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Anti crispr

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https://www.readbyqxmd.com/read/28215705/kras-allelic-imbalance-enhances-fitness-and-modulates-map-kinase-dependence-in-cancer
#1
Michael R Burgess, Eugene Hwang, Rana Mroue, Craig M Bielski, Anica M Wandler, Benjamin J Huang, Ari J Firestone, Amy Young, Jennifer A Lacap, Lisa Crocker, Saurabh Asthana, Elizabeth M Davis, Jin Xu, Keiko Akagi, Michelle M Le Beau, Qing Li, Benjamin Haley, David Stokoe, Deepak Sampath, Barry S Taylor, Marie Evangelista, Kevin Shannon
Investigating therapeutic "outliers" that show exceptional responses to anti-cancer treatment can uncover biomarkers of drug sensitivity. We performed preclinical trials investigating primary murine acute myeloid leukemias (AMLs) generated by retroviral insertional mutagenesis in Kras(G12D) "knockin" mice with the MEK inhibitor PD0325901 (PD901). One outlier AML responded and exhibited intrinsic drug resistance at relapse. Loss of wild-type (WT) Kras enhanced the fitness of the dominant clone and rendered it sensitive to MEK inhibition...
February 16, 2017: Cell
https://www.readbyqxmd.com/read/28196870/biallelic-insertion-of-a-transcriptional-terminator-via-crispr-cas9-efficiently-silences-expression-of-protein-coding-and-non-coding-rna-genes
#2
Yangyang Liu, Xiao Han, Junting Yuan, Tuoyu Geng, Shihao Chen, Xuming Hu, Isabelle H Cui, Hengmi Cui
The type II bacterial CRISPR/Cas9 system is a simple, convenient and powerful tool for gene editing that allows for gene targeting. Here, we describe a CRISPR/Cas9-based approach for silencing both protein-coding and non-protein-coding genes by biallelic integration of a PolyA signal. Because of the integration of a BGH PolyA signal into the target genes, gene expression was drastically terminated. Two anti-antibiotic genes were used as markers in the selection of clonal cell lines with biallelic integration of a PolyA signal...
February 14, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28159786/bacteriophage-%C3%AE-m1-of-pectobacterium-evolves-to-escape-two-bifunctional-type-iii-toxin-antitoxin-and-abortive-infection-systems-through-mutations-in-a-single-viral-gene
#3
Tim R Blower, Ray Chai, Rita Przybilski, Shahzad Chindhy, Xinzhe Fang, Samuel E Kidman, Hui Tan, Ben F Luisi, Peter C Fineran, George P C Salmond
: Some bacteria, when infected by their viral parasites (bacteriophages), undergo a suicidal response that also terminates productive viral replication (abortive infection; Abi). This response can be viewed as an altruistic act protecting the uninfected bacterial clonal population. Abortive infection can occur through the action of Type III protein-RNA toxin-antitoxin (TA) systems, such as ToxINPa from the phytopathogen, Pectobacterium atrosepticum Rare spontaneous mutants evolved in the generalized transducing phage, ΦM1, which escaped ToxINPa-mediated abortive infection in P...
February 3, 2017: Applied and Environmental Microbiology
https://www.readbyqxmd.com/read/28148555/targeting-toxoplasma-gondii-cpsf3-as-a-new-approach-to-control-toxoplasmosis
#4
Andrés Palencia, Alexandre Bougdour, Marie-Pierre Brenier-Pinchart, Bastien Touquet, Rose-Laurence Bertini, Cristina Sensi, Gabrielle Gay, Julien Vollaire, Véronique Josserand, Eric Easom, Yvonne R Freund, Hervé Pelloux, Philip J Rosenthal, Stephen Cusack, Mohamed-Ali Hakimi
Toxoplasma gondii is an important food and waterborne pathogen causing toxoplasmosis, a potentially severe disease in immunocompromised or congenitally infected humans. Available therapeutic agents are limited by suboptimal efficacy and frequent side effects that can lead to treatment discontinuation. Here we report that the benzoxaborole AN3661 had potent in vitro activity against T. gondii Parasites selected to be resistant to AN3661 had mutations in TgCPSF3, which encodes a homologue of cleavage and polyadenylation specificity factor subunit 3 (CPSF-73 or CPSF3), an endonuclease involved in mRNA processing in eukaryotes...
