EMMANUEL DIAS NETO
Projetos de Pesquisa
Unidades Organizacionais
LIM/27 - Laboratório de Neurociências, Hospital das Clínicas, Faculdade de Medicina
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conferenceObject MOLECULAR CHARACTERIZATION OF THE LARVAL PHASE OF SCHISTOSOMA MANSONI IN BIOMPHALARIA GLABRATA MOLLUSKS UNDER EXPERIMENTAL CONDITIONS(2017) CASOTTI, Marcia Oliveira; TUAN, Roseli Tuan; GOMES, Michele; DIAS-NETO, Emmanuel; PINHO, Joao Renato Rebello; PAULA, Fabiana Martins; CARRILHO, Flair Jose Carrilho Jose; LUNA, Expedito Jose Albuquerque; GRYSCHEK, Ronaldo Cesar Borges Borges; ESPIRITO-SANTO, Maria Cristina- PRUNE2 and PCA3 expression in paired non-malignant and tumor specimens from radical prostatectomy patients with gleason score 7 prostate cancer.(2017) LAUER, Richard C.; BARRY, Marc; WU, Jin; LEE, Ji-Hyun; MCCANCE, Dennis J.; DU, Ruofei; RAO, Arpit; DOBROFF, Andrey S.; DIAS-NETO, Emmanuel; CHEN, Isan; PASQUALINI, Renata; ARAP, Wadih
- PCA3 upregulation in prostate cancer: Analysis in a cohort of 497 subjects from TCGA.(2017) DIAS-NETO, Emmanuel; NUNES, Diana N.; THOMAS, Andrew M.; SMITH, Tracey L.; RAO, Arpit; LAUER, Richard C.; CHEN, Isan; ARAP, Wadih; PASQUALINI, Renata
- Exome sequencing of multiple-sclerosis patients and their unaffected first-degree relatives(2017) GARCIA-ROSA, S.; AMORIM, M. G. De; VALIERIS, R.; MARQUES, V. D.; LORENZI, J. C. C.; TOLLER, V. B.; OLIVAL, G. S. Do; SILVA JUNIOR, W. A. Da; SILVA, I. T. Da; BARREIRA, A. A.; NUNES, D. N.; DIAS-NETO, E.Objectives: The understanding of complex multifactorial diseases requires the availability of a variety of data for a large-number of affected individuals. In this data note here we provide whole exome sequencing data from a set of non-familiar multiple-sclerosis (MS) patients as well as their unaffected first-degree relatives. This data might help the identification of genomic alterations, including single nucleotide polymorphisms, de novo variations and structural genomic variations, such as copy-number alterations that may impact this disease. Data description: This dataset comprises the full exome of 28 Brazilian subjects grouped in eight distinct families, consisting of four complete trios (mother-patient-father) plus another four complete trios with one added unaffected sibling. In total, we present the full exome data of eight patients diagnosed with recurrent remittent multiple sclerosis. Diagnoses were made by experienced neurologists and all enrolled patients had at least 5 years of follow up and specific MS treatment. Exomes were sequenced from leukocyte-derived DNA, after the capture of exons using biotinylated probes, in the Ion Proton platform. For each exome we generated an average of 66.1 million good quality mapped reads with an average length of ~ 160nt. On average, for 90% of the exome a vertical coverage above 20× was reached. © 2017 The Author(s).
- Prophylactic Supplementation of Bifidobacterium longum 5(1A) Protects Mice from Ovariectomy-Induced Exacerbated Allergic Airway Inflammation and Airway Hyperresponsiveness(2017) MENDES, Eduardo; ACETTURI, Beatriz G.; THOMAS, Andrew M.; MARTINS, Flaviano dos S.; CRISMA, Amanda R.; MURATA, Gilson; BRAGA, TarcioT; CAMARA, Niels O. S.; FRANCO, Adriana L. dos S.; SETUBAL, Joao C.; RIBEIRO, Willian R.; VALDUGA, Claudete J.; CURI, Rui; DIAS-NETO, Emmanuel; TAVARES-DE-LIMA, Wothan; FERREIRA, Caroline M.Asthma is a chronic inflammatory disease that affects more females than males after puberty, and its symptoms and severity in women change during menstruation and menopause. Recently, evidence has demonstrated that interactions among the microbiota, female sex hormones, and immunity are associated with the development of autoimmune diseases. However, no studies have investigated if therapeutic gut microbiota modulation strategies could affect asthma exacerbation during menstruation and menopause. Here we aimed to examine the preventive effects of a probiotic, Bifidobacterium longum 5(1A), on airway inflammation exacerbation in allergic ovariectomized mice. We first evaluated the gut microbiota composition and diversity in mice 10 days after ovariectomy. Next, we examined whether re-exposure of ovariectomized allergic mice to antigen (ovalbumin) would lead to exacerbation of lung inflammation. Finally, we evaluated the preventive and treatment effect of B. longum 5(1A) on lung inflammation and airway hyperresponsiveness. Our results showed that whereas ovariectomy caused no alterations in the gut microbiota composition and diversity in this animal model, 10 days after ovariectomy, preventive use administration of B. longum 5(1A), rather than its use after surgery was capable of attenuate the exacerbated lung inflammation and hyperresponsiveness in ovariectomized allergic mice. This prophylactic effect of B. longum 5(1A) involves acetate production, which led to increased fecal acetate levels and, consequently, increased Treg cells in ovariectomized allergic mice.
