The odyssey of the TR(i)P journey to the cellular membrane.

Ion channels are integral membrane proteins mediating ion flow in response to changes in their environment. Among the different types of ion channels reported to date, the super-family of TRP channels stands out since its members have been linked to many pathophysiological processes. The family comprises 6 subfamilies and 28 members in mammals, which are widely distributed throughout most tissues and organs and have an important role in several aspects of cellular physiology. It has been evidenced that abnormal expression, post-translational modifications, and channel trafficking are associated with several pathologies, such as cancer, cardiovascular disease, diabetes, and brain disorders, among others. In this review, we present an updated summary of the mechanisms involved in the subcellular trafficking of TRP channels, with a special emphasis on whether different post-translational modifications and naturally occurring mutagenesis affect both expression and trafficking. Additionally, we describe how such changes have been associated with the development and progress of diverse pathologies associated with the gain or loss of functional phenotypes. The study of these processes will not only contribute to a better understanding the role of TRP channels in the different tissues but will also present novel possible therapeutic targets in diseases where their activity is dysregulated.

Assessing RNA-Seq Workflow Methodologies Using Shannon Entropy.

RNA-seq faces persistent challenges due to the ongoing, expanding array of data processing workflows, none of which have yet achieved standardization to date. It is imperative to determine which method most effectively preserves biological facts. Here, we used Shannon entropy as a tool for depicting the biological status of a system. Thus, we assessed the measurement of Shannon entropy by several RNA-seq workflow approaches, such as DESeq2 and edgeR, but also by combining nine normalization methods with log2 fold change on paired samples of TCGA RNA-seq representing datasets of 515 patients and spanning 12 different cancer types with 5-year overall survival rates ranging from 20% to 98%. Our analysis revealed that TPM, RLE, and TMM normalization, coupled with a threshold of log2 fold change ≥1, for identifying differentially expressed genes, yielded the best results. We propose that Shannon entropy can serve as an objective metric for refining the optimization of RNA-seq workflows and mRNA sequencing technologies.

The Effect of Dexlansoprazole on Gastroesophageal Reflux Disease: A Systematic Review and Meta-Analysis.

This systematic review and meta-analysis evaluated the efficacy of dexlansoprazole (a proton pump inhibitor-PPI) in resolving heartburn, reflux, and other symptoms and complications resulting from gastroesophageal reflux disease (GERD). The study followed PRISMA 2020 and was registered in PROSPERO (CRD42020206513). The search strategy used MeSH and free terms appropriately adapted for each database. Only randomized clinical trials (RCTs) were included. The Cochrane tool (RoB 2.0) was used to assess the risk of bias, and the certainty of evidence was rated using GRADE. Ten RCTs were included. Dexlansoprazole outperformed the placebo and other PPIs in the resolution of heartburn and reflux symptoms in patients with GERD, with benefits during and after treatment, especially in those with moderate and severe symptoms. The meta-analyses indicated that dexlansoprazole at doses of 30 and 60 mg had more 24 h heartburn-free days and nights compared to the placebo medications; no difference was reported between dexlansoprazole at doses of 30 and 60 mg in heartburn-free nights. A low bias risk and a moderate certainty of evidence were observed. This review confirms the therapeutic effect of dexlansoprazole (placebo-controlled) and its improvements in GERD symptoms compared to another PPI. However, the interpretation of the results should be carried out cautiously due to the small number of included studies and other reported limitations.

State of the art in protein-protein interactions within the fungi kingdom.

Proteins rarely exert their function by themselves. Protein-protein interactions (PPIs) regulate virtually every biological process that takes place in a cell. Such interactions are targets for new therapeutic agents against all sorts of diseases, through the screening and design of a variety of inhibitors. Here we discuss several aspects of PPIs that contribute to prediction of protein function and drug discovery. As the high-throughput techniques continue to release biological data, targets for fungal therapeutics that rely on PPIs are being proposed worldwide. Computational approaches have reduced the time taken to develop new therapeutic approaches. The near future brings the possibility of developing new PPI and interaction network inhibitors and a revolution in the way we treat fungal diseases.