February 1, 2017: EMBO Molecular Medicine
https://www.readbyqxmd.com/read/28130450/rab8a-recruited-pi3k%C3%AE-regulates-signaling-and-cytokine-outputs-from-endosomal-toll-like-receptors
#5
Adam A Wall, Lin Luo, Yu Hung, Samuel J Tong, Nicholas D Condon, Antje Blumenthal, Matthew J Sweet, Jennifer L Stow
Lipopolysaccharide (LPS)-mediated activation of Toll-like receptor 4 (TLR4) in macrophages results in the coordinated release of proinflammatory cytokines, followed by regulatory mediators, to ensure that this potentially destructive pathway is tightly regulated. We previously showed that Rab8a recruits PI3Kγ for Akt-dependent signaling during TLR4 activation to limit the production of the pro-inflammatory cytokines IL-6 and IL-12p40, while enhancing the release of the regulatory/anti-inflammatory cytokine IL-10...
January 27, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28122981/transgenic-crispr-cas9-mediated-viral-gene-targeting-for-antiviral-therapy-of-bombyx-mori-nucleopolyhedrovirus-bmnpv
#6
Shuqing Chen, Chengxiang Hou, Honglun Bi, Yueqiang Wang, Jun Xu, Muwang Li, Anthony A James, Yongping Huang, Anjiang Tan
: We developed a novel anti-viral strategy by combining transposon-based transgenesis and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated 9 (Cas9) system for direct cleavage of the Bombyx mori nucleopolyhedrovirus (BmNPV) genome DNA to promote virus clearance in silkworms. We demonstrate that transgenic silkworms constitutively-expressing Cas9 and guide RNAs (gRNAs) targeting the BmNPV immediate early-1 (ie-1) gene and me53 gene effectively induce target-specific cleavage and subsequent mutagenesis, especially large segment deletions (∼ 7 kilobase-pairs [kb]) in BmNPV genomes and thus exhibit a robust suppression of BmNPV proliferation...
January 25, 2017: Journal of Virology
https://www.readbyqxmd.com/read/28110021/the-application-of-crispr-technology-to-high-content-screening-in-primary-neurons
#7
Ben L Callif, Brian Maunze, Nick L Krueger, Matthew T Simpson, Murray G Blackmore
Axon growth is coordinated by multiple interacting proteins that remain incompletely characterized. High content screening (HCS), in which manipulation of candidate genes is combined with rapid image analysis of phenotypic effects, has emerged as a powerful technique to identify key regulators of axon outgrowth. Here we explore the utility of a genome editing approach referred to as CRISPR (Clustered Regularly Interspersed Palindromic Repeats) for knockout screening in primary neurons. In the CRISPR approach a DNA-cleaving Cas enzyme is guided to genomic target sequences by user-created guide RNA (sgRNA), where it initiates a double-stranded break that ultimately results in frameshift mutation and loss of protein production...
January 18, 2017: Molecular and Cellular Neurosciences
https://www.readbyqxmd.com/read/28104689/identification-of-apilimod-as-a-first-in-class-pikfyve-kinase-inhibitor-for-treatment-of-b-cell-non-hodgkin-lymphoma
#8
Sophia Gayle, Sean Landrette, Neil Beeharry, Chris Conrad, Marylens Hernandez, Paul Beckett, Shawn M Ferguson, Talya Mandelkern, Meiling Zheng, Tian Xu, Jonathan Rothberg, Henri Lichenstein
We identified apilimod as an anti-proliferative compound by high-throughput screening of clinical stage drugs. Apilimod exhibits exquisite specificity for PIKfyve lipid kinase and has selective cytotoxic activity in B-cell non-Hodgkin lymphoma (B-NHL) compared to normal cells. Apilimod displays nanomolar activity in vitro, and in vivo studies demonstrate single agent efficacy as well as synergy with approved B-NHL drugs. Using biochemical and knockdown approaches, and discovery of a kinase domain mutation conferring resistance, we demonstrate that apilimod-mediated cytotoxicity is driven by PIKfyve inhibition...
