results The sterility test showed no evidence of bacterial or fungal growth in any of the samples during 14 days of incubation. Also, residual solvent testing indicated no sign of residual solvents in the samples. Conclusion Antler-derived xenograft was safe to use in terms of the sterility and removal of residual solvents. Further studies should be carried out regarding other important laboratory tests as well as the animal and clinical studies

Modeling the combined effect of RNA-binding proteins and microRNAs in post-transcriptional regulation

Recent studies show that RNA-binding proteins (RBPs) and microRNAs (miRNAs) function in coordination with each other to control post-transcriptional regulation (PTR). Despite this, the majority of research to date has focused on the regulatory effect of individual RBPs or miRNAs. Here, we mapped both RBP and miRNA binding sites on human 3′UTRs and utilized this collection to better understand PTR. We show that the transcripts that lack competition for HuR binding are destabilized more after HuR depletion. We also confirm this finding for PUM1(2) by measuring genome-wide expression changes following the knockdown of PUM1(2) in HEK293 cells. Next, to find potential cooperative interactions, we identified the pairs of factors whose sites co-localize more often than expected by random chance. Upon examining these results for PUM1(2), we found that transcripts where the sites of PUM1(2) and its interacting miRNA form a stem-loop are more stabilized upon PUM1(2) depletion. Finally, using dinucleotide frequency and counts of regulatory sites as features in a regression model, we achieved an AU-ROC of 0.86 in predicting mRNA half-life in BEAS-2B cells. Altogether, our results suggest that future studies of PTR must consider the combined effects of RBPs and miRNAs, as well as their interactions.No sponso

Towards High Quality Single-cell Experiments: Approaches, Applications and Performance

[eng] Single-cell RNA sequencing has revolutionized the way molecular mechanisms were being studied by allowing the dissection of gene expression at single-cell resolution. The data acquired from scRNA-seq provides great opportunities for scientist to push the limits and go beyond technological boundaries to address biological questions. However, a thoroughly thought experimental design, protocol selection and data analysis strategies are necessary to get the best out of this high potential technology. In this thesis we start with summarizing current methodological and analytical options, and discuss their suitability for a range of research scenarios. We provide information about best practices in every step from separating cells and RNA library preparation to data generation, normalization and analysis. Next, we try to address a biological phenomenon using scRNA-seq. We demonstrate how a correctly designed scRNA-seq experiment and analysis is able to capture in details the process of dermal fibroblast aging. Observing the data produced by different scRNA-seq protocols, their important differences and the challenge to analyse them together, raised the question of their suitability specially in cell atlas projects. Hence, in a big multi-center systematic study we compared 13 commonly used single-cell and single-nucleus RNA-seq protocols using a highly heterogeneous reference sample resource. We pointed at their accuracy, application across distinct cell properties, potential to disclose tissue heterogeneity, reproducibility and integratability with other methods; features in which should be considered when defining guidelines and standards for international consortia, such as the Human Cell Atlas project. Finally, we propose an approach to elevate the data from poor-performing protocols to the quality of the best data coming from best-performing ones using variational autoencoders and vector arithmetic