Integrated bioinformatics approach reveals methylation-regulated differentially expressed genes in obesity.

Objective: To identify DNA methylation and gene expression profiles involved in obesity by implementing an integrated bioinformatics approach. Materials and methods: Gene expression (GSE94752, GSE55200, and GSE48964) and DNA methylation (GSE67024 and GSE111632) datasets were obtained from the GEO database. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) in subcutaneous adipose tissue of patients with obesity were identified using GEO2R. Methylation-regulated DEGs (MeDEGs) were identified by overlapping DEGs and DMGs. The protein-protein interaction (PPI) network was constructed with the STRING database and analyzed using Cytoscape. Functional modules and hub-bottleneck genes were identified by using MCODE and CytoHubba plugins. Functional enrichment analyses were performed based on Gene Ontology terms and KEGG pathways. To prioritize and identify candidate genes for obesity, MeDEGs were compared with obesity-related genes available at the DisGeNET database. Results: A total of 54 MeDEGs were identified after overlapping the lists of significant 274 DEGs and 11,556 DMGs. Of these, 25 were hypermethylated-low expression genes and 29 were hypomethylated-high expression genes. The PPI network showed three hub-bottleneck genes (PTGS2, TNFAIP3, and FBXL20) and one functional module. The 54 MeDEGs were mainly involved in the regulation of fibroblast growth factor production, the molecular function of arachidonic acid, and ubiquitin-protein transferase activity. Data collected from DisGeNET showed that 11 of the 54 MeDEGs were involved in obesity. Conclusion: This study identifies new MeDEGs involved in obesity and assessed their related pathways and functions. These results data may provide a deeper understanding of methylation-mediated regulatory mechanisms of obesity.

Age-related changes in prepulse inhibition of the startle response.

Introduction: Acoustic prepulse inhibition of the startle response (PPI) is a phenomenon characterized by the reduction in the startle reflex caused by the presence of weak and brief stimulus before an intense and sudden stimulus (pulse). These phenomena can be observed in several species, but in humans it is commonly measured by the eyeblink using electromyography. PPI works as an operational measure of sensorimotor gating, which is the ability to suppress motor responses for sensory stimulus. Healthy aging is marked by several changes in neural processing, like inhibitory functioning decline. In this line, PPI measure can be a potential biomarker for changes related to the aging process. Methods: In this research we aim to investigate if PPI is reduced with aging and if this reduction would be associated with cognitive functioning of older adults. To this aim, we compared PPI levels of older adults (over 60 years old) with PPI levels of young adults (from 18 to 28 years old). Results: With that, we found, significantly lower PPI level (F[1,25] = 7.44 p = 0.01) and lower startle amplitude startle amplitude: (U = 26.000 p = 0.001) in older adults than in young adults. However, we did not find differences in levels of habituation (T = -1.1 p = 0.28) and correlation between PPI and cognition within the sample of healthy older adults. Discussion: Our results demonstrate that aging is a factor that affects PPI and that it does not seem to predict cognition, however, future studies should explore the potential of using PPI for monitoring cognitive changes associated with techniques such as cognitive training.

Shared Molecular Signatures Across Zika Virus Infection and Multiple Sclerosis Highlight AP-1 Transcription Factor as a Potential Player in Post-ZIKV MS-Like Phenotypes.

