Cellular Modifications Research Articles

IDH1R132H Promotes Malignant Transformation of Benign Prostatic Epithelium by Dysregulating MicroRNAs: Involvement of IGF1R-AKT/STAT3 Signaling Pathway

Risk stratification using molecular features could potentially help distinguish indolent from aggressive prostate cancer (PCa). Mutations in isocitrate dehydrogenase (IDH) acquire an abnormal enzymatic activity, resulting in the production of 2-hydroxyglutarate and alterations in cellular metabolism, histone modification, and DNA methylation. Mutant IDH1 has been identified in various human malignancies, and IDH1R132H constituted the vast majority of mutational events of IDH1. Most recent studies suggested that IDH1 mutations define a methylator subtype in PCa. However, the function of IDH1R132H in PCa development and progression is largely unknown. In this study, we showed that the prevalence of IDH1R132H in Chinese PCa patients is 0.6% (2/336). Of note, IDH1R132H-mutant PCa patients lacked other canonical genomic lesions (e.g., ERG rearrangement, PTEN deletion) that are common in most other PCa patients. The in vitro experiment suggested that IDH1R132H can promote proliferation of benign prostate epithelial cell RWPE-1 when under the situation of low cytokine. It could also promote migration capacity of RWPE-1 cells. Mechanistically, IDH1R132H was an important regulator of insulin-like growth factor 1receptor (IGF1R) by downregulating a set of microRNAs (miR-141-3p, miR-7-5p, miR-223-3p). These microRNAs were repressed by the alteration of epigenetic modification to decrease the enrichment of active marker H3K4me3 or to increase repressive marker H3K27me3 at their promoters. Collectively, we proposed a novel model for an IDH1R132H-microRNAs-IGF1R regulatory axis, which might provide insight into the function of IDH1R132H in PCa development.

Cellular metabolism modification of 2, 3, 5, 4'-Tetrahydroxystilbene-2-O-β-D-glucoside through Nrf2 Related Gene Expression

Cellular metabolism modification of 2, 3, 5, 4'-Tetrahydroxystilbene-2-O-β-D-glucoside through Nrf2 Related Gene Expression

Association of Genetic Variants of Small Non-Coding RNAs with Survival in Colorectal Cancer.

Background: Single nucleotide polymorphisms (SNPs) of small non-coding RNAs (sncRNAs) can influence sncRNA function and target gene expression to mediate the risk of certain diseases. The aim of the present study was to evaluate the prognostic relevance of sncRNA SNPs for colorectal cancer, which has not been well characterized to date.Methods: We comprehensively examined 31 common SNPs of sncRNAs, and assessed the impact of these variants on survival in a cohort of 188 patients with colorectal cancer.Results: Three SNPs were significantly associated with survival of patients with colorectal cancer after correction for multiple testing, and two of the SNPs (hsa-mir-196a-2 rs11614913 and U85 rs714775) remained significant in multivariate analyses. Additional in silico analysis provided further evidence of this association, since the expression levels of the target genes of the hsa-miR-196a (HOXA7, HOXB8, and AKT1) were significantly correlated with colorectal cancer progression. Furthermore, Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses indicated that hsa-miR-196a is associated with well-known oncogenic pathways, including cellular protein modification process, mitotic cell cycle, adherens junction, and extracellular matrix receptor interaction pathways.Conclusion: Our results suggest that SNPs of sncRNAs could play a critical role in cancer progression, and that hsa-miR-196a might be a valuable biomarker or therapeutic target for colorectal cancer patients.

Complexity of WGBS Data Caused by Cellular Heterogeneity and Multiple Cytosine Modifications

DNA methylation is an important epigenetic modification that plays an important role in many biological processes such as transcriptional regulation, gene imprinting, X chromosome inactivation, transposon silencing, and embryonic development. With the development of next-generation sequencing technology, a large number of high-throughput methylation data are constantly emerging, and the processing and analysis of these data is an urgent problem to be solved. This review discussed the difficulties and challenges encountered in the analysis of WGBS methylation data from four levels: (i) Cytosines to Reads: Technology based on bisulfite conversion; (ii) Reads to Methylation level: BS-seq Sequence alignment; (iii) Methylation level to Region: Characteristics of the methylation group; (iv) Muticle methylomes: Differential methylation. In particular, we discussed the effects of cellular heterogeneity, other cytosine modifications at the site, region, and multiple methylation levels on WGBS methylation data.

