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https://www.readbyqxmd.com/read/29691470/crispr-cas9-genome-editing-technology-significantly-accelerated-herpes-simplex-virus-research
#1
REVIEW
Dong Wang, Xian-Wang Wang, Xiao-Chun Peng, Ying Xiang, Shi-Bao Song, Ying-Ying Wang, Lin Chen, Victoria W Xin, Yan-Ning Lyu, Jiafu Ji, Zhao-Wu Ma, Cheng-Bin Li, Hong-Wu Xin
Herpes simplex viruses (HSVs) are important pathogens and ideal for gene therapy due to its large genome size. Previous researches on HSVs were hampered because the technology to construct recombinant HSVs were based on DNA homology-dependent repair (HDR) and plaque assay, which are inefficient, laborious, and time-consuming. Fortunately, clustered regularly interspaced short palindromic repeat/CRISPR-associated protein 9 (CRISPR/Cas9) recently provided the possibility to precisely, efficiently, and rapidly edit genomes and indeed is successfully being used in HSVs...
April 25, 2018: Cancer Gene Therapy
https://www.readbyqxmd.com/read/29690620/silk-route-to-the-acceptance-and-re-implementation-of-bacteriophage-therapy-part-ii
#2
Wilbert Sybesma, Christine Rohde, Pavol Bardy, Jean-Paul Pirnay, Ian Cooper, Jonathan Caplin, Nina Chanishvili, Aidan Coffey, Daniel De Vos, Amber Hartman Scholz, Shawna McCallin, Hilke Marie Püschner, Roman Pantucek, Rustam Aminov, Jiří Doškař, D İpek Kurtbӧke
This perspective paper follows up on earlier communications on bacteriophage therapy that we wrote as a multidisciplinary and intercontinental expert-panel when we first met at a bacteriophage conference hosted by the Eliava Institute in Tbilisi, Georgia in 2015. In the context of a society that is confronted with an ever-increasing number of antibiotic-resistant bacteria, we build on the previously made recommendations and specifically address how the Nagoya Protocol might impact the further development of bacteriophage therapy...
April 23, 2018: Antibiotics
https://www.readbyqxmd.com/read/29687998/5s-rrna-promoter-for-guide-rna-expression-enabled-highly-efficient-crispr-cas9-genome-editing-in-aspergillus-niger
#3
Xiaomei Zheng, Ping Zheng, Kun Zhang, Timothy Charlie Cairns, Vera Meyer, Jibin Sun, Yanhe Ma
The CRISPR/Cas9 system is a revolutionary genome editing tool. However, in eukaryotes, search and optimization of a suitable promoter for guide RNA expression is a significant technical challenge. Here we used the industrially important fungus, Aspergillus niger, to demonstrate that the 5S rRNA gene, which is both highly conserved and efficiently expressed in eukaryotes, can be used as a guide RNA promoter. The gene editing system was established with 100% rates of precision gene modifications among dozens of transformants using short (40-bp) homologous donor DNA...
April 24, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/29687035/pharmacology-of-recombinant-adeno-associated-virus-production
#4
REVIEW
Magalie Penaud-Budloo, Achille François, Nathalie Clément, Eduard Ayuso
Recombinant adeno-associated viral (rAAV) vectors have been used in more than 150 clinical trials with a good safety profile and significant clinical benefit in many genetic diseases. In addition, due to their ability to infect non-dividing and dividing cells and to serve as efficient substrate for homologous recombination, rAAVs are being used as a tool for gene-editing approaches. However, manufacturing of these vectors at high quantities and fulfilling current good manufacturing practices (GMP) is still a challenge, and several technological platforms are competing for this niche...
