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Genome Editing human

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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
#1
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
#2
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/29673141/subunit-specific-role-of-nf-%C3%AE%C2%BAb-in-cancer
#3
REVIEW
Barbara Kaltschmidt, Johannes F W Greiner, Hussamadin M Kadhim, Christian Kaltschmidt
The transcription factor NF-κB is a key player in inflammation, cancer development, and progression. NF-κB stimulates cell proliferation, prevents apoptosis, and could promote tumor angiogenesis as well as metastasis. Extending the commonly accepted role of NF-κB in cancer formation and progression, different NF-κB subunits have been shown to be active and of particular importance in distinct types of cancer. Here, we summarize overexpression data of the NF-κB subunits RELA, RELB, and c-REL (referring to the v-REL, which is the oncogene of Reticuloendotheliosis virus strain T) as well as of their upstream kinase inhibitor, namely inhibitor of κB kinases (IKK), in different human cancers, assessed by database mining...
April 17, 2018: Biomedicines
https://www.readbyqxmd.com/read/29672669/crispr-cas9-cleavage-efficiency-regression-through-boosting-algorithms-and-markov-sequence-profiling
#4
Hui Peng, Yi Zheng, Michael Blumenstein, Dacheng Tao, Jinyan Li
Motivation: CRISPR/Cas9 system is a widely used genome editing tool. A prediction problem of great interests for this system is: how to select optimal single guide RNAs (sgRNAs) such that its cleavage efficiency is high meanwhile the off-target effect is low. Results: This work proposed a two-step averaging method (TSAM) for the regression of cleavage efficiencies of a set of sgRNAs by averaging the predicted efficiency scores of a boosting algorithm and those by a support vector machine (SVM)...
April 16, 2018: Bioinformatics
https://www.readbyqxmd.com/read/29672586/selection-on-the-regulation-of-sympathetic-nervous-activity-in-humans-and-chimpanzees
#5
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/29670305/germline-genetic-modification-and-identity-the-mitochondrial-and-nuclear-genomes
#6
COMMENT
Rosamund Scott, Stephen Wilkinson
In a legal 'first', the UK removed a prohibition against modifying embryos in human reproduction, to enable mitochondrial replacement techniques (MRTs), a move the Government distanced from 'germline genetic modification', which it aligned with modifying the nuclear genome. This paper (1) analyzes the uses and meanings of this term in UK/US legal and policy debates; and (2) evaluates related ethical concerns about identity. It shows that, with respect to identity, MRTs and nuclear genome editing techniques such as CRISPR/Cas-9 (now a policy topic), are not as different as has been supposed...
December 2017: Oxford Journal of Legal Studies
https://www.readbyqxmd.com/read/29666931/genome-editing-and-induced-pluripotent-stem-cell-technologies-for-personalized-study-of-cardiovascular-diseases
#7
REVIEW
Young Wook Chun, Matthew D Durbin, Charles C Hong
PURPOSE OF REVIEW: The goal of this review is to highlight the potential of induced pluripotent stem cell (iPSC)-based modeling as a tool for studying human cardiovascular diseases. We present some of the current cardiovascular disease models utilizing genome editing and patient-derived iPSCs. RECENT FINDINGS: The incorporation of genome-editing and iPSC technologies provides an innovative research platform, providing novel insight into human cardiovascular disease at molecular, cellular, and functional level...
April 17, 2018: Current Cardiology Reports
https://www.readbyqxmd.com/read/29666172/genetic-editing-of-colonic-organoids-provides-a-molecularly-distinct-and-orthotopic-preclinical-model-of-serrated-carcinogenesis
#8
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/29663926/polyethylenimine-mediated-ccr5-gene-knockout-using-transcription-activator-like-effector-nucleases
#9
Lian Jin, Yan Deng, Nongyue He, Lijun Wang, Mengling Weng
CCR5 acts as one of the key coreceptors for human immunodeficiency virus infection, which leads to acquired immune deficiency syndrome. CCR5 gene knockout comes up as an alternative method for treatment of the disease. Transcription activator-like effector nuclease is a powerful gene editing tool characterized by the ease of design, high rates of cleavage activity, and the accessibility of all ranges of transcription activator-like effector nucleases. In this study, transcription activator-like effector nuclease plasmids specifically targeting to knock out CCR5 gene were designed, constructed and then transfected to Hela and HEK293T cell lines with the assistance of the well-established gene delivery carrier polyethylenimine...
March 1, 2018: Journal of Biomedical Nanotechnology
https://www.readbyqxmd.com/read/29663920/advances-in-the-engineering-of-the-gene-editing-enzymes-and-the-genomes-understanding-and-handling-the-off-target-effects-of-crispr-cas9
#10
Yufang Yin, Qian Wang, Li Xiao, Fengjiao Wang, Zhuo Song, Cuilan Zhou, Xuan Liu, Chungen Xing, Nongyue He, Kai Li, Yan Feng, Jia Zhang
In the past decades, significant progresses have been achieved in genetic engineering of nucleases. Among the genetically engineered nucleases, zinc finger nucleases, transcription activator-like (TAL) effector nucleases, and CRIPSPR/Cas9 system form a new field of gene editing. The gene editing efficiency or targeting effect and the off-target effect are the two major determinant factors in evaluating the usefulness of a new enzyme. Engineering strategies in improving these gene editing enzymes, particularly in minimizing their off-target effects, are the focus of this paper...