Ocular findings in Zucker Diabetic Fatty rats emphasize the key role of neuroglia degeneration in diabetic retinopathy pathophysiology.

Ocular findings in Zucker Diabetic Fatty rats emphasize the key role of neuroglia degeneration in diabetic retinopathy pathophysiology.

Regenerative Medicine/Cardiac Cell Therapy: Adult/Somatic Progenitor Cells.

Preclinical data suggested that somatic stem or progenitor cells derived induce and/or support endogenous repair mechanisms of the myocardium. Such cell populations were clearly shown to promote neovascularization in postischemic tissue, and some evidence also indicated transdifferentiation into cardiomyocytes. In the clinical setting, however, many attempts to regenerate damaged myocardium with a variety of autologous and allogeneic somatic progenitors have failed to generate the expected therapeutic efficacy. Currently, efforts are being made to select specific cellular subpopulations, modify somatic cells to augment their regenerative capacity, improve delivery methods, and develop markers selection of potentially responding patients. Cardiac surgical groups have pioneered and continue to advance the field of cellular therapies. While the initial excitement has subsided, the field has evolved into one of the pillars of surgical research and benefits from novel methods such as cellular reprogramming, genetic modification, and pluripotent stem cell technology. This review highlights developments and controversies in somatic cardiac cell therapy and provides a comprehensive overview of completed and ongoing clinical trials.

Regulation of PD-1/PD-L1 pathway and resistance to PD-1/PD-L1 blockade.

Immune checkpoint blockades, such as inhibitors against programmed death 1 (PD-1) and its ligand (PD-L1), have received extensive attention in the past decade because of their dramatic clinical outcomes in advanced malignancies. However, both primary and acquired resistance becomes one of the major obstacles, which greatly limits the long-lasting effects and wide application of PD-1/PD-L1 blockade therapy. PD-1/PD-L1 both regulates and is regulated by cellular signaling pathways and epigenetic modification, thus inhibiting the proliferation and effector function of T and B cells. The lack of tumor antigens and effective antigen presentation, aberrant activation of oncogenic pathways, mutations in IFN-γ signaling, immunosuppressive tumor microenvironment such as regulatory T cells, myeloid-derived suppressor cells, M2 macrophages, and immunoinhibitory cytokines can lead to resistance to PD-1/PD-L1 blockade. In this review, we describe PD-1 related signaling pathways, essential factors contributing to the resistance of PD-1 blockade, and discuss strategies to increase the efficacy of immunotherapy. Furthermore, we discuss the possibility of combined epigenetic therapy with PD-1 blockade as a potential promising approach for cancer treatment.

Self-perceived oral health status and cytomorphological changes in individuals with addictive oral habits: assessed by WHO oral health questionnaire for adults

Background: Oral diseases related to tobacco use are relatively widespread and common in the Pakistani community but epidemiological data regarding maintenance of oral hygiene and suggested treatment is scarce. Therefore, this study was conducted in an under developed district (Muzaffargarh) of Punjab, Pakistan to evaluate oral health status and to determine frequency of cytomorphological changes in buccal mucosa of habitual tobacco users. Methods: Oral examination of all the subjects was carried out using mouth mirrors and gauze under good illumination. Cytology samples were taken from buccal mucosa. The smears were later stained with Papanicolaou stain and microscopy was performed. All the cytological data was recorded in the respective proformas. Data was analysed using IBM SPSS software version 20. Descriptive statistical analysis was performed. A p value of ≤0.05 was considered significant. Results: When cross relations were studied among the demographics, addictive habits and cytological variables, soft drink usage was associated with epithelial atypia (p=0.05), marijuana usage was associated with inflammatory infiltrate on cytology (p=0.047) and snuff/niswar usage was associated with inflammatory atypia (p=0.048). No associations were found among the other studied variables. Conclusions: The results of cellular changes in the smears from subjects with addictive habits can be utilized as an educational and screening tool in cessation therapy. The results attained in this study proposed that tobacco addictive habits produce cellular modifications in clinically normal mucosa on exfoliation cytology.