March 16, 2018: Molecular Therapy. Methods & Clinical Development
https://www.readbyqxmd.com/read/29685812/the-cf-canada-sick-kids-program-in-individual-cf-therapy-a-resource-for-the-advancement-of-personalized-medicine-in-cf
#5
Paul D W Eckford, Jacqueline McCormack, Lise Munsie, Gengming He, Sanja Stanojevic, Sergio L Pereira, Karen Ho, Julie Avolio, Claire Bartlett, Jin Ye Yang, Amy P Wong, Leigh Wellhauser, Ling Jun Huan, Jia Xin Jiang, Hong Ouyang, Kai Du, Michelle Klingel, Lianna Kyriakopoulou, Tanja Gonska, Theo J Moraes, Lisa J Strug, Janet Rossant, Felix Ratjen, Christine E Bear
BACKGROUND: Therapies targeting certain CFTR mutants have been approved, yet variations in clinical response highlight the need for in-vitro and genetic tools that predict patient-specific clinical outcomes. Toward this goal, the CF Canada-Sick Kids Program in Individual CF Therapy (CFIT) is generating a "first of its kind", comprehensive resource containing patient-specific cell cultures and data from 100 CF individuals that will enable modeling of therapeutic responses. METHODS: The CFIT program is generating: 1) nasal cells from drug naïve patients suitable for culture and the study of drug responses in vitro, 2) matched gene expression data obtained by sequencing the RNA from the primary nasal tissue, 3) whole genome sequencing of blood derived DNA from each of the 100 participants, 4) induced pluripotent stem cells (iPSCs) generated from each participant's blood sample, 5) CRISPR-edited isogenic control iPSC lines and 6) prospective clinical data from patients treated with CF modulators...
April 20, 2018: Journal of Cystic Fibrosis: Official Journal of the European Cystic Fibrosis Society
https://www.readbyqxmd.com/read/29683383/lipid-nanoparticles-enabling-gene-therapies-from-concepts-to-clinical-utility
#6
Jayesh A Kulkarni, Pieter R Cullis, Roy van der Meel
Genetic drugs based on RNA or DNA have remarkable therapeutic potential as virtually any disease can be treated by silencing a pathological gene, expressing a beneficial protein, or by editing defective genes. However, therapies based on nucleic acid polymers require sophisticated delivery systems to deliver these macromolecules to the interior of target cells. In this study, we review progress in developing nonviral lipid nanoparticle (LNP) delivery systems that have attractive properties, including ease of manufacture, reduced immune responses, multidosing capabilities, larger payloads, and flexibility of design...
April 23, 2018: Nucleic Acid Therapeutics
https://www.readbyqxmd.com/read/29680088/clustered-regularly-interspaced-short-palindromic-repeat-crispr-crispr-associated-endonuclease-cas9-mediated-homology-independent-integration-for-generating-quality-control-materials-for-clinical-molecular-genetic-testing
#7
Guigao Lin, Kuo Zhang, Rongxue Peng, Yanxi Han, Jiehong Xie, Jinming Li
Genome-edited human cell lines are important resources for producing quality control materials for clinical molecular genetic testing. Generating cell lines with defined mutations through homology-directed repair-based methods are inefficient and can lead to unwanted insertions and deletions in the target loci. Nonhomologous end joining in the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated endonuclease Cas9 (Cas9) system was harnessed to generate genome-engineered cell lines harboring target mutations...
May 2018: Journal of Molecular Diagnostics: JMD
https://www.readbyqxmd.com/read/29676720/mutagenic-repair-of-double-stranded-dna-breaks-in-vaccinia-virus-genomes-requires-cellular-dna-ligase-iv-activity-in-the-cytosol
#8
Rutger David Luteijn, Ingo Drexler, Geoffrey L Smith, Robert Jan Lebbink, Emmanuel J H J Wiertz
Poxviruses comprise a group of large dsDNA viruses that include members relevant to human and animal health, such as variola virus, monkeypox virus, cowpox virus and vaccinia virus (VACV). Poxviruses are remarkable for their unique replication cycle, which is restricted to the cytoplasm of infected cells. The independence from the host nucleus requires poxviruses to encode most of the enzymes involved in DNA replication, transcription and processing. Here, we use the CRISPR/Cas9 genome engineering system to induce DNA damage to VACV (strain Western Reserve) genomes...
April 20, 2018: Journal of General Virology
https://www.readbyqxmd.com/read/29672770/clustered-regularly-interspaced-short-palindromic-repeats-crispr-crispr-associated-protein-9-with-improved-proof-reading-enhances-homology-directed-repair
#9
Tomoko Kato-Inui, Gou Takahashi, Szuyin Hsu, Yuichiro Miyaoka
Genome editing using clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) predominantly induces non-homologous end joining (NHEJ), which generates random insertions or deletions, whereas homology-directed repair (HDR), which generates precise recombination products, is useful for wider applications. However, the factors that determine the ratio of HDR to NHEJ products after CRISPR/Cas9 editing remain unclear, and methods by which the proportion of HDR products can be increased have not yet been fully established...