Zika virus (ZIKV) is an arbovirus of the Flaviviridae genus that has rapidly disseminated from across the Pacific to the Americas. Robust evidence has indicated a crucial role of ZIKV in congenital virus syndrome, including neonatal microcephaly. Moreover, emerging evidence suggests an association between ZIKV infection and the development of an extensive spectrum of central nervous system inflammatory demyelinating diseases (CNS IDD), such as multiple sclerosis-like clinical phenotypes. However, the underlying mechanisms of host-pathogen neuro-immune interactions remain to be elucidated. This study aimed to identify common transcriptional signatures between multiple sclerosis (MS) and ZIKV infection to generate molecular interaction networks, thereby leading to the identification of deregulated processes and pathways, which could give an insight of these underlying molecular mechanisms. Our investigation included publicly available transcriptomic data from MS patients in either relapse or remission (RR-MS) and datasets of subjects acutely infected by ZIKV for both immune peripheral cells and central nervous system cells. The protein-protein interaction (PPI) analysis showed upregulated AP-1 transcription factors (JUN and FOS) among the top hub and bottleneck genes in RR-MS and ZIKV data. Gene enrichment analysis retrieved a remarkable presence of ontologies and pathways linked to oxidative stress responses, immune cell function, inflammation, interleukin signaling, cell division, and transcriptional regulation commonly enriched in both scenarios. Considering the recent findings concerning AP-1 function in immunological tolerance breakdown, regulation of inflammation, and its function as an oxidative stress sensor, we postulate that the ZIKV trigger may contribute as a boost for the activation of such AP-1-regulated mechanisms that could favor the development of MS-like phenotypes following ZIKV infection in a genetically susceptible individual.

Zinc/iron-regulated transporter-like protein gene family in Theobroma cacao L: Characteristics, evolution, function and 3D structure analysis.

The zinc/iron-regulated transporter-like protein (ZIP) gene family first identified in plants is highly distributed in the plant kingdom. This family has previously been reported to transport several essential and non-essential cationic elements, including those toxic to many economically important crops such as cacao (Theobroma cacao L.). In this article, we present a detailed study on physicochemical properties, evolution, duplication, gene structure, promoter region and TcZIP family three-dimensional protein structure. A total of 11 TcZIP genes have been identified to encode proteins from 309 to 435 aa, with localization in the plasma membrane and chloroplast, containing 6-9 putative domains (TM). Interspecies phylogenetic analysis subdivided the ZIP proteins into four groups. Segmental duplication events significantly contributed to the expansion of TcZIP genes. These genes underwent high pressure of purifying selection. The three-dimensional structure of the proteins showed that α helix conformations are predominant with several pocket sites, containing the metal binding site, with the residues leucine (LEU), alanine (ALA), glycine (GLY), serine (SER), lysine (LYS) and histidine (HIS) the most predicted. Regarding the analysis of the protein-protein interaction and enrichment of the gene ontology, four biological processes were assigned, the most important being the cation transport. These new discoveries expand the knowledge about the function, evolution, protein structures and interaction of ZIP family proteins in cacao and contribute to develop cacao genotypes enriched with important mineral nutrients as well as genotypes that bioaccumulate or exclude toxic metals.

Integrated bioinformatics approach reveals methylation-regulated differentially expressed genes in obesity

ABSTRACT Objective: To identify DNA methylation and gene expression profiles involved in obesity by implementing an integrated bioinformatics approach. Materials and methods: Gene expression (GSE94752, GSE55200, and GSE48964) and DNA methylation (GSE67024 and GSE111632) datasets were obtained from the GEO database. Differentially expressed genes (DEGs) and differentially methylated genes (DMGs) in subcutaneous adipose tissue of patients with obesity were identified using GEO2R. Methylation-regulated DEGs (MeDEGs) were identified by overlapping DEGs and DMGs. The protein-protein interaction (PPI) network was constructed with the STRING database and analyzed using Cytoscape. Functional modules and hub-bottleneck genes were identified by using MCODE and CytoHubba plugins. Functional enrichment analyses were performed based on Gene Ontology terms and KEGG pathways. To prioritize and identify candidate genes for obesity, MeDEGs were compared with obesity-related genes available at the DisGeNET database. Results: A total of 54 MeDEGs were identified after overlapping the lists of significant 274 DEGs and 11,556 DMGs. Of these, 25 were hypermethylated-low expression genes and 29 were hypomethylated-high expression genes. The PPI network showed three hub-bottleneck genes (PTGS2, TNFAIP3, and FBXL20) and one functional module. The 54 MeDEGs were mainly involved in the regulation of fibroblast growth factor production, the molecular function of arachidonic acid, and ubiquitin-protein transferase activity. Data collected from DisGeNET showed that 11 of the 54 MeDEGs were involved in obesity. Conclusion: This study identifies new MeDEGs involved in obesity and assessed their related pathways and functions. These results data may provide a deeper understanding of methylation-mediated regulatory mechanisms of obesity.

