A model for accurate quantification of CRISPR effects in pooled FACS screens.

CRISPR screens are powerful tools to identify key genes that underlie biological processes. One important type of screen uses fluorescence activated cell sorting (FACS) to sort perturbed cells into bins based on the expression level of marker genes, followed by guide RNA (gRNA) sequencing. Analysis of these data presents several statistical challenges due to multiple factors including the discrete nature of the bins and typically small numbers of replicate experiments. To address these challenges, we developed a robust and powerful Bayesian random effects model and software package called Waterbear. Furthermore, we used Waterbear to explore how various experimental design parameters affect statistical power to establish principled guidelines for future screens. Finally, we experimentally validated our experimental design model findings that, when using Waterbear for analysis, high power is maintained even at low cell coverage and a high multiplicity of infection. We anticipate that Waterbear will be of broad utility for analyzing FACS-based CRISPR screens.

Systematic decoding of cis gene regulation defines context-dependent control of the multi-gene costimulatory receptor locus in human T cells.

Cis-regulatory elements (CREs) interact with trans regulators to orchestrate gene expression, but how transcriptional regulation is coordinated in multi-gene loci has not been experimentally defined. We sought to characterize the CREs controlling dynamic expression of the adjacent costimulatory genes CD28, CTLA4 and ICOS, encoding regulators of T cell-mediated immunity. Tiling CRISPR interference (CRISPRi) screens in primary human T cells, both conventional and regulatory subsets, uncovered gene-, cell subset- and stimulation-specific CREs. Integration with CRISPR knockout screens and assay for transposase-accessible chromatin with sequencing (ATAC-seq) profiling identified trans regulators influencing chromatin states at specific CRISPRi-responsive elements to control costimulatory gene expression. We then discovered a critical CCCTC-binding factor (CTCF) boundary that reinforces CRE interaction with CTLA4 while also preventing promiscuous activation of CD28. By systematically mapping CREs and associated trans regulators directly in primary human T cell subsets, this work overcomes longstanding experimental limitations to decode context-dependent gene regulatory programs in a complex, multi-gene locus critical to immune homeostasis.

Systematic discovery and perturbation of regulatory genes in human T cells reveals the architecture of immune networks.

Gene regulatory networks ensure that important genes are expressed at precise levels. When gene expression is sufficiently perturbed, it can lead to disease. To understand how gene expression disruptions percolate through a network, we must first map connections between regulatory genes and their downstream targets. However, we lack comprehensive knowledge of the upstream regulators of most genes. Here, we developed an approach for systematic discovery of upstream regulators of critical immune factors-IL2RA, IL-2 and CTLA4-in primary human T cells. Then, we mapped the network of the target genes of these regulators and putative cis-regulatory elements using CRISPR perturbations, RNA-seq and ATAC-seq. These regulators form densely interconnected networks with extensive feedback loops. Furthermore, this network is enriched for immune-associated disease variants and genes. These results provide insight into how immune-associated disease genes are regulated in T cells and broader principles about the structure of human gene regulatory networks.

The Effect of Therapeutic Hypothermia after Cardiac Arrest on the Neurological Outcome and Survival-A Systematic Review of RCTs Published between 2016 and 2020.

Therapeutic hypothermia is a treatment used for patients who have suffered cardiorespiratory arrest and remain conscious after the recovery of spontaneous circulation. However, its effectiveness is controversial. The objective of this systematic review is to summarize the scientific evidence available about the effect of therapeutic hypothermia on neurological status and survival in this type of patients. METHODOLOGY: A primary search in CINAHL, CUIDEN, Pubmed, Web of Science, and Scopus databases was carried out. Randomized clinical trials (RCT) published from 2016 to 2020 were selected. RESULTS: 17 studies were selected for inclusion and most relevant data were extracted. Methodological quality was assessed by the RoB tool. CONCLUSIONS: Although therapeutic hypothermia is a safe technique with few adverse and manageable effects, it has not shown to improve survival rate and neurological status of adult nor pediatric patients. It is possible that its positive effect on neuroprotection could be achieved only by preventing hyperthermia although further investigation is needed.

Avicin G is a potent sphingomyelinase inhibitor and blocks oncogenic K- and H-Ras signaling.

K-Ras must interact primarily with the plasma membrane (PM) for its biological activity. Therefore, disrupting K-Ras PM interaction is a tractable approach to block oncogenic K-Ras activity. Here, we found that avicin G, a family of natural plant-derived triterpenoid saponins from Acacia victoriae, mislocalizes K-Ras from the PM and disrupts PM spatial organization of oncogenic K-Ras and H-Ras by depleting phosphatidylserine (PtdSer) and cholesterol contents, respectively,  at the inner PM leaflet. Avicin G also inhibits oncogenic K- and H-Ras signal output and the growth of K-Ras-addicted pancreatic and non-small cell lung cancer cells. We further identified that avicin G perturbs lysosomal activity, and disrupts cellular localization and activity of neutral and acid sphingomyelinases (SMases), resulting in elevated cellular sphingomyelin (SM) levels and altered SM distribution. Moreover, we show that neutral SMase inhibitors disrupt the PM localization of K-Ras and PtdSer and oncogenic K-Ras signaling. In sum, this study identifies avicin G as a new potent anti-Ras inhibitor, and suggests that neutral SMase can be a tractable target for developing anti-K-Ras therapeutics.

Acylpeptide hydrolase is a novel regulator of KRAS plasma membrane localization and function.