IDNAProt-ES: Identification of DNA-binding Proteins Using Evolutionary and Structural Features

DNA-binding proteins play a very important role in the structural composition of the DNA. In addition, they regulate and effect various cellular processes like transcription, DNA replication, DNA recombination, repair and modification. The experimental methods used to identify DNA-binding proteins are expensive and time consuming and thus attracted researchers from computational field to address the problem. In this paper, we present iDNAProt-ES, a DNA-binding protein prediction method that utilizes both sequence based evolutionary and structure based features of proteins to identify their DNA-binding functionality. We used recursive feature elimination to extract an optimal set of features and train them using Support Vector Machine (SVM) with linear kernel to select the final model. Our proposed method significantly outperforms the existing state-of-the-art predictors on standard benchmark dataset. The accuracy of the predictor is 90.18% using jack knife test and 88.87% using 10-fold cross validation on the benchmark dataset. The accuracy of the predictor on the independent dataset is 80.64% which is also significantly better than the state-of-the-art methods. iDNAProt-ES is a novel prediction method that uses evolutionary and structural based features. We believe the superior performance of iDNAProt-ES will motivate the researchers to use this method to identify DNA-binding proteins. iDNAProt-ES is publicly available as a web server at: http://brl.uiu.ac.bd/iDNAProt-ES/.

Histologic Characterization of Retina Neuroglia Modifications in Diabetic Zucker Diabetic Fatty Rats.

The purpose of this study was to characterize retinal degenerative morphologic modifications in Zucker Diabetic Fatty (ZDF) rats, a genetic model of type 2 diabetes, by histologic and immunohistochemical evaluation. Male lean (?/+; n = 10) and ZDF (fa/fa; n = 20) rats were used. At 24 weeks of age, body weights and blood glucose levels were determined. Eyes were removed and processed for paraffin wax embedding. Sections through the optic disc were stained for hematoxylin and eosin or immunostained for TUNEL, advanced glycation end products (AGEs), glial fibrillary acidic protein (GFAP), glutamate/aspartate transporter (GLAST), isolectin B4, recoverin, retinal pigment epithelium-specific 65-kDa protein, rhodopsin, vimentin, and zonula occludens protein 1. Retinal morphometry, cell counts, glial activation degree and immunoreactivity of AGEs and GLAST were also determined. ZDF rats were observed to be diabetic from week 9 and by week 24. These animals showed retinal morphologic degenerative changes, increased neuroretinal thickness, and decreased number of nuclei. Glial cells activation with massive GFAP upregulation was present. Cellular morphologic modifications were also observed. GLAST immunofluorescence was decreased, whereas AGEs were increased in comparison with lean rats. Spontaneous development of diabetes in ZDF rats results in neuroglia morphologic degenerative changes at 24 weeks of age. This animal model may be useful to understand the pathogenesis of diabetic retinopathy and to screen neuroprotective drugs in diabetes.

Citrus Fruit-Cracking: Causes and Occurrence

Citrus fruit creasing or cracking is a complex pre-harvest physiological disorder that causes significant economic losses. Recent studies have indicated that citrus fruit creasing or cracking is caused not only by genetic factors but also by environmental factors. By reviewing the relationship between citrus fruit creasing or cracking and peel mechanical properties, the cellular wall ultrastructure, cellular wall metabolism and modification, this paper summarized the mechanism of citrus creasing or cracking and further explained the effects of genetic factors and environmental factors (light, temperature, humidity, mineral nutrition and plant growth regulators) on citrus fruit creasing or cracking rate. Further studies were proposed to provide a sound theoretical basis on citrus fruit creasing or cracking.

Chemoradiation Cancer Therapy: Molecular Mechanisms of Cisplatin Radiosensitization

Sensitization of malignant cells to ionizing radiation plays a key role in cancer treatments that combine chemotherapy and radiation therapy. Enhancement by chemotherapeutic agents of DNA base damages and clustered damage, which are among the most detrimental cellular modifications, is expected to contribute significantly to the radiosensitization process; however, with the exception of double-strand breaks (DSBs), no measurements exist on the enhancement of such damages induced by the abundant secondary low-energy electrons (LEEs) created by ionizing radiation. This lack of information restricts our global understanding of the molecular mechanisms involved in chemoradiation therapy. Here we measure the enhancements of LEE-induced damages resulting from the binding of cisplatin to plasmid DNA (pGEM-3Zf(−), 3197 bp). The enhancement factors (EFs) are reported for base damages (BDs) on one strand and clustered damages consisting of BDs and single-strand break (SSBs) with adjacent BDs on the opposite strand....