Computational Design of Inhibitors Targeting the Catalytic ß Subunit of Escherichia coli FOF1-ATP Synthase.

With the uncontrolled growth of multidrug-resistant bacteria, there is an urgent need to search for new therapeutic targets, to develop drugs with novel modes of bactericidal action. FoF1-ATP synthase plays a crucial role in bacterial bioenergetic processes, and it has emerged as an attractive antimicrobial target, validated by the pharmaceutical approval of an inhibitor to treat multidrug-resistant tuberculosis. In this work, we aimed to design, through two types of in silico strategies, new allosteric inhibitors of the ATP synthase, by targeting the catalytic ß subunit, a centerpiece in communication between rotor subunits and catalytic sites, to drive the rotary mechanism. As a model system, we used the F1 sector of Escherichia coli, a bacterium included in the priority list of multidrug-resistant pathogens. Drug-like molecules and an IF1-derived peptide, designed through molecular dynamics simulations and sequence mining approaches, respectively, exhibited in vitro micromolar inhibitor potency against F1. An analysis of bacterial and Mammalia sequences of the key structural helix-turn-turn motif of the C-terminal domain of the ß subunit revealed highly and moderately conserved positions that could be exploited for the development of new species-specific allosteric inhibitors. To our knowledge, these inhibitors are the first binders computationally designed against the catalytic subunit of FOF1-ATP synthase.

Association of Early Life Prescriptions for Antibiotics and Acid Suppressants with Childhood Psychotropic Prescriptions.

OBJECTIVE: To examine the association between antibiotic and acid suppressant prescriptions in the first 2 years of life and subsequent treatment for childhood psychiatric disorders. STUDY DESIGN: This was a retrospective cohort study of children born between October 2001 and September 2012 in the Military Health System enrolled in TRICARE past age 2 years and within 35 days of birth, with an initial hospital stay <7 days, and without psychotropic agents dispensed during the first 2 years of life. Exposure was defined as a filled prescription for an antibiotic or acid suppressant before age 2 years, and the outcome was defined as a filled prescription for a psychotropic agent after age 2 years. RESULTS: For the 804 920 patients (51% males and 49% female) composing the study population, the mean age at first psychotropic prescription was 6.8 years. A total of 24 176 children (3%) were prescribed a proton pump inhibitor (PPI), 79 243 (10%) were prescribed a histamine-2 receptor antagonist (H2RA), and 607 348 (76%) were prescribed an antibiotic during the first 2 years of life. The adjusted hazard ratio (aHR) of a psychotropic prescription was significantly increased in children prescribed any H2RA (1.79; 95% CI, 1.63-1.96), PPI (1.47; 95% CI, 1.26-1.71), or antibiotic (1.71; 95% CI, 1.59-1.84). The aHR of psychotropic prescriptions increased commensurately with each additional antibiotic class added and with each additional class of medication (H2RA, PPI, or antibiotics) prescribed. CONCLUSIONS: Children prescribed antibiotic and acid suppressants in the first 2 years of life have a significant increase in future prescriptions for psychotropics, with a dose-related effect observed. This association represents a potential risk of early exposure to antibiotics and acid suppressants.

The potential mechanism of Chebulae Fructus in the treatment of hepatocellular carcinoma on the basis of network pharmacology.

