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Genome scale screen

Nicholas J Slipek, Jyotika Varshney, David A Largaespada
Since the advent of large-scale, detailed descriptive cancer genomics studies at the beginning of the century, such as The Cancer Genome Atlas (TCGA), labs around the world have been working to make this data useful. Data like these can be made more useful by comparison with complementary functional genomic data. One new example is the application of CRISPR/Cas9-based library screening for cancer-related traits in cell lines. Such screens can reveal genome-wide suppressors of tumorigenesis and metastasis. Here we describe the use of widely available lentiviral libraries for such screens in cultured cell lines...
2019: Methods in Molecular Biology
Yujia Zheng, Yulin Liu, Songfeng Zhao, Zhetian Zheng, Chunyi Shen, Li An, Yongliang Yuan
Background: Hepatocellular carcinoma (HCC) is a major cause of cancer mortality and an increasing incidence worldwide; however, there are very few effective diagnostic approaches and prognostic biomarkers. Materials and methods: One hundred forty-nine pairs of HCC samples from Gene Expression Omnibus (GEO) were obtained to screen differentially expressed genes (DEGs) between HCC and normal samples. The Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, Gene ontology enrichment analyses, and protein-protein interaction network were used...
2018: Cancer Management and Research
Amanda Balboni Iniguez, Gabriela Alexe, Emily Jue Wang, Giovanni Roti, Sarvagna Patel, Liying Chen, Samuel Kitara, Amy Conway, Amanda L Robichaud, Björn Stolte, Pratiti Bandopadhayay, Amy Goodale, Sasha Pantel, Yenarae Lee, Dorian M Cheff, Matthew D Hall, Rajarshi Guha, Mindy I Davis, Marie Menard, Nicole Nasholm, William A Weiss, Jun Qi, Rameen Beroukhim, Federica Piccioni, Cory Johannessen, Kimberly Stegmaier
Drug resistance represents a major challenge to achieving durable responses to cancer therapeutics. Resistance mechanisms to epigenetically targeted drugs remain largely unexplored. We used bromodomain and extra-terminal domain (BET) inhibition in neuroblastoma as a prototype to model resistance to chromatin modulatory therapeutics. Genome-scale, pooled lentiviral open reading frame (ORF) and CRISPR knockout rescue screens nominated the phosphatidylinositol 3-kinase (PI3K) pathway as promoting resistance to BET inhibition...
December 10, 2018: Cancer Cell
Megan C McDonald, Melanie Renkin, Merrin Spackman, Beverly Orchard, Daniel Croll, Peter S Solomon, Andrew Milgate
Zymoseptoria tritici is a globally distributed fungal pathogen, which causes Septoria tritici blotch on wheat. Management of the disease is attempted through the deployment of resistant wheat cultivars and the application of fungicides. However, fungicide resistance is commonly observed in Z. tritici populations and continuous monitoring is required to detect breakdowns in fungicide efficacy. We recently reported azole resistant isolates in Australia, however it remained unknown whether resistance was brought into the continent through gene flow or whether resistance emerged independently...
December 7, 2018: Applied and Environmental Microbiology
Kristen M Cunanan, Alexia Iasonos, Ronglai Shen, Mithat Gönen
BACKGROUND: In the era of targeted therapies, clinical trials in oncology are rapidly evolving, wherein patients from multiple diseases are now enrolled and treated according to their genomic mutation(s). In such trials, known as basket trials, the different disease cohorts form the different baskets for inference. Several approaches have been proposed in the literature to efficiently use information from all baskets while simultaneously screening to find individual baskets where the drug works...
December 7, 2018: Clinical Trials: Journal of the Society for Clinical Trials
Gaia Chiara Mannino, Francesco Andreozzi, Giorgio Sesti
Type 2 diabetes mellitus (T2DM) is a chronic disease that has reached the levels of a global epidemic. In order to achieve optimal glucose control it is often necessary to rely on combination therapy of multiple drugs or insulin, because uncontrolled glucose levels result in T2DM progression and enhanced risk of complications and mortality. Several anti-hyperglycemic agents have been developed over time, and T2DM pharmacotherapy should be prescribed based on suitability for the individual patient's characteristics...
December 4, 2018: Diabetes/metabolism Research and Reviews
Lucrecia Carrera-Quintanar, Daniel Ortuño-Sahagún, Noel N Franco-Arroyo, Juan M Viveros-Paredes, Adelaida S Zepeda-Morales, Rocio I Lopez-Roa
Obesity is a noncommunicable disease that affects a considerable part of humanity. Recently, it has been recognized that gut microbiota constitutes a fundamental factor in the triggering and development of a large number of pathologies, among which obesity is one of the most related to the processes of dysbiosis. In this review, different animal model approaches, methodologies, and genome scale metabolic databases were revisited to study the gut microbiota and its relationship with metabolic disease. As a data source, PubMed for English-language published material from 1 January 2013, to 22 August 2018, were screened...