Sustained efficacy of closed loop electrical stimulation for long-term treatment of absence epilepsy in rats

Closed-loop brain stimulation is a promising alternative to treat drug-resistant epilepsies. In contrast to optogenetic interventions, transcranial electrical stimulation (TES) does not require cellular modification of neurons to be effective, and it is less invasive compared to deep brain stimulation. Furthermore, on-demand TES of targeted brain regions allows the potential for normal function of these networks during interictal periods, a possibility that is eliminated by resective surgical treatment approaches. To further explore the translation of closed-loop TES for treatment of epilepsy, we show here for the first time that unsupervised closed-loop TES in rats can consistently interrupt seizures for 6 weeks and has the potential to control seizure activity up to 4 months (longest periods examined). On-demand TES significantly reduced the time spent in seizure and the individual seizure duration, although significantly higher seizure rate was observed during the treatment. The 6 week long stimulation had no residual adverse effects on the electrophysiologic characteristics of the brain after the termination of the treatment and did not induce glial remodelling in the brain. Our findings demonstrate the safety and effectiveness of minimally invasive, potentially lifelong TES treatment of epilepsy either alone or as a complement to drug treatments.

Genes of cellular components of morphogenesis in porcine oocytes before and after IVM.

Proper oocyte maturation in mammals produces an oocyte capable of monospermic fertilization and embryo preimplantation. The cumulus-oocyte complexes (COCs), surrounding an oocyte, play a significant role in oocyte maturation. During this process, when the COCs undergo cumulus expansion wherein tightly compact cumulus cells (CCs) form a dispersed structure, permanent biochemical and molecular modifications occur in the maturing oocytes, indicating that the gene expression between immature and mature oocytes differs significantly. This study focuses on the genes responsible for the cellular components of morphogenesis within the developing oocyte. Brilliant cresyl blue (BCB) was used to determine the developmental capability of porcine oocytes. The immature oocytes (GV stage) were compared with matured oocytes (MII stage), using microarray and qRT-PCR analysis to track changes in the genetic expression profile of transcriptome genes. The data showed substantial upregulation of genes influencing oocyte's morphology, cellular migration and adhesion, intracellular communication, as well as plasticity of nervous system. Conversely, downregulation involved genes related to microtubule reorganization, regulation of adhesion, proliferation, migration and cell differentiation processes in oocytes. This suggests that most genes recruited in morphogenesis in porcine oocyte in vitro, may have cellular maturational capability, since they have a higher level of expression before the oocyte's matured form. It shows the process of oocyte maturation and developmental capacity is orchestrated by significant cellular modifications during morphogenesis.

Activity-Dependent Gating of Parvalbumin Interneuron Function by the Perineuronal Net Protein Brevican

Activity-dependent neuronal plasticity is a fundamental mechanism through which the nervous system adapts to sensory experience. Several lines of evidence suggest that parvalbumin (PV+) interneurons are essential in this process, but the molecular mechanisms underlying the influence of experience on interneuron plasticity remain poorly understood. Perineuronal nets (PNNs) enwrapping PV+ cells are long-standing candidates for playing such a role, yet their precise contribution has remained elusive. We show that the PNN protein Brevican is a critical regulator of interneuron plasticity. We find that Brevican simultaneously controls cellular and synaptic forms of plasticity in PV+ cells by regulating the localization of potassium channels and AMPA receptors, respectively. By modulating Brevican levels, experience introduces precise molecular and cellular modifications in PV+ cells that are required for learning and memory. These findings uncover a molecular program through which a PNN protein facilitates appropriate behavioral responses to experience by dynamically gating PV+ interneuron function.

Dynamic ubiquitin signaling in cell cycle regulation.

The cell division cycle is driven by a collection of enzymes that coordinate DNA duplication and separation, ensuring that genomic information is faithfully and perpetually maintained. The activity of the effector proteins that perform and coordinate these biological processes oscillates by regulated expression and/or posttranslational modifications. Ubiquitylation is a cardinal cellular modification and is long known for driving cell cycle transitions. In this review, we emphasize emerging concepts of how ubiquitylation brings the necessary dynamicity and plasticity that underlie the processes of DNA replication and mitosis. New studies, often focusing on the regulation of chromosomal proteins like DNA polymerases or kinetochore kinases, are demonstrating that ubiquitylation is a versatile modification that can be used to fine-tune these cell cycle events, frequently through processes that do not involve proteasomal degradation. Understanding how the increasing variety of identified ubiquitin signals are transduced will allow us to develop a deeper mechanistic perception of how the multiple factors come together to faithfully propagate genomic information. Here, we discuss these and additional conceptual challenges that are currently under study toward understanding how ubiquitin governs cell cycle regulation.