INTRODUCTION AND OBJECTIVES: Hepatocellular carcinoma (HCC) ranks third on the list of the leading cause for cancer death globally. The treatment of HCC patients is unsatisfactory. However, the traditional Chinese medicine Chebulae Fructus has potential efficacy in the treatment of HCC. MATERIALS AND METHODS: We mined the active ingredients of Chebulae Fructus and its main targets from the Traditional Chinese Medicine Systems Pharmacology database. HCC-related datasets were downloaded from The Cancer Genome Atlas database and differentially expressed genes (DEGs) in HCC were obtained by differential expression analysis. Top10 small molecule compounds capable of reversing HCC pathology were screened by the Connectivity Map database based on DEGs. Ellipticine, an extract of Chebulae Fructus, had the potential to reverse HCC pathology. Protein-Protein Interaction (PPI) networks of DEGs in HCC were constructed using STRING. Eighteen potential targets of Chebulae Fructus for the treatment of HCC were obtained by taking intersection of DEGs in HCC with targets corresponding to the active constituents of Chebulae Fructus. In addition, MTT assay was also employed to examine the effect of ellipticine on HCC cell viability. RESULTS: It has been shown that ellipticine and ellagic acid have antitumor activity. Random Walk with Restart analysis of PPI networks was performed using potential targets as seeds, and the genes with the top 50 affinity coefficients were selected to construct a drug-active constituent-gene interaction network. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes enrichment analyses of key genes involved in the treatment of HCC with Chebulae Fructus demonstrated that these genes were mainly enriched in signaling pathways related to tumor metabolism such as cAMP signaling pathway and Ras signaling pathway. Finally, it was verified by MTT assay that proliferation of HCC cells could be remarkably hindered. CONCLUSIONS: We excavated ellipticine, a key active constituent of Chebulae Fructus, by network pharmacology, and elucidated the signaling pathways involved in Chebulae Fructus, providing a theoretical basis for the use of Chebulae Fructus for HCC clinical application.

Early Schizophrenia and Bipolar Disorder Patients Display Reduced Neural Prepulse Inhibition.

BACKGROUND: Altered sensorimotor gating has been demonstrated by Prepulse Inhibition (PPI) tests in patients with psychosis. Recent advances in signal processing methods allow assessment of neural PPI through electroencephalogram (EEG) recording during acoustic startle response measures (classic muscular PPI). Simultaneous measurements of muscular (eye-blink) and neural gating phenomena during PPI test may help to better understand sensorial processing dysfunctions in psychosis. In this study, we aimed to assess simultaneously muscular and neural PPI in early bipolar disorder and schizophrenia patients. METHOD: Participants were recruited from a population-based case-control study of first episode psychosis. PPI was measured using electromyography (EMG) and EEG in pulse alone and prepulse + pulse with intervals of 30, 60, and 120 ms in early bipolar disorder (n = 18) and schizophrenia (n = 11) patients. As control group, 15 socio-economically matched healthy subjects were recruited. All subjects were evaluated with Rating Scale, Hamilton Rating Scale for Depression, and Young Mania Rating Scale questionnaires at recruitment and just before PPI test. Wilcoxon ranked sum tests were used to compare PPI test results between groups. RESULTS: In comparison to healthy participants, neural PPI was significantly reduced in PPI 30 and PPI60 among bipolar and schizophrenia patients, while muscular PPI was reduced in PPI60 and PPI120 intervals only among patients with schizophrenia. CONCLUSION: The combination of muscular and neural PPI evaluations suggested distinct impairment patterns among schizophrenia and bipolar disorder patients. Simultaneous recording may contribute with novel information in sensory gating investigations.

PPI-MASS: An Interactive Web Server to Identify Protein-Protein Interactions From Mass Spectrometry-Based Proteomics Data.

Mass spectrometry-based proteomics methods are widely used to identify and quantify protein complexes involved in diverse biological processes. Specifically, tandem mass spectrometry methods represent an accurate and sensitive strategy for identifying protein-protein interactions. However, most of these approaches provide only lists of peptide fragments associated with a target protein, without performing further analyses to discriminate physical or functional protein-protein interactions. Here, we present the PPI-MASS web server, which provides an interactive analytics platform to identify protein-protein interactions with pharmacological potential by filtering a large protein set according to different biological features. Starting from a list of proteins detected by MS-based methods, PPI-MASS integrates an automatized pipeline to obtain information of each protein from freely accessible databases. The collected data include protein sequence, functional and structural properties, associated pathologies and drugs, as well as location and expression in human tissues. Based on this information, users can manipulate different filters in the web platform to identify candidate proteins to establish physical contacts with a target protein. Thus, our server offers a simple but powerful tool to detect novel protein-protein interactions, avoiding tedious and time-consuming data postprocessing. To test the web server, we employed the interactome of the TRPM4 and TMPRSS11a proteins as a use case. From these data, protein-protein interactions were identified, which have been validated through biochemical and bioinformatic studies. Accordingly, our web platform provides a comprehensive and complementary tool for identifying protein-protein complexes assisting the future design of associated therapies.