April 17, 2018: Nucleic Acids Research
https://www.readbyqxmd.com/read/29672693/metabolic-and-genomic-characterization-of-stress-tolerant-industrial-saccharomyces-cerevisiae-strains-from-talens-assisted-multiplex-editing
#10
Yuman Gan, Yuping Lin, Yufeng Guo, Xianni Qi, Qinhong Wang
TALENs-assisted multiplex editing (TAME) toolbox was previously established and used to successfully enhance ethanol-stress tolerance of S. cerevisiae laboratory strain. Here, the TAME toolbox was harnessed to improve and elucidate stress tolerances of S. cerevisiae industrial strain. One osmotolerant strain and one thermotolerant strain were selected from the mutant library generated by TAME at corresponding stress conditions, and exhibited 1.2- to 1.3-fold increases of fermentation capacities, respectively...
April 17, 2018: FEMS Yeast Research
https://www.readbyqxmd.com/read/29672640/differential-impact-of-transplantation-on-peripheral-and-tissue-associated-viral-reservoirs-implications-for-hiv-gene-therapy
#11
Christopher W Peterson, Jianbin Wang, Claire Deleage, Sowmya Reddy, Jasbir Kaur, Patricia Polacino, Andreas Reik, Meei-Li Huang, Keith R Jerome, Shiu-Lok Hu, Michael C Holmes, Jacob D Estes, Hans-Peter Kiem
Autologous transplantation and engraftment of HIV-resistant cells in sufficient numbers should recapitulate the functional cure of the Berlin Patient, with applicability to a greater number of infected individuals and with a superior safety profile. A robust preclinical model of suppressed HIV infection is critical in order to test such gene therapy-based cure strategies, both alone and in combination with other cure strategies. Here, we present a nonhuman primate (NHP) model of latent infection using simian/human immunodeficiency virus (SHIV) and combination antiretroviral therapy (cART) in pigtail macaques...
April 2018: PLoS Pathogens
https://www.readbyqxmd.com/read/29672586/selection-on-the-regulation-of-sympathetic-nervous-activity-in-humans-and-chimpanzees
#12
Kang Seon Lee, Paramita Chatterjee, Eun-Young Choi, Min Kyung Sung, Jaeho Oh, Hyejung Won, Seong-Min Park, Youn-Jae Kim, Soojin V Yi, Jung Kyoon Choi
Adrenergic α2C receptor (ADRA2C) is an inhibitory modulator of the sympathetic nervous system. Knockout mice for this gene show physiological and behavioural alterations that are associated with the fight-or-flight response. There is evidence of positive selection on the regulation of this gene during chicken domestication. Here, we find that the neuronal expression of ADRA2C is lower in human and chimpanzee than in other primates. On the basis of three-dimensional chromatin structure, we identified a cis-regulatory region whose DNA sequences have been significantly accelerated in human and chimpanzee...
April 2018: PLoS Genetics
https://www.readbyqxmd.com/read/29670286/pluripotency-factors-functionally-premark-cell-type-restricted-enhancers-in-es-cells
#13
Hong Sook Kim, Yuliang Tan, Wubin Ma, Daria Merkurjev, Eugin Destici, Qi Ma, Tom Suter, Kenneth Ohgi, Meyer Friedman, Dorota Skowronska-Krawczyk, Michael G Rosenfeld
Enhancers for embryonic stem (ES) cell-expressed genes and lineage-determining factors are characterized by conventional marks of enhancer activation in ES cells1-3 , but it remains unclear whether enhancers destined to regulate cell-type-restricted transcription units might also have distinct signatures in ES cells. Here we show that cell-type-restricted enhancers are 'premarked' and activated as transcription units by the binding of one or two ES cell transcription factors, although they do not exhibit traditional enhancer epigenetic marks in ES cells, thus uncovering the initial temporal origins of cell-type-restricted enhancers...