The primary site for KRAS signaling is the inner leaflet of the plasma membrane (PM). We previously reported that oxanthroquinone G01 (G01) inhibited KRAS PM localization and blocked KRAS signaling. In this study, we identified acylpeptide hydrolase (APEH) as a molecular target of G01. APEH formed a stable complex with biotinylated G01, and the enzymatic activity of APEH was inhibited by G01. APEH knockdown caused profound mislocalization of KRAS and reduced clustering of KRAS that remained PM localized. APEH knockdown also disrupted the PM localization of phosphatidylserine (PtdSer), a lipid critical for KRAS PM binding and clustering. The mislocalization of KRAS was fully rescued by ectopic expression of APEH in knockdown cells. APEH knockdown disrupted the endocytic recycling of epidermal growth factor receptor and transferrin receptor, suggesting that abrogation of recycling endosome function was mechanistically linked to the loss of KRAS and PtdSer from the PM. APEH knockdown abrogated RAS-RAF-MAPK signaling in cells expressing the constitutively active (oncogenic) mutant of KRAS (KRASG12V), and selectively inhibited the proliferation of KRAS-transformed pancreatic cancer cells. Taken together, these results identify APEH as a novel drug target for a potential anti-KRAS therapeutic.

Identification of novel ΔNp63α-regulated miRNAs using an optimized small RNA-Seq analysis pipeline.

Advances in high-throughput sequencing have enabled profiling of microRNAs (miRNAs), however, a consensus pipeline for sequencing of small RNAs has not been established. We built and optimized an analysis pipeline using Partek Flow, circumventing the need for analyzing data via scripting languages. Our analysis assessed the effect of alignment reference, normalization method, and statistical model choice on biological data. The pipeline was evaluated using sequencing data from HaCaT cells transfected with either a non-silencing control or siRNA against ΔNp63α, a p53 family member protein which is highly expressed in non-melanoma skin cancer and shown to regulate a number of miRNAs. We posit that 1) alignment and quantification to the miRBase reference provides the most robust quantitation of miRNAs, 2) normalizing sample reads via Trimmed Mean of M-values is the most robust method for accurate downstream analyses, and 3) use of the lognormal with shrinkage statistical model effectively identifies differentially expressed miRNAs. Using our pipeline, we identified previously unrecognized regulation of miRs-149-5p, 18a-5p, 19b-1-5p, 20a-5p, 590-5p, 744-5p and 93-5p by ΔNp63α. Regulation of these miRNAs was validated by RT-qPCR, substantiating our small RNA-Seq pipeline. Further analysis of these miRNAs may provide insight into ΔNp63α's role in cancer progression. By defining the optimal alignment reference, normalization method, and statistical model for analysis of miRNA sequencing data, we have established an analysis pipeline that may be carried out in Partek Flow or at the command line. In this manner, our pipeline circumvents some of the major hurdles encountered during small RNA-Seq analysis.

[USE, EFFECTS, AND KNOWLEDGE OF THE NUTRITIONAL SUPPLEMENTS FOR THE SPORT IN UNIVERSITY STUDENTS]. / USO, EFECTOS Y CONOCIMIENTOS DE LOS SUPLEMENTOS NUTRICIONALES PARA EL DEPORTE EN ESTUDIANTES UNIVERSITARIOS.

BACKGROUND: consumption and marketing of supplements that help improve athletic performance has increased in semi-professional sport. Moreover, in the market are increasingly a wide variety of such products pressure and high performance requirements push many young athletes to have recourse to the use of supplements to improve your fitness. However, this type of treatment should be advised and guided by an expert since improper use of such supplements favors the appearance of adverse effects and can be harmful to the health of the individual. OBJECTIVE: to know the use of supplements to improve athletic performance by college athletes methods: was a systematic review in the Pubmed database, care, BIREME CUIDEN, BIREME (IBECS y Scielo) and CINHAL limited to articles published in the last ten years. RESULTS: 25 articles were analyzed. The main themes were found in the literature reviewed have been three: the "levels of supplements to increase athletic performance in college students", "effect of sports supplements" and "knowledge, behaviors and motivations for sports supplements". CONCLUSIONS: taking into account that the around 55% of University athletes using supplements but show a lack significant knowledge is necessary to provide a health education on such supplements.

Introducción: el consumo y comercialización de suplementos que ayudan a mejorar el rendimiento físico ha aumentado en el ámbito deportivo semiprofesional. Además, la comercialización de este tipo de productos en el mercado cada vez es más variada. La presión y las altas exigencias de rendimiento personal empujan a muchos jóvenes estudiantes y deportistas a recurrir al uso de suplementos con objeto de mejorar su forma física. Sin embargo, este proceso debiera ser aconsejado y guiado por un experto, puesto que un uso incorrecto de dichos suplementos favorece la aparición de efectos adversos, con el consecuente perjuicio para la salud del individuo. Objetivo: conocer el grado de conocimientos, usos y efectos de los suplementos para la mejora del rendimiento deportivo por parte de estudiantes universitarios. Métodos: se efectuó una revisión sistemática en las bases de datos de Pubmed, CUIDEN, BIREME (IBECS y Scielo), CINHAL y Scopus limitada a artículos publicados en los últimos diez años. Resultados: se analizaron 32 artículos. Las temáticas principales encontradas en la literatura revisada han sido tres: los "niveles de consumo de suplementos para aumentar el rendimiento deportivo en estudiantes universitarios", el "efecto del consumo de suplementos deportivos" y los "conocimientos, conductas y motivaciones para el consumo de suplementos deportivos". Conclusiones: existe una gran heterogeneidad sobre el consumo de suplementos para la mejora del rendimiento deportivo y son muchas las sustancias que se ponen a prueba para comprobar su verdadero efecto, no consiguiendo en múltiples ocasiones el objetivo de mejorar dicho rendimiento.