Impact of treatment optimization in patients with gastroesophageal reflux disease who do not respond to esomeprazole / Impacto de la optimización del tratamiento en pacientes con enfermedad por reflujo gastroesofágico que no responden a esomeprazol

Abstract Introduction: gastroesophageal reflux disease (GERD) affects one out of eight people in Colombia. Its characteristic symptoms are heartburn and reflux. The cornerstone of treatment is proton pump inhibitors (PPIs), with a clinical response in 58-80% of patients. Of those who do not respond, 75-90% have a superimposed functional disorder and could be treated by adding visceral neuromodulators. Objective: to evaluate the impact of optimizing the treatment of patients with GERD when there is no response to esomeprazole (ESO). Materials and methods: a prospective study in patients with no clinical response (more than two reflux episodes per week) who were treated with 40 mg of ESO half an hour before breakfast along with the recommendation to lose weight if BMI >25, stop smoking and manage stress; and, finally, increasing the ESO dose to 40 mg on an empty stomach and before dinner. When all of this was done and symptoms persisted, 12.5 mg of amitriptyline were added at night. The response was evaluated every 12 weeks. Results: a total of 529 patients were eligible and 149 met the inclusion criteria. With treatment optimization, 111 patients had a clinical response without using amitriptyline (74.5%; 95%CI 67.2 81.4). Amitriptyline was added in 22 patients (14.8%), 15 of whom responded (68.2%; 95%CI 47.04-89.32%). Eight patients experienced drowsiness (53.3%). A relationship was found between PPI treatment compliance and clinical response (p<0.0001). Conclusions: in patients with GERD, PPI treatment optimization improves 74.5% (95%CI 67.2 81.4) of the patients, and adding amitriptyline for those who do not improve achieves improvement in 68.2% of those who did not improve with two doses of ESO. Sequential management achieved a cumulative improvement in symptom control in 85% (95%CI 78.6-90.4) of the patients. (Acta Med Colomb 2021; 46. DOI: https://doi.org/10.36104/amc.2021.2041).

Resumen Introducción: la enfermedad por reflujo gastroesofágico (ERGE) afecta a una de cada ocho personas en Colombia. Sus síntomas característicos son pirosis y regurgitación. La piedra angular del tratamiento son los inhibidores de bomba de protones (IBP) con respuesta clínica en 58-80%. En quienes no responden 75-90% tienen un trastorno funcional superpuesto y se podrían tratar adicionando neuromoduladores viscerales. Objetivo: evaluar el impacto que tiene optimizar el tratamiento en pacientes con ERGE cuando no hay respuesta a esomeprazol (ESO). Material y métodos: estudio prospectivo en pacientes sin respuesta clínica (más de dos episodios de reflujo por semana) tratados con ESO 40 mg media hora antes del desayuno y simultáneamente recomendaciones para bajar de peso si IMC >25, dejar de fumar y controlar el estrés, y finalmente aumentado la dosis de ESO a 40 mg en ayunas y antes de la cena. Cuando se cumplió todo lo anterior y persistían los síntomas, se adicionó amitriptilina 12.5 mg por la noche. Cada 12 semanas se evaluaba la respuesta. Resultados: hubo 529 pacientes elegibles y 149 cumplieron los criterios de inclusión. Optimizando el tratamiento 111 pacientes tuvieron respuesta clínica sin la utilización de amitriptilina (74.5%; IC95% 67.2-81.4). En 22 se adicionó amitriptilina (14.8%) y de estos respondieron 15 pacientes, 68.2% (IC95% 47.04-89.32%). En ocho pacientes hubo somnolencia (53.3%). Se encontró relación entre el cumplimiento del tratamiento con IBP y la respuesta clínica (p<0.0001). Conclusiones: en pacientes con ERGE la optimización del tratamiento con IBP mejora el 74.5% (IC95% 67.2-81.4) de los pacientes y la adición de amitriptilina a quienes no mejoran, logra mejorar el 68.2% de quienes no mejoraban con dos dosis de ESO. Con el manejo secuencial se logró mejoría acumulativa en el control de los síntomas de 85% (IC95% 78.6-90.4) de los pacientes. (Acta Med Colomb 2021; 46. DOI:https://doi.org/10.36104/amc.2021.2041).

