Um fluxo de análise quantitativa de dados de transcriptômica de células únicas no contexo de células-tronco pluripotentes induzidas

TCC(graduação) - Universidade Federal de Santa Catarina. Centro de Ciências Biológicas. Biologia.Células-tronco pluripotentes induzidas são células reprogramadas a partir de células somáticas de modo a adquirir pluripotência – a capacidade de se diferenciar em qualquer tipo de célula. Com um protocolo de diferenciação adequado, podemos transformá-las em diversas outras células do organismo. Desde sua criação, diversos avanços em protocolos e técnicas laboratoriais permitem seu uso em pesquisa e terapias celulares. Contudo, o processo de diferenciação é falho e nem todas as células se transformam nas células alvo intencionadas. Nesse contexto, o sequenciamento de transcriptômica de células únicas se mostra uma poderosa ferramenta para a obtenção de informações. Ferramentas de bioinformática são fundamentais nesse processo, nos permitindo analisar a expressão gênica de uma célula e inferir seu tipo celular. Diversas ferramentas são utilizadas em diferentes passos do processo de análise. De modo geral, essas ferramentas são reprodutíveis. No entanto, é comum que o usuário tenha dificuldades em instalar a ferramenta e utilizar scripts fora do contexto onde foram escritos. Para que não ocorram situações como essas, estruturamos o uso dessas ferramentas em uma pipeline de análise. Boas práticas de construção de pipeline mostram a necessidade de desenvolvê-la de forma modular, reprodutível e compartimentalizada. Para tal, é necessário o uso de ferramentas de gerenciamento de fluxo de trabalho e containers de dependências dos pacotes. Este trabalho buscou construir uma pipeline de análise de dados de transcriptômica de células únicas no contexto de células-tronco pluripotentes induzidas. Além disso, visou criar um score que avalia a importância que determinado gene teve na classificação de uma amostra. As ferramentas de análise utilizadas na pipeline foram FUSCA, singleCellNet, Seurat e Symphony. Os recursos utilizados para a construção da estrutura da pipeline foram o gerenciador de fluxo de trabalho Snakemake e o container Singularity. A avaliação de eficácia da pipeline foi medida com sua aplicação em dados de células únicas de neurônios dopaminérgicos derivados de células-tronco pluripotentes induzidas, utilizando um conjunto de dados de células da região ventral do mesencéfalo de embriões humanos. A pipeline foi capaz de identificar os tipos celulares das células em questão e esses foram compatíveis com a tipagem feita pelos autores. As figuras geradas são acessíveis e podem ser utilizadas para a construção de um relatório ou trabalho científico. Por fim, a pipeline está disponível para acesso e uso público em https://github.com/gacrestani/ipsc-pipeline.Induced pluripotent stem cells (iPSCs) are cells reprogrammed from somatic cells to acquire pluripotency – the ability to differentiate into any cell type of an organism. With a differentiation protocol, one can transform them into those several other cells. Since their creation, several advances in laboratory protocols and techniques allow their use in biomedical research and cell therapies. However, the differentiation process is flawed and not all cells turn into the intended target cells. In this context, single cell transcriptomics sequencing proves to be a powerful tool for obtaining information. Bioinformatics tools are fundamental in this process, allowing us to analyze the gene expression of a cell and, by it, infer its cell type. Several tools are used in different steps of the analysis process. In general, these tools are reproducible. However, it is common for the user to have difficulties installing the tool and using scripts outside the context where they were written. To minimize those situations, we have structured the use of these tools in an analysis pipeline. Good pipeline construction practices state the need to develop it in a modular, reproducible and compartmentalized way. To do so, it is necessary to use workflow management tools and package dependency containers. This work aimed to build a pipeline for analyzing single cell transcriptomics data in the context of induced pluripotent stem cells. In addition, it aimed to create a score that assesses the importance that a given gene had in the classification of a sample. The analysis tools used in the pipeline were FUSCA, singleCellNet, Seurat and Symphony. The resources used to build the pipeline structure were the workflow manager Snakemake and the container manager Singularity. The evaluation of the effectiveness of the pipeline was measured with its application to single cell data from dopaminergic neurons derived from induced pluripotent stem cells, using a dataset of cells from the ventral region of the midbrain of human embryos. The pipeline was able to identify the cell types of the cells in question and these were compatible with the types found by the authors. The generated figures are accessible and can be used to build a report or scientific work. Finally, the pipeline is available for public use on https://github.com/gacrestani/ipsc-pipeline

Telehealth in Urology: A Systematic Review of the Literature. How Much Can Telemedicine Be Useful During and After the COVID-19 Pandemic?