Comparative muscle transcriptome associated with carcass traits of Nellore cattle

BackgroundCommercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits.ResultsBy comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis.ConclusionIn this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production.

Non-alcoholic fatty liver disease, to struggle with the strangle: Oxygen availability in fatty livers

Nonalcoholic fatty liver diseases (NAFLD) is one of the most common chronic liver disease in Western countries. Oxygen is a central component of the cellular microenvironment, which participate in the regulation of cell survival, differentiation, functions and energy metabolism. Accordingly, sufficient oxygen supply is an important factor for tissue durability, mainly in highly metabolic tissues, such as the liver. Accumulating evidence from the past few decades provides strong support for the existence of interruptions in oxygen availability in fatty livers. This outcome may be the consequence of both, impaired systemic microcirculation and cellular membrane modifications which occur under steatotic conditions. This review summarizes current knowledge regarding the main factors which can affect oxygen supply in fatty liver.

Low-dose exposure to bisphenols A, F and S of human primary adipocyte impacts coding and non-coding RNA profiles.

Bisphenol A (BPA) exposure has been suspected to be associated with deleterious effects on health including obesity and metabolically-linked diseases. Although bisphenols F (BPF) and S (BPS) are BPA structural analogs commonly used in many marketed products as a replacement for BPA, only sparse toxicological data are available yet. Our objective was to comprehensively characterize bisphenols gene targets in a human primary adipocyte model, in order to determine whether they may induce cellular dysfunction, using chronic exposure at two concentrations: a “low-dose” similar to the dose usually encountered in human biological fluids and a higher dose. Therefore, BPA, BPF and BPS have been added at 10 nM or 10 μM during the differentiation of human primary adipocytes from subcutaneous fat of three non-diabetic Caucasian female patients. Gene expression (mRNA/lncRNA) arrays and microRNA arrays, have been used to assess coding and non-coding RNA changes. We detected significantly deregulated mRNA/lncRNA and miRNA at low and high doses. Enrichment in “cancer” and “organismal injury and abnormalities” related pathways was found in response to the three products. Some long intergenic non-coding RNAs and small nucleolar RNAs were differentially expressed suggesting that bisphenols may also activate multiple cellular processes and epigenetic modifications. The analysis of upstream regulators of deregulated genes highlighted hormones or hormone-like chemicals suggesting that BPS and BPF can be suspected to interfere, just like BPA, with hormonal regulation and have to be considered as endocrine disruptors. All these results suggest that as BPA, its substitutes BPS and BPF should be used with the same restrictions.

Tetrahydrofolate Modulates Floral Transition through Epigenetic Silencing.

Folates, termed from tetrahydrofolate (THF) and its derivatives, function as coenzymes in one-carbon transfer reactions and play a central role in synthesis of nucleotides and amino acids. Dysfunction of cellular folate metabolism leads to serious defects in plant development; however, the molecular mechanisms of folate-mediated cellular modifications and physiological responses in plants are still largely unclear. Here, we reported that THF controls flowering time by adjusting DNA methylation-regulated gene expression in Arabidopsis (Arabidopsis thaliana). Wild-type seedlings supplied with THF as well as the high endogenous THF content mutant dihydrofolate synthetase folypoly-Glu synthetase homolog B exhibited significant up-regulation of the flowering repressor of Flowering Wageningen and thereby delaying floral transition in a dose-dependent manner. Genome-wide transcripts and DNA methylation profiling revealed that THF reduces DNA methylation so as to manipulate gene expression activity. Moreover, in accompaniment with elevated cellular ratios between monoglutamylated and polyglutamylated folates under increased THF levels, the content of S-adenosylhomo-Cys, a competitive inhibitor of methyltransferases, was obviously higher, indicating that enhanced THF accumulation may disturb cellular homeostasis of the concerted reactions between folate polyglutamylation and folate-dependent DNA methylation. In addition, we found that the loss-of-function mutant of CG DNA methyltransferase MET1 displayed much less responsiveness to THF-associated flowering time alteration. Taken together, our studies revealed a novel regulatory role of THF on epigenetic silencing, which will shed lights on the understanding of interrelations in folate homeostasis, epigenetic variation, and flowering control in plants.