Shared Neurodevelopmental Perturbations Can Lead to Intellectual Disability in Individuals with Distinct Rare Chromosome Duplications.

Chromosomal duplications are associated with a large group of human diseases that arise mainly from dosage imbalance of genes within the rearrangements. Phenotypes range widely but are often associated with global development delay, intellectual disability, autism spectrum disorders, and multiple congenital abnormalities. How different contiguous genes from a duplicated genomic region interact and dynamically affect the expression of each other remains unclear in most cases. Here, we report a genomic comparative delineation of genes located in duplicated chromosomal regions 8q24.13q24.3, 18p11.32p11.21, and Xq22.3q27.2 in three patients followed up at our genetics service who has the intellectual disability (ID) as a common phenotype. We integrated several genomic data levels by identification of gene content within the duplications, protein-protein interactions, and functional analysis on specific tissues. We found functional relationships among genes from three different duplicated chromosomal regions, reflecting interactions of protein-coding genes and their involvement in common cellular subnetworks. Furthermore, the sharing of common significant biological processes associated with ID has been demonstrated between proteins from the different chromosomal regions. Finally, we elaborated a shared model of pathways directly or indirectly related to the central nervous system (CNS), which could perturb cognitive function and lead to ID in the three duplication conditions.

Large-Scale Protein Interactions Prediction by Multiple Evidence Analysis Associated With an In-Silico Curation Strategy.

Predicting the physical or functional associations through protein-protein interactions (PPIs) represents an integral approach for inferring novel protein functions and discovering new drug targets during repositioning analysis. Recent advances in high-throughput data generation and multi-omics techniques have enabled large-scale PPI predictions, thus promoting several computational methods based on different levels of biological evidence. However, integrating multiple results and strategies to optimize, extract interaction features automatically and scale up the entire PPI prediction process is still challenging. Most procedures do not offer an in-silico validation process to evaluate the predicted PPIs. In this context, this paper presents the PredPrIn scientific workflow that enables PPI prediction based on multiple lines of evidence, including the structure, sequence, and functional annotation categories, by combining boosting and stacking machine learning techniques. We also present a pipeline (PPIVPro) for the validation process based on cellular co-localization filtering and a focused search of PPI evidence on scientific publications. Thus, our combined approach provides means to extensive scale training or prediction of new PPIs and a strategy to evaluate the prediction quality. PredPrIn and PPIVPro are publicly available at https://github.com/YasCoMa/predprin and https://github.com/YasCoMa/ppi_validation_process.

EsxA mainly contributes to the miR-155 overexpression in human monocyte-derived macrophages and potentially affect the immune mechanism of macrophages through miRNA dysregulation.

BACKGROUND/PURPOSE: Mycobacterium tuberculosis is a successful intracellular pathogen that uses multiple proteins to survive within macrophages, one of the most remarkable is the virulence factor EsxA. In this study, we evaluate the participation of EsxA in the miRNAs expression profile of human monocyte-derived macrophages (hMDM), to mapping out the contribution of this virulence factor in the miRNA profile and how these changes can influence and alter immune-related processes and pathways. METHODS: The cytotoxic effect of rEsxA on hMDM was evaluated by the neutral red assay. The evaluation of miRNA expression profile in infected and rEsxA-stimulated hMDM was done using TaqMan Low Density Assays, and in silico analyses was carried on to construct Protein-Protein Interaction network of miRNAs targets. RESULTS: miR-155 was the only miRNA upregulated consistently in hMDM infected with M. tuberculosis H37Rv or stimulated with rEsxA. In hMDM stimulated with rEsxA, we found 25 miRNA's dysregulated (8 up-regulated and 17 down-regulated). The most significant were the miR-155 and miR-622 that has been observed in the analysis carried out with two different endogenous controls (U6 snRNA and RNU44) for the normalization of expression analysis. This result suggests that rEsxA induces the deregulation of miRNAs that potentially target genes in key pathways for the infection control, like the MAPK signaling pathway, cytokines, and chemokine signaling pathways, and several connected pathways involved in mycobacterial uptake, vesicular traffic, and endosome maturation. CONCLUSION: Higher expression levels of miR-155 suggest potential roles of these miRNA in EsxA-dependent immune subversion.