April 18, 2018: Nature
https://www.readbyqxmd.com/read/29668265/receptor-mediated-delivery-of-crispr-cas9-endonuclease-for-cell-type-specific-gene-editing
#14
Romain Rouet, Benjamin A Thuma, Marc D Roy, Nathanael G Lintner, David M Rubitski, James E Finley, Hanna M Wisniewska, Rima Mendonsa, Ariana Hirsh, Lorena de Oñate, Joan Compte, Thomas J Mclellan, Justin Bellenger, Xidong Feng, Alison Varghese, Boris A Chrunyk, Kris A Borzilleri, Kevin D Hesp, Kaihong Zhou, Nannan Ma, Meihua Tu, Robert Dullea, Kim F Mcclure, Ross C Wilson, Spiros Liras, Vincent Mascitti, Jennifer A Doudna
CRISPR-Cas RNA-guided endonucleases hold great promise for disrupting or correcting genomic sequences through site-specific DNA cleavage and repair. However, the lack of methods for cell- and tissue-selective delivery currently limits both research and clinical uses of these enzymes. We report the design and in vitro evaluation of S. pyogenes Cas9 proteins harboring asialoglycoprotein receptor ligands (ASGPrL). In particular, we demonstrate that the resulting ribonucleoproteins (Cas9-ASGPrL RNP) can be engineered to be preferentially internalized into cells expressing the corresponding receptor on their surface...
April 18, 2018: Journal of the American Chemical Society
https://www.readbyqxmd.com/read/29668111/efficient-in-planta-gene-targeting-in-tomato-using-geminiviral-replicons-and-the-crispr-cas9-system
#15
Tal Dahan-Meir, Shdema Filler-Hayut, Cathy Melamed-Bessudo, Samuel Bocobza, Henryk Czosnek, Asaph Aharoni, Avraham A Levy
Current breeding relies mostly on random mutagenesis and recombination to generate novel genetic variation. However, targeted genome editing is becoming an increasingly important tool for precise plant breeding. Using the CRISPR-Cas system combined with the bean yellow dwarf virus rolling circle replicon we optimized a method for targeted mutagenesis and gene replacement in tomato. The carotenoid isomerase (CRTISO) and phytoene synthase 1 (PSY1) genes from the carotenoid biosynthesis pathway were chosen as targets due to their easily detectable change of phenotype...
April 18, 2018: Plant Journal: for Cell and Molecular Biology
https://www.readbyqxmd.com/read/29666172/genetic-editing-of-colonic-organoids-provides-a-molecularly-distinct-and-orthotopic-preclinical-model-of-serrated-carcinogenesis
#16
Tamsin R M Lannagan, Young K Lee, Tongtong Wang, Jatin Roper, Mark L Bettington, Lochlan Fennell, Laura Vrbanac, Lisa Jonavicius, Roshini Somashekar, Krystyna Gieniec, Miao Yang, Jia Q Ng, Nobumi Suzuki, Mari Ichinose, Josephine A Wright, Hiroki Kobayashi, Tracey L Putoczki, Yoku Hayakawa, Simon J Leedham, Helen E Abud, Ömer H Yilmaz, Julie Marker, Sonja Klebe, Pratyaksha Wirapati, Siddhartha Mukherjee, Sabine Tejpar, Barbara A Leggett, Vicki L J Whitehall, Daniel L Worthley, Susan L Woods
OBJECTIVE: Serrated colorectal cancer (CRC) accounts for approximately 25% of cases and includes tumours that are among the most treatment resistant and with worst outcomes. This CRC subtype is associated with activating mutations in the mitogen-activated kinase pathway gene, BRAF , and epigenetic modifications termed the CpG Island Methylator Phenotype, leading to epigenetic silencing of key tumour suppressor genes. It is still not clear which (epi-)genetic changes are most important in neoplastic progression and we begin to address this knowledge gap herein...