- signeR: an empirical Bayesian approach to mutational signature discovery(2017) ROSALES, Rafael A.; DRUMMOND, Rodrigo D.; VALIERIS, Renan; DIAS-NETO, Emmanuel; SILVA, Israel T. daMotivation: Mutational signatures can be used to understand cancer origins and provide a unique opportunity to group tumor types that share the same origins and result from similar processes. These signatures have been identified from high throughput sequencing data generated from cancer genomes by using non-negative matrix factorisation (NMF) techniques. Current methods based on optimization techniques are strongly sensitive to initial conditions due to high dimensionality and nonconvexity of the NMF paradigm. In this context, an important question consists in the determination of the actual number of signatures that best represent the data. The extraction of mutational signatures from high-throughput data still remains a daunting task. Results: Here we present a new method for the statistical estimation of mutational signatures based on an empirical Bayesian treatment of the NMF model. While requiring minimal intervention from the user, our method addresses the determination of the number of signatures directly as a model selection problem. In addition, we introduce two new concepts of significant clinical relevance for evaluating the mutational profile. The advantages brought by our approach are shown by the analysis of real and synthetic data. The later is used to compare our approach against two alternative methods mostly used in the literature and with the same NMF parametrization as the one considered here. Our approach is robust to initial conditions and more accurate than competing alternatives. It also estimates the correct number of signatures even when other methods fail. Results on real data agree well with current knowledge.
- A total transcriptome profiling method for plasma-derived extracellular vesicles: applications for liquid biopsies(2017) AMORIM, Maria G.; VALIERIS, Renan; DRUMMOND, Rodrigo D.; PIZZI, Melissa P.; FREITAS, Vanessa M.; SINIGAGLIA-COIMBRA, Rita; CALIN, George A.; PASQUALINI, Renata; ARAP, Wadih; SILVA, Israel T.; DIAS-NETO, Emmanuel; NUNES, Diana N.Extracellular vesicles (EVs) are key mediators of intercellular communication. Part of their biological effects can be attributed to the transfer of cargos of diverse types of RNAs, which are promising diagnostic and prognostic biomarkers. EVs found in human biofluids are a valuable source for the development of minimally invasive assays. However, the total transcriptional landscape of EVs is still largely unknown. Here we develop a new method for total transcriptome profiling of plasma-derived EVs by next generation sequencing (NGS) from limited quantities of patient-derived clinical samples, which enables the unbiased characterization of the complete RNA cargo, including both small- and long-RNAs, in a single library preparation step. This approach was applied to RNA extracted from EVs isolated by ultracentrifugation from the plasma of five healthy volunteers. Among the most abundant RNAs identified we found small RNAs such as tRNAs, miRNAs and miscellaneous RNAs, which have largely unknown functions. We also identified protein-coding and long noncoding transcripts, as well as circular RNA species that were also experimentally validated. This method enables, for the first time, the full spectrum of transcriptome data to be obtained from minute patient-derived samples, and will therefore potentially allow the identification of cell-to-cell communication mechanisms and biomarkers.
- Going viral? Linking the etiology of human prostate cancer to the PCA3 long noncoding RNA and oncogenic viruses(2017) TEIXEIRA, Andre A.; MARCHIO, Serena; DIAS-NETO, Emmanuel; NUNES, Diana N.; SILVA, Israel T. da; CHACKERIAN, Bryce; BARRY, Marc; LAUER, Richard C.; GIORDANO, Ricardo J.; SIDMAN, Richard L.; WHEELER, Cosette M.; CAVENEE, Webster K.; PASQUALINI, Renata; ARAP, Wadih
- Evaluation of PRUNE2 and PCA3 expression as metastasis predictors in Gleason 7 prostate cancer(2017) LAUER, Richard C.; BARRY, Marc; WU, Jin; LEE, Ji-Hyun; MCCANCE, Dennis J.; DU, Ruofei; RAO, Arpit; DOBROFF, Andrey S.; DIAS-NETO, Emmanuel; CHEN, Isan; PASQUALINI, Renata; ARAP, Wadih