Meta-Analysis of Sensorimotor Gating Deficits in Patients With Schizophrenia Evaluated by Prepulse Inhibition Test.

Prepulse inhibition (PPI) of startle is an operational measure of sensorimotor gating that is often impaired in patients with schizophrenia. Despite the large number of studies, there is considerable variation in PPI outcomes reported. We conducted a systematic review and meta-analysis investigating PPI impairment in patients with schizophrenia compared with healthy control subjects, and examined possible explanations for the variation in results between studies. Major databases were screened for observational studies comparing healthy subjects and patients with schizophrenia for the prepulse and pulse intervals of 60 and 120 ms as primary outcomes, ie, PPI-60 and PPI-120. Standardized mean difference (SMD) and 95% confidence intervals (CI) were extracted and pooled using random effects models. We then estimated the mean effect size of these measures with random effects meta-analyses and evaluated potential PPI heterogeneity moderators, using sensitivity analysis and meta-regressions. Sixty-seven primary studies were identified, with 3685 healthy and 4290 patients with schizophrenia. The schizophrenia group showed reduction in sensorimotor gating for both PPI-60 (SMD = -0.50, 95% CI = [-0.61, -0.39]) and PPI-120 (SMD = -0.44, 95% CI = [-0.54, -0.33]). The sensitivity and meta-regression analysis showed that sample size, gender proportion, imbalance for gender, source of control group, and study continent were sources of heterogeneity (P < .05) for both PPI-60 and PPI-120 outcomes. Our findings confirm a global sensorimotor gating deficit in schizophrenia patients, with overall moderate effect size for PPI-60 and PPI-120. Methodological consistency should decrease the high level of heterogeneity of PPI results between studies.

Novel LRAP-binding partner revealing the plasminogen activation system as a regulator of cementoblast differentiation and mineral nodule formation in vitro.

Amelogenin isoforms, including full-length amelogenin (AMEL) and leucine-rich amelogenin peptide (LRAP), are major components of the enamel matrix, and are considered as signaling molecules in epithelial-mesenchymal interactions regulating tooth development and periodontal regeneration. Nevertheless, the molecular mechanisms involved are still poorly understood. The aim of the present study was to identify novel binding partners for amelogenin isoforms in the cementoblast (OCCM-30), using an affinity purification assay (GST pull-down) followed by mass spectrometry and immunoblotting. Protein-protein interaction analysis for AMEL and LRAP evidenced the plasminogen activation system (PAS) as a potential player regulating OCCM-30 response to amelogenin isoforms. For functional assays, PAS was either activated (plasmin) or inhibited (ε-aminocaproic acid [aminocaproic]) in OCCM-30 cells and the cell morphology, mineral nodule formation, and gene expression were assessed. PAS inhibition (EACA 100 mM) dramatically decreased mineral nodule formation and expression of OCCM-30 differentiation markers, including osteocalcin (Bglap), bone sialoprotein (Ibsp), osteopontin (Spp1), tissue-nonspecific alkaline phosphatase (Alpl) and collagen type I (Col1a1), and had no effect on runt-related transcription factor 2 (Runx2) and Osterix (Osx) mRNA levels. PAS activation (plasmin 5 µg/µl) significantly increased Col1a1 and decreased Bglap mRNA levels (p < .05). Together, our findings shed new light on the potential role of plasminogen signaling pathway in the control of the amelogenin isoform-mediated response in cementoblasts and provide new insights into the development of targeted therapies.