January 19, 2017: Blood
https://www.readbyqxmd.com/read/28101903/development-and-characterization-of-anti-glycopeptide-monoclonal-antibodies-against-human-podoplanin-using-glycan-deficient-cell-lines-generated-by-crispr-cas9-and-talen
#9
Mika K Kaneko, Takuro Nakamura, Ryusuke Honma, Satoshi Ogasawara, Yuki Fujii, Shinji Abe, Michiaki Takagi, Hiroyuki Harada, Hiroyoshi Suzuki, Yasuhiko Nishioka, Yukinari Kato
Human podoplanin (hPDPN), which binds to C-type lectin-like receptor-2 (CLEC-2), is involved in platelet aggregation and cancer metastasis. The expression of hPDPN in cancer cells or cancer-associated fibroblasts indicates poor prognosis. Human lymphatic endothelial cells, lung-type I alveolar cells, and renal glomerular epithelial cells express hPDPN. Although numerous monoclonal antibodies (mAbs) against hPDPN are available, they recognize peptide epitopes of hPDPN. Here, we generated a novel anti-hPDPN mAb, LpMab-21...
January 19, 2017: Cancer Medicine
https://www.readbyqxmd.com/read/28067257/enhanced-tumor-targeting-selectivity-by-modulating-bispecific-antibody-binding-affinity-and-format-valence
#10
Yariv Mazor, Kris F Sachsenmeier, Chunning Yang, Anna Hansen, Jessica Filderman, Kathy Mulgrew, Herren Wu, William F Dall'Acqua
Bispecific antibodies are considered attractive bio-therapeutic agents owing to their ability to target two distinct disease mediators. Cross-arm avidity targeting of antigen double-positive cancer cells over single-positive normal tissue is believed to enhance the therapeutic efficacy, restrict major escape mechanisms and increase tumor-targeting selectivity, leading to reduced systemic toxicity and improved therapeutic index. However, the interplay of factors regulating target selectivity is not well understood and often overlooked when developing clinically relevant bispecific therapeutics...
January 9, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28044228/reduced-il-37-production-increases-spontaneous-chemokine-expressions-in-colon-epithelial-cells
#11
Sezin Günaltay, Mohammed Ghiboub, Olof Hultgren, Elisabeth Hultgren Hörnquist
BACKGROUND AND AIM: Microscopic colitis, comprising collagenous colitis and lymphocytic colitis, is a common cause of chronic diarrhea. Previously, we showed enhanced chemokine productions in microscopic colitis patients, indicating dysregulated immune cell chemotaxis in the immunopathogenesis. We also showed decreased mRNA of IL-37, mainly regarded as an anti-inflammatory cytokine, in the colonic mucosa of these patients, potentially an important factor for the chronicity of the colitis...
January 2, 2017: Digestive Diseases and Sciences
https://www.readbyqxmd.com/read/28041849/inhibition-of-crispr-cas9-with-bacteriophage-proteins
#12
Benjamin J Rauch, Melanie R Silvis, Judd F Hultquist, Christopher S Waters, Michael J McGregor, Nevan J Krogan, Joseph Bondy-Denomy
Bacterial CRISPR-Cas systems utilize sequence-specific RNA-guided nucleases to defend against bacteriophage infection. As a countermeasure, numerous phages are known that produce proteins to block the function of class 1 CRISPR-Cas systems. However, currently no proteins are known to inhibit the widely used class 2 CRISPR-Cas9 system. To find these inhibitors, we searched cas9-containing bacterial genomes for the co-existence of a CRISPR spacer and its target, a potential indicator for CRISPR inhibition. This analysis led to the discovery of four unique type II-A CRISPR-Cas9 inhibitor proteins encoded by Listeria monocytogenes prophages...