Coronavirus disease 2019 (COVID-19) pandemic has caused increased interest in the application of telehealth to provide care without exposing patients and physicians to the risk of contagion. The urological literature on the topic is sparse

Urology practice during the COVID-19 vaccination campaign

The current scenario of the COVID-19 pandemic is significantly different from that of the first, emergency phase. Several countries in the world are experiencing a second, or even a third, wave of contagion, while awaiting the effects of mass vaccination campaigns. The aim of this report was to provide an update of previously released recommendations on prioritization and restructuring of urological activities

Como os computadores podem ajudar a curar o câncer?

Divulgação Científica para a comunidade. Universidade Federal de Santa Catarina.Como os computadores auxiliam a pesquisa do cânce

Mecanismos oxidativos na neuropatia periférica induzida por quimioterápicos

Seminário de Iniciação Científica e Tecnológica. Universidade Federal de Santa Catarina. Centro de Ciências Biológicas.O paclitaxel (PTX) é um dos antitumorais mais utilizados no tratamento de diferentes tipos tumorais. Contudo, um efeito adverso muito frequente com o uso desse fármaco é o desenvolvimento de neuropatia periférica induzida por quimioterapia (NPIQ), a qual pode afetar significativamente a qualidade de vida dos pacientes em tratamento quimioterápico, bem como pode gerar casos de resistência ao fármaco e afetar a eficácia terapêutica. Estudos mostram que animais com neuropatia periférica induzida por quimioterapia, neste caso por paclitaxel, apresentam danos em mitocôndrias, levando ao aumento de espécies reativas de oxigênio (ERO) e nitrogênio (ERN) e, consequentemente, desenvolvimento de um quadro de estresse oxidativo. Com isso, o objetivo deste trabalho foi avaliar o efeito da N-acetilcisteína (NAC), ácido lipoico (AL) e vitamina E, todos antioxidantes, na hiperalgesia mecânica e alodinia ao frio em modelo de neuropatia periférica induzida pelo paclitaxel em camundongos fêmeas da linhagem Swiss. A neuropatia foi induzida através da administração intraperitoneal de paclitaxel 5 mg/kg e o tratamento com os antioxidantes foi realizado por via oral, todos na dose de 50 mg/kg, durante 14 dias. Para avaliar a nocicepção mecânica e térmica foram utilizados os testes de Von Frey e da placa fria, respectivamente. Além disso, através do implante de tumores subcutâneos de Ehrlich, avaliamos se os antioxidantes possuem efeitos anti ou pró-tumorais in vivo. O tratamento com os antioxidantes reduziu a nocicepção mecânica e alodinia ao frio induzida pelo paclitaxel quando iniciado concomitante com o quimioterápico. Em modelos de tumor subcutâneo, o crescimento tumoral não foi negativamente afetado pelo uso dos antioxidantes, porém a linhagem celular implantada mostrou-se resistente ao paclitaxel. Sendo assim, os dados mostram que o uso da NAC, ácido lipoico e vitamina E pode ter relevância farmacológica no tratamento da NPIQ de acordo com od dados deste estudo não-clínico