March 1, 2018: Journal of Biomedical Nanotechnology
https://www.readbyqxmd.com/read/29662087/accurate-identification-of-rna-editing-sites-from-primitive-sequence-with-deep-neural-networks
#11
Zhangyi Ouyang, Feng Liu, Chenghui Zhao, Chao Ren, Gaole An, Chuan Mei, Xiaochen Bo, Wenjie Shu
RNA editing is a post-transcriptional RNA sequence alteration. Current methods have identified editing sites and facilitated research but require sufficient genomic annotations and prior-knowledge-based filtering steps, resulting in a cumbersome, time-consuming identification process. Moreover, these methods have limited generalizability and applicability in species with insufficient genomic annotations or in conditions of limited prior knowledge. We developed DeepRed, a deep learning-based method that identifies RNA editing from primitive RNA sequences without prior-knowledge-based filtering steps or genomic annotations...
April 16, 2018: Scientific Reports
https://www.readbyqxmd.com/read/29659822/development-and-application-of-crispr-cas9-technologies-in-genomic-editing
#12
Zhang Cui, Quan Renfu, Wang Jinfu
Genomic editing to correct disease-causing mutations is a promising approach for the treatment of human diseases. As a simple and programmable nuclease-based genomic editing tool, the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has substantially improved the ability to make precise changes in the human genome. Rapid development of CRISPR-based technologies in recent years has expanded its application scope and promoted CRISPR-based therapies in preclinical trails...
April 6, 2018: Human Molecular Genetics
https://www.readbyqxmd.com/read/29651774/genome-editing-for-the-treatment-of-tumorigenic-viral-infections-and-virus-related-carcinomas
#13
REVIEW
Lan Yu, Xun Tian, Chun Gao, Ping Wu, Liming Wang, Bei Feng, Xiaomin Li, Hui Wang, Ding Ma, Zheng Hu
Viral infections cause at least 10%-15% of all human carcinomas. Over the last century, the elucidation of viral oncogenic roles in many cancer types has provided fundamental knowledge on carcinogenetic mechanisms and established a basis for the early intervention of virus-related cancers. Meanwhile, rapidly evolving genomeediting techniques targeting viral DNA/RNA have emerged as novel therapeutic strategies for treating virusrelated carcinogenesis and have begun showing promising results. This review discusses the recent advances of genome-editing tools for treating tumorigenic viruses and their corresponding cancers, the challenges that must be overcome before clinically applying such genome-editing technologies, and more importantly, the potential solutions to these challenges...
April 12, 2018: Frontiers of Medicine
https://www.readbyqxmd.com/read/29650777/-mll-leukemia-induction-by-t-9-11-chromosomal-translocation-in-human-hematopoietic-stem-cells-using-genome-editing
#14
Corina Schneidawind, Johan Jeong, Dominik Schneidawind, In-Suk Kim, Jesús Duque-Afonso, Stephen Hon Kit Wong, Masayuki Iwasaki, Erin H Breese, James L Zehnder, Matthew Porteus, Michael L Cleary
Genome editing provides a potential approach to model de novo leukemogenesis in primary human hematopoietic stem and progenitor cells (HSPCs) through induction of chromosomal translocations by targeted DNA double-strand breaks. However, very low efficiency of translocations and lack of markers for translocated cells serve as barriers to their characterization and model development. Here, we used transcription activator-like effector nucleases to generate t(9;11) chromosomal translocations encoding MLL-AF9 and reciprocal AF9-MLL fusion products in CD34+ human cord blood cells...
April 24, 2018: Blood Advances
https://www.readbyqxmd.com/read/29643508/aspm-knockout-ferret-reveals-an-evolutionary-mechanism-governing-cerebral-cortical-size
#15
Matthew B Johnson, Xingshen Sun, Andrew Kodani, Rebeca Borges-Monroy, Kelly M Girskis, Steven C Ryu, Peter P Wang, Komal Patel, Dilenny M Gonzalez, Yu Mi Woo, Ziying Yan, Bo Liang, Richard S Smith, Manavi Chatterjee, Daniel Coman, Xenophon Papademetris, Lawrence H Staib, Fahmeed Hyder, Joseph B Mandeville, P Ellen Grant, Kiho Im, Hojoong Kwak, John F Engelhardt, Christopher A Walsh, Byoung-Il Bae
The human cerebral cortex is distinguished by its large size and abundant gyrification, or folding. However, the evolutionary mechanisms that drive cortical size and structure are unknown. Although genes that are essential for cortical developmental expansion have been identified from the genetics of human primary microcephaly (a disorder associated with reduced brain size and intellectual disability) 1 , studies of these genes in mice, which have a smooth cortex that is one thousand times smaller than the cortex of humans, have provided limited insight...