January 12, 2017: Cell
https://www.readbyqxmd.com/read/27984732/perturb-seq-dissecting-molecular-circuits-with-scalable-single-cell-rna-profiling-of-pooled-genetic-screens
#13
Atray Dixit, Oren Parnas, Biyu Li, Jenny Chen, Charles P Fulco, Livnat Jerby-Arnon, Nemanja D Marjanovic, Danielle Dionne, Tyler Burks, Raktima Raychowdhury, Britt Adamson, Thomas M Norman, Eric S Lander, Jonathan S Weissman, Nir Friedman, Aviv Regev
Genetic screens help infer gene function in mammalian cells, but it has remained difficult to assay complex phenotypes-such as transcriptional profiles-at scale. Here, we develop Perturb-seq, combining single-cell RNA sequencing (RNA-seq) and clustered regularly interspaced short palindromic repeats (CRISPR)-based perturbations to perform many such assays in a pool. We demonstrate Perturb-seq by analyzing 200,000 cells in immune cells and cell lines, focusing on transcription factors regulating the response of dendritic cells to lipopolysaccharide (LPS)...
December 15, 2016: Cell
https://www.readbyqxmd.com/read/27984730/naturally-occurring-off-switches-for-crispr-cas9
#14
April Pawluk, Nadia Amrani, Yan Zhang, Bianca Garcia, Yurima Hidalgo-Reyes, Jooyoung Lee, Alireza Edraki, Megha Shah, Erik J Sontheimer, Karen L Maxwell, Alan R Davidson
CRISPR-Cas9 technology would be enhanced by the ability to inhibit Cas9 function spatially, temporally, or conditionally. Previously, we discovered small proteins encoded by bacteriophages that inhibit the CRISPR-Cas systems of their host bacteria. These "anti-CRISPRs" were specific to type I CRISPR-Cas systems that do not employ the Cas9 protein. We posited that nature would also yield Cas9 inhibitors in response to the evolutionary arms race between bacteriophages and their hosts. Here, we report the discovery of three distinct families of anti-CRISPRs that specifically inhibit the CRISPR-Cas9 system of Neisseria meningitidis...
December 15, 2016: Cell
https://www.readbyqxmd.com/read/27943633/integrated-genome-and-protein-editing-swaps-%C3%AE-2-6-sialylation-for-%C3%AE-2-3-sialic-acid-on-recombinant-antibodies-from-cho
#15
Cheng-Yu Chung, Qiong Wang, Shuang Yang, Bojiao Yin, Hui Zhang, Michael Betenbaugh
Immunoglobin G with α-2,6 sialylation has been reported to have an impact on antibody-dependent cellular cytotoxicity and anti-inflammatory efficacy. However, production of antibodies with α-2,6 sialylation from Chinese hamster ovary cells is challenging due to the inaccessibility of sialyltransferases for the heavy chain N-glycan site and the presence of exclusively α-2,3 sialyltransferases. In this study, combining mutations on the Fc regions to allow sialyltransferase accessibility with overexpression of α-2,6 sialyltransferase produced IgG with significant levels of both α-2,6 and α-2,3 sialylation...
December 12, 2016: Biotechnology Journal
https://www.readbyqxmd.com/read/27926730/integrin-yap-taz-jnk-cascade-mediates-atheroprotective-effect-of-unidirectional-shear-flow
#16
Li Wang, Jiang-Yun Luo, Bochuan Li, Xiao Yu Tian, Li-Jing Chen, Yuhong Huang, Jian Liu, Dan Deng, Chi Wai Lau, Song Wan, Ding Ai, King-Lun Kingston Mak, Ka Kui Tong, Kin Ming Kwan, Nanping Wang, Jeng-Jiann Chiu, Yi Zhu, Yu Huang
The Yorkie homologues YAP (Yes-associated protein) and TAZ (transcriptional coactivator with PDZ-binding motif, also known as WWTR1), effectors of the Hippo pathway, have been identified as mediators for mechanical stimuli. However, the role of YAP/TAZ in haemodynamics-induced mechanotransduction and pathogenesis of atherosclerosis remains unclear. Here we show that endothelial YAP/TAZ activity is regulated by different patterns of blood flow, and YAP/TAZ inhibition suppresses inflammation and retards atherogenesis...