November 30, 2018: International Journal of Molecular Sciences
Miguel A Matilla, Abdelali Daddaoua, Andrea Chini, Bertrand Morel, Tino Krell
The majority of clinically used antibiotics originate from bacteria. As the need for new antibiotics grows, large-scale genome sequencing and mining approaches are being used to identify novel antibiotics. However, this task is hampered by the fact that many antibiotic biosynthetic clusters are not expressed under laboratory conditions. One strategy to overcome this limitation is the identification of signals that activate the expression of silent biosynthetic pathways. Here, we report the use of high-throughput screening to identify signals that control the biosynthesis of the acetyl-CoA carboxylase inhibitor antibiotic andrimid in the broad-range antibiotic-producing rhizobacterium Serratia plymuthica A153...
November 30, 2018: Nucleic Acids Research
Björn E Langer, Michael Hiller
Changes in gene regulation are important for phenotypic and in particular morphological evolution. However, it remains challenging to identify the transcription factors (TFs) that contribute to differences in gene regulation and thus to phenotypic differences between species. Here, we present TFforge (Transcription Factor forward genomics), a computational method to identify TFs that are involved in the loss of phenotypic traits. TFforge screens an input set of regulatory genomic regions to detect TFs that exhibit a significant binding site divergence signature in species that lost a particular phenotypic trait...
November 28, 2018: Nucleic Acids Research
Susana Campino, Alejandro Marin-Menendez, Alison Kemp, Nadia Cross, Laura Drought, Thomas D Otto, Ernest Diez Benavente, Matt Ravenhall, Frank Schwach, Gareth Girling, Magnus Manske, Michel Theron, Kelda Gould, Eleanor Drury, Taane G Clark, Dominic P Kwiatkowski, Alena Pance, Julian C Rayner
Invasion of human erythrocytes is essential for Plasmodium falciparum parasite survival and pathogenesis, and is also a complex phenotype. While some later steps in invasion appear to be invariant and essential, the earlier steps of recognition are controlled by a series of redundant, and only partially understood, receptor-ligand interactions. Reverse genetic analysis of laboratory adapted strains has identified multiple genes that when deleted can alter invasion, but how the relative contributions of each gene translate to the phenotypes of clinical isolates is far from clear...
November 29, 2018: PLoS Pathogens
Ludwig Lausser, Lea Siegle, Wolfgang Rottbauer, Derk Frank, Steffen Just, Hans A Kestler
Genetic model organisms have the potential of removing blind spots from the underlying gene regulatory networks of human diseases. Allowing analyses under experimental conditions they complement the insights gained from observational data. An inevitable requirement for a successful trans-species transfer is an abstract but precise high-level characterization of experimental findings. In this work, we provide a large-scale analysis of seven weak contractility/heart failure genotypes of the model organism zebrafish which all share a weak contractility phenotype...
November 26, 2018: Biomolecules
Li Xue, Bin Tang, Wei Chen, Jiesi Luo
The CRISPR-Cas9 system derived from adaptive immunity in bacteria and archaea has been developed into a powerful tool for genome engineering with wide-ranging applications. Optimizing single guide RNA (sgRNA) design to improve efficiency of target cleavage is a key step for successful gene editing using the CRISPR-Cas9 system. Because not all sgRNAs that cognate to a given target gene are equally effective, computational tools have been developed based on experimental data to increase the likelihood of selecting effective sgRNAs...
November 28, 2018: Journal of Chemical Information and Modeling
Agustina Rimondi, Ana S Gonzalez-Reiche, Valeria S Olivera, Julieta Decarre, Gabriel J Castresana, Marcelo Romano, Martha I Nelson, Harm van Bakel, Ariel J Pereda, Lucas Ferreri, Ginger Geiger, Daniel R Perez
Wild aquatic birds are the major reservoir of influenza A virus. Cloacal swabs and feces samples (n = 6595) were collected from 62 bird species in Argentina from 2006 to 2016 and screened for influenza A virus. Full genome sequencing of 15 influenza isolates from 6 waterfowl species revealed subtypes combinations that were previously described in South America (H1N1, H4N2, H4N6 (n = 3), H5N3, H6N2 (n = 4), and H10N7 (n = 2)), and new ones not previously identified in the region (H4N8, H7N7 and H7N9)...