Urology practice during COVID-19 pandemic

The severe acute respiratory syndrome coronavirus 2 and the disease it causes, coronavirus disease 2019 (COVID-19) is generating a rapid and tragic health emergency in Italy due to the need to provide assistance to an overwhelming number of infected patients and, at the same time, treat all the non-deferrable oncological and benign conditions. A panel of Italian urologists has agreed on possible strategies for the reorganization of urological routine practice and on a set of recommendations that should facilitate the process of rescheduling both surgical and outpatient activities during the COVID-19 pandemic and in the subsequent phases. This document could be a valid tool to be used in routine clinical practice and, possibly, a cornerstone for further discussion on the topic also considering the further evolution of the COVID-19 pandemic. It also may provide useful recommendations for national and international urological societies in a condition of emergency

Clinical Pathways for Urology Patients During the COVID-19 Pandemic

The public health emergency caused by the Coronavirus Disease 2019 (COVID-19) pandemic has resulted in a significant reallocation of health resources with a consequent reorganization of the clinical activities also in several urological centers. A panel of Italian urologists has agreed on a set of recommendations on pathways of pre-, intra- and post-operative care for urological patients undergoing urgent procedures or non-deferrable oncological interventions during the COVID-19 pandemic. Simplification of the diagnostic and staging pathway has to be prioritized in order to reduce hospital visits and consequently the risk of contagion. In absence of strict uniform regulations that impose the implementation of nasopharyngeal swabs, we recommend that an accurate triage for possible COVID-19 symptoms be performed both by telephone at home before hospitalization and at the time of hospitalization. We recommend that during hospital stay patients should be provided with as many instructions as possible to facilitate their return to, and stay at, home. Patients should be discharged under stable good conditions in order to minimize the risk of readmission. It is advisable to reduce or reschedule post-discharge controls and implement an adequate system of communication for telemonitoring discharged patients in order to reduce hospital visits

Telehealth in Urology: A Systematic Review of the Literature. How Much Can Telemedicine Be Useful During and After the COVID-19 Pandemic?

Context: Coronavirus disease 2019 (COVID-19) pandemic has caused increased interest in the application of telehealth to provide care without exposing patients and physicians to the risk of contagion. The urological literature on the topic is sparse. Objective: To perform a systematic review of the literature and evaluate all the available studies on urological applications of telehealth. Evidence acquisition: After registration on PROSPERO, we searched PubMed and Scopus databases to collect any kind of studies evaluating any telehealth interventions in any urological conditions. The National Toxicology Program/Office of Health Assessment and Translation Risk of Bias Rating Tool for Human and Animal Studies was used to estimate the risk of bias. A narrative synthesis was performed. Evidence synthesis: We identified 45 studies (11 concerning prostate cancer [PCa], three hematuria management, six urinary stones, 14 urinary incontinence [UI], five urinary tract infections [UTIs], and six other conditions), including 12 randomized controlled trials. The available literature indicates that telemedicine has been implemented successfully in several common clinical scenarios, including the decision-making process following a diagnosis of nonmetastatic PCa, follow-up care of patients with localized PCa after curative treatments, initial diagnosis of hematuria, management diagnosis and follow-up care of uncomplicated urinary stones and uncomplicated UTIs, and initial evaluation, behavioral therapies, and pelvic floor muscle training in UI patients, as well as follow-up care after surgical treatments of stress urinary incontinence or pelvic organ prolapse. The methodological quality of most of the reports was good. Conclusions: Telehealth has been implemented successfully in selected patients with PCa, UI, pelvic organ prolapse, uncomplicated urinary stones, and UTIs. Many urological conditions are suitable for telehealth, but more studies are needed on other highly prevalent urological malignant and benign conditions. Likely, the COVID-19 pandemic will give a significant boost to the use of telemedicine. More robust data on long-term efficacy, safety, and health economics are necessary. Patient summary: The diffusion of coronavirus disease 2019 (COVID-19) infections has recently increased the interest in telehealth, which is the adoption of telecommunication to deliver any health care activity. The available literature indicates that telemedicine has been adopted successfully in selected patients with several common clinical urological conditions, including prostate cancer, uncomplicated urinary stones, uncomplicated urinary infections, urinary incontinence, or pelvic organ prolapse. Likely, the COVID-19 pandemic will give a significant boost to the use of telemedicine, but more robust data on long-term efficacy, safety, and costs are necessary