December 7, 2016: Nature
https://www.readbyqxmd.com/read/27896818/coupling-immunity-and-programmed-cell-suicide-in-prokaryotes-life-or-death-choices
#17
Eugene V Koonin, Feng Zhang
Host-pathogen arms race is a universal, central aspect of the evolution of life. Most organisms evolved several distinct yet interacting strategies of anti-pathogen defense including resistance to parasite invasion, innate and adaptive immunity, and programmed cell death (PCD). The PCD is the means of last resort, a suicidal response to infection that is activated when resistance and immunity fail. An infected cell faces a decision between active defense and altruistic suicide or dormancy induction, depending on whether immunity is "deemed" capable of preventing parasite reproduction and consequent infection of other cells...
January 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/27862436/redefining-the-phenotype-of-heat-shock-protein-90-hsp90-inhibitors
#18
Yao Wang, Yen Chin Koay, Shelli R McAlpine
The phenotypes produced when cells are treated with the heat shock protein 90 (Hsp90) inhibitors AUY922 or 17-AAG (classical inhibitors) are different to those produced when cells are knocked down with Hsp90α. Pull-down assays using classical inhibitors suggest that these molecules bind to multiple targets other than Hsp90. Classical inhibitors also induce similar protein markers as other anti-cancer therapies cisplatin and bortezomib that do not target Hsp90. Together these data suggest that AUY922 and 17-AAG acts on multiple targets and likely kills cells through multiple mechanisms...
November 8, 2016: Chemistry: a European Journal
https://www.readbyqxmd.com/read/27837168/editor-s-highlight-microbial-derived-1-4-dihydroxy-2-naphthoic-acid-and-related-compounds-as-aryl-hydrocarbon-receptor-agonists-antagonists-structure-activity-relationships-and-receptor-modeling
#19
Yating Cheng, Un-Ho Jin, Laurie A Davidson, Robert S Chapkin, Arul Jayaraman, Phanourios Tamamis, Asuka Orr, Clint Allred, Michael S Denison, Anatoly Soshilov, Evelyn Weaver, Stephen Safe
1,4-Dihydroxy-2-naphthoic acid (1,4-DHNA) is a bacterial-derived metabolite that binds the aryl hydrocarbon receptor (AhR) and exhibits anti-inflammatory activity in the gut. The structure-dependent AhR activity of hydroxyl/carboxy-substituted naphthoic acids (NAs) was determined in young adult mouse colonic (YAMC) cells and human Caco2 colon cancer cells using CYP1A1/CYP1B1 mRNAs as Ah-responsive genes. Compounds used in this study include 1,4-, 3,5-, and 3,7-DHNA, 1,4-dimethoxy-2-naphthoic acid (1,4-DMNA), 1- and 4-hydroxy-2-naphthoic acid (1-HNA, 4-HNA), 1- and 2-naphthoic acid (1-NA, 2-NA), and 1- and 2-naphthol (1-NOH, 2-NOH)...
February 2017: Toxicological Sciences: An Official Journal of the Society of Toxicology
https://www.readbyqxmd.com/read/27815355/multiplex-genome-editing-to-generate-universal-car-t-cells-resistant-to-pd1-inhibition
#20
Jiangtao Ren, Xiaojun Liu, Chongyun Fang, Shuguang Jiang, Carl H June, Yangbing Zhao
PURPOSE: Using gene-disrupted allogeneic T cells as universal effector cells provides an alternative to and potentially improves current chimeric antigen receptor (CAR) T cell therapy against cancers and infectious diseases. EXPERIMENTAL DESIGN: The CRISPR/Cas9 system has recently emerged as a simple and efficient way for multiplex genome engineering. By combining the lentiviral delivery of CAR and CRISPR RNA electroporation to co-introduce RNA encoding the Cas9 and gRNAs targeting endogenous TCR, beta-2 microglobulin (B2M) and PD1 simultaneously, to generate gene-disrupted allogeneic CAR T cells deficient of TCR, HLA class I molecule and PD1...
November 4, 2016: Clinical Cancer Research: An Official Journal of the American Association for Cancer Research
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