April 17, 2018: Gut
https://www.readbyqxmd.com/read/29664911/hpv-relatedness-definitions-for-classifying-hpv-related-oropharyngeal-cancer-patient-do-impact-on-tnm-classification-and-patients-survival
#17
Miren Taberna, Marisa Mena, Sara Tous, Miquel Angel Pavón, Marc Oliva, Xavier León, Jacinto Garcia, Marta Guix, Rafael Hijano, Teresa Bonfill, Antón Aguilà, Laia Alemany, Ricard Mesía
BACKGROUND: Given the different nature and better outcomes of oropharyngeal carcinoma (OPC) associated with human papillomavirus (HPV) infection, a novel clinical stage classification for HPV-related OPC has been accepted for the 8th edition AJCC TNM (ICON-S model). However, it is still unclear the HPV-relatedness definition with best diagnostic accuracy and prognostic value. MATERIAL AND METHODS: The aim of this study was to compare different staging system models proposed for HPV-related OPC patients: 7th edition AJCC TNM, RPA stage with non-anatomic factors (Princess Margaret), RPA with N categories for nasopharyngeal cancer (MD-Anderson) and AHR-new (ICON-S), according to different HPV-relatedness definitions: HPV-DNA detection plus an additional positive marker (p16INK4a or HPV-mRNA), p16INK4a positivity alone or the combination of HPV-DNA/p16INK4a positivity as diagnostic tests...
2018: PloS One
https://www.readbyqxmd.com/read/29662676/-toxoplasma-gondii-exposure-and-epilepsy-a-matched-case-control-study-in-a-public-hospital-in-northern-mexico
#18
Cosme Alvarado-Esquivel, Yazmin Del Rosario Rico-Almochantaf, Jesús Hernández-Tinoco, Gerardo Quiñones-Canales, Luis Francisco Sánchez-Anguiano, Jorge Torres-González, Eda Guadalupe Ramírez-Valles, Andrea Minjarez-Veloz
Objectives: This study aimed to determine the association between infection with Toxoplasma gondii and epilepsy in patients attended to in a public hospital in the northern Mexican city of Durango. Methods: We performed an age- and gender-matched case-control study of 99 patients suffering from epilepsy and 99 without epilepsy. Sera of participants were analyzed for anti- T. gondii IgG and IgM antibodies using commercially available enzyme-linked immunoassays. Seropositive samples to T...
2018: SAGE Open Medicine
https://www.readbyqxmd.com/read/29657966/engineering-complexity-in-bacterial-regulatory-circuits-for-biotechnological-applications
#19
Cauã Antunes Westmann, María-Eugenia Guazzaroni, Rafael Silva-Rocha
Engineering microbial systems allows the generation of new technologies having significant impact in the biotechnological industry and on human health. In the past few years, several synthetic biology approaches have been implemented in bacteria to allow precise engineering of novel regulatory circuits for several applications. The advent of high-throughput technologies and clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9-based DNA editing techniques have been pivotal in this process. Yet, despite the tremendous advances experienced recently, there are still a number of bottlenecks that need to be overcome in order to generate high-performance redesigned living machines, and the use of novel computer-aided approaches would be essential for this task...
March 2018: MSystems
https://www.readbyqxmd.com/read/29655782/lithocholic-acid-a-bacterial-metabolite-reduces-breast-cancer-cell-proliferation-and-aggressiveness
#20
Edit Mikó, András Vida, Tünde Kovács, Gyula Ujlaki, György Trencsényi, Judit Márton, Zsanett Sári, Patrik Kovács, Anita Boratkó, Zoltán Hujber, Tamás Csonka, Péter Antal-Szalmás, Mitsuhiro Watanabe, Imre Gombos, Balazs Csoka, Borbála Kiss, László Vígh, Judit Szabó, Gábor Méhes, Anna Sebestyén, James J Goedert, Péter Bai
Our study aimed at finding a mechanistic relationship between the gut microbiome and breast cancer. Breast cancer cells are not in direct contact with these microbes, but disease could be influenced by bacterial metabolites including secondary bile acids that are exclusively synthesized by the microbiome and known to enter the human circulation. In murine and bench experiments, a secondary bile acid, lithocholic acid (LCA), reduced cancer cell proliferation (by 10-20%) and VEGF production (by 37%), aggressiveness and metastatic potential of primary tumors through inducing mesenchymal-to-epithelial transition, increased antitumor immune response, OXPHOS and the TCA cycle...
April 12, 2018: Biochimica et Biophysica Acta
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