November 28, 2018: Emerging Microbes & Infections
Andrea Chai, Ana M Mateus, Fazal Oozeer, Rita Sousa-Nunes
Studies in genetic model organisms have revealed much about the development and pathology of complex tissues. Most have focused on cell-intrinsic gene functions and mechanisms. Much less is known about how transformed, or otherwise functionally disrupted, cells interact with healthy ones towards a favorable or pathological outcome. This is largely due to technical limitations. We developed new genetic tools in Drosophila melanogaster that permit efficient multiplexed gain- and loss-of-function genetic perturbations with separable spatial and temporal control...
November 27, 2018: ELife
Zheng-Shan Chong, Shuhei Ohnishi, Kosuke Yusa, Gavin J Wright
Extracellular interactions between cell surface receptors are necessary for signaling and adhesion but identifying them remains technically challenging. We describe a cell-based genome-wide approach employing CRISPR activation to identify receptors for a defined ligand. We show receptors for high-affinity antibodies and low-affinity ligands can be unambiguously identified when used in pools or as individual binding probes. We apply this technique to identify ligands for the adhesion G-protein-coupled receptors and show that the Nogo myelin-associated inhibitory proteins are ligands for ADGRB1...
November 26, 2018: Genome Biology
Chiara Rezzoagli, David Wilson, Michael Weigert, Stefan Wyder, Rolf Kümmerli
Lay Summary: We probed the evolutionary robustness of two antivirulence drugs, gallium and flucytosine, targeting the iron-scavenging pyoverdine in the opportunistic pathogen Pseudomonas aeruginosa . Using an experimental evolution approach in human serum, we showed that antivirulence treatments are not evolutionarily robust per se, but vary in their propensity to select for resistance. Background and objectives: Treatments that inhibit the expression or functioning of bacterial virulence factors hold great promise to be both effective and exert weaker selection for resistance than conventional antibiotics...
2018: Evolution, Medicine, and Public Health
Wenyu Li, Zheran Liu, Bowen Liang, Siyang Chen, Xinping Zhang, Xiaoqin Tong, Weiming Lou, Lulu Le, Xiaoli Tang, Fen Fu
BACKGROUND: Epithelial ovarian cancer is one of the most severe public health threats in women. Since it is still challenging to screen in early stages, identification of core genes that play an essential role in epithelial ovarian cancer initiation and progression is of vital importance. RESULTS: Seven gene expression datasets (GSE6008, GSE18520, GSE26712, GSE27651, GSE29450, GSE36668, and GSE52037) containing 396 ovarian cancer samples and 54 healthy control samples were analyzed to identify the significant differentially expressed genes (DEGs)...
November 19, 2018: Journal of Ovarian Research
Eric Shifrut, Julia Carnevale, Victoria Tobin, Theodore L Roth, Jonathan M Woo, Christina T Bui, P Jonathan Li, Morgan E Diolaiti, Alan Ashworth, Alexander Marson
Human T cells are central effectors of immunity and cancer immunotherapy. CRISPR-based functional studies in T cells could prioritize novel targets for drug development and improve the design of genetically reprogrammed cell-based therapies. However, large-scale CRISPR screens have been challenging in primary human cells. We developed a new method, single guide RNA (sgRNA) lentiviral infection with Cas9 protein electroporation (SLICE), to identify regulators of stimulation responses in primary human T cells...
November 13, 2018: Cell
Qing Liu, Chun Wang, Xiaozhen Jiao, Huawei Zhang, Lili Song, Yanxin Li, Caixia Gao, Kejian Wang
The CRISPR/Cas system has been extensively applied to make precise genetic modifications in various organisms. Despite its importance and widespread use, large-scale mutation screening remains time-consuming, labour-intensive and costly. Here, we developed Hi-TOM (available at ), an online tool to track the mutations with precise percentage for multiple samples and multiple target sites. We also described a corresponding next-generation sequencing (NGS) library construction strategy by fixing the bridge sequences and barcoding primers...
November 13, 2018: Science China. Life Sciences
Dylan T Blaha, Scott D Anderson, Daniel M Yoakum, Marlies V Hager, Yuanyuan Zha, Thomas F Gajewski, David Kranz
Mutated peptides (neoantigens) from a patient's cancer genome can serve as targets for T-cell immunity, but identifying which peptides can be presented by an MHC molecule and elicit T cells has been difficult. Although algorithms that predict MHC binding exist, they are not yet able to distinguish experimental differences in half-lives of the complexes (an immunologically relevant parameter, referred to here as kinetic stability). Improvement in determining actual neoantigen peptide/MHC stability could be important, as only a small fraction of peptides in most current vaccines are capable of eliciting CD8+ T-cell responses...
November 13, 2018: Cancer Immunology Research
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