April 11, 2018: Nature
https://www.readbyqxmd.com/read/29628199/genome-editing-using-crispr-cas9-targeted-mutagenesis-an-opportunity-for-yield-improvements-of-crop-plants-grown-under-environmental-stresses
#16
Mostafa Abdelrahman, Abdullah M Al-Sadi, Alireza Pour-Aboughadareh, David J Burritt, Lam-Son Phan Tran
Developing more crops able to sustainably produce high yields when grown under biotic/abiotic stresses is an important goal, if crop production and food security are to be guaranteed in the face of ever-increasing human population and unpredictable global climatic conditions. However, conventional crop improvement, through random mutagenesis or genetic recombination, is time-consuming and cannot keep pace with increasing food demands. Targeted genome editing (GE) technologies, especially clustered regularly interspaced short palindromic repeats (CRISPR)/(CRISPR)-associated protein 9 (Cas9), have great potential to aid in the breeding of crops that are able to produce high yields under conditions of biotic/abiotic stress...
March 12, 2018: Plant Physiology and Biochemistry: PPB
https://www.readbyqxmd.com/read/29625676/rapid-and-low-cost-strategy-for-detecting-genome-editing-induced-deletion-a-single-copy-case
#17
Nan Cheng, Qin Wang, Ying Shang, Yuancong Xu, Kunlun Huang, Zhansen Yang, Dengke Pan, Wentao Xu, Yunbo Luo
Genome editing techniques have been implemented in human daily lives, which has created a high demand for the development of new gene-edited product analysis methods. Conventional assays are time-consuming, labor-intensive, and costly. This paper proposes a rapid and low-cost strategy for detecting genome-editing induced deletion which works by integrating rapid-multiplex ligation-dependent probe amplification (MLPA) with a dual-lateral flow nucleic acid biosensor (LFNAB) cascade in a single-copy case. A rapid-MLPA was first introduced to the LFNAB system as a replacement for the conventional PCR for enhanced specificity and accuracy...
August 17, 2018: Analytica Chimica Acta
https://www.readbyqxmd.com/read/29625575/targeted-genome-engineering-in-human-induced-pluripotent-stem-cells-from-patients-with-hemophilia-b-using-the-crispr-cas9-system
#18
Cuicui Lyu, Jun Shen, Rui Wang, Haihui Gu, Jianping Zhang, Feng Xue, Xiaofan Liu, Wei Liu, Rongfeng Fu, Liyan Zhang, Huiyuan Li, Xiaobing Zhang, Tao Cheng, Renchi Yang, Lei Zhang
BACKGROUND: Replacement therapy for hemophilia remains a lifelong treatment. Only gene therapy can cure hemophilia at a fundamental level. The clustered regularly interspaced short palindromic repeats-CRISPR associated nuclease 9 (CRISPR-Cas9) system is a versatile and convenient genome editing tool which can be applied to gene therapy for hemophilia. METHODS: A patient's induced pluripotent stem cells (iPSCs) were generated from their peripheral blood mononuclear cells (PBMNCs) using episomal vectors...
April 6, 2018: Stem Cell Research & Therapy
https://www.readbyqxmd.com/read/29622803/simultaneous-reprogramming-and-gene-editing-of-human-fibroblasts
#19
Sara E Howden, James A Thomson, Melissa H Little
The utility of human induced pluripotent stem cells (iPSCs) is enhanced by an ability to precisely modify a chosen locus with minimal impact on the remaining genome. However, the derivation of gene-edited iPSCs typically involves multiple steps requiring lengthy culture periods and several clonal events. Here, we describe a one-step protocol for reliable generation of clonally derived gene-edited iPSC lines from human fibroblasts in the absence of drug selection or FACS enrichment. Using enhanced episomal-based reprogramming and CRISPR/Cas9 systems, gene-edited and passage-matched unmodified iPSC lines are obtained following a single electroporation of human fibroblasts...
May 2018: Nature Protocols
https://www.readbyqxmd.com/read/29622802/design-and-assessment-of-engineered-crispr-cpf1-and-its-use-for-genome-editing
#20
Bin Li, Chunxi Zeng, Yizhou Dong
Cpf1, a CRISPR endonuclease discovered in Prevotella and Francisella 1 bacteria, offers an alternative platform for CRISPR-based genome editing beyond the commonly used CRISPR-Cas9 system originally discovered in Streptococcus pyogenes. This protocol enables the design of engineered CRISPR-Cpf1 components, both CRISPR RNAs (crRNAs) to guide the endonuclease and Cpf1 mRNAs to express the endonuclease protein, and provides experimental procedures for effective genome editing using this system. We also describe quantification of genome-editing activity and off-target effects of the engineered CRISPR-Cpf1 in human cell lines using both T7 endonuclease I (T7E1) assay and targeted deep sequencing...
May 2018: Nature Protocols
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