Genome engineering in human pluripotent stem cells
Tài liệu tham khảo
Thomson, 1998, Embryonic stem cell lines derived from human blastocysts, Science, 282, 1145, 10.1126/science.282.5391.1145
Takahashi, 2006, Induction of pluripotent stem cells from mouse embryonic and adult fibroblast cultures by defined factors, Cell, 126, 663, 10.1016/j.cell.2006.07.024
Sterneckert, 2014, Investigating human disease using stem cell models, Nat Rev Genet, 15, 625, 10.1038/nrg3764
Santostefano, 2015, A practical guide to induced pluripotent stem cell research using patient samples, Lab Investig, 95, 4, 10.1038/labinvest.2014.104
Theodoris, 2015, Human disease modeling reveals integrated transcriptional and epigenetic mechanisms of NOTCH1 haploinsufficiency, Cell, 160, 1072, 10.1016/j.cell.2015.02.035
Gonzales, 2016, CRISPR/Cas9 genome editing in human pluripotent stem cells: harnessing human genetics in a dish, Dev Dyn, 1
FitzPatrick, 2015, Genome editing in stem cells, Curr Stem Cell Reports, 1, 31, 10.1007/s40778-014-0009-6
Lancaster, 2014, Organogenesis in a dish: modeling development and disease using organoid technologies, Science, 345, 1247125, 10.1126/science.1247125
Deglincerti, 2016, Self-organization of the in vitro attached human embryo, Nature, 533, 251, 10.1038/nature17948
Caiazzo, 2016, Defined three-dimensional microenvironments boost induction of pluripotency, Nat Mater, 15, 344, 10.1038/nmat4536
Rouet, 1994, Introduction of double-strand breaks into the genome of mouse cells by expression of a rare-cutting endonuclease, Mol Cell Biol, 14, 8096, 10.1128/MCB.14.12.8096
Rouet, 1994, Expression of a site-specific endonuclease stimulates homologous recombination in mammalian cells, Proc Natl Acad Sci U S A, 91, 6064, 10.1073/pnas.91.13.6064
Urnov, 2010, Genome editing with engineered zinc finger nucleases, Nat Rev Genet, 11, 636, 10.1038/nrg2842
Joung, 2012, TALENs: a widely applicable technology for targeted genome editing, Nat Rev Mol Cell Biol, 14, 49, 10.1038/nrm3486
Marraffini, 2015, CRISPR-Cas immunity in prokaryotes, Nature, 526, 55, 10.1038/nature15386
Mali, 2013, Cas9 as a versatile tool for engineering biology, Nat Methods, 10, 957, 10.1038/nmeth.2649
Jinek, 2012, A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity, Science, 337, 816, 10.1126/science.1225829
Gong, 2005, Mechanism of nonhomologous end-joining in mycobacteria: a low-fidelity repair system driven by Ku, ligase D and ligase C, Nat Struct Mol Biol, 12, 304, 10.1038/nsmb915
Byrne, 2015
Liao, 2015, Targeted disruption of DNMT1, DNMT3A and DNMT3B in human embryonic stem cells, Nat Genet, 47, 469, 10.1038/ng.3258
Ran, 2013, Double nicking by RNA-guided CRISPR Cas9 for enhanced genome editing specificity, Cell, 154, 1380, 10.1016/j.cell.2013.08.021
Chapman, 2012, Playing the end game: DNA double-strand break repair pathway choice, Mol Cell, 47, 497, 10.1016/j.molcel.2012.07.029
Jang, 2016, Gene correction in patient-specific iPSCs for therapy development and disease modeling, Hum Genet, 135, 1041, 10.1007/s00439-016-1691-5
Chen, 2011, High-frequency genome editing using ssDNA oligonucleotides with zinc-finger nucleases, Nat Methods, 8, 753, 10.1038/nmeth.1653
González, 2014, An iCRISPR platform for rapid, multiplexable, and inducible genome editing in human pluripotent stem cells, Cell Stem Cell, 15, 215, 10.1016/j.stem.2014.05.018
Merkle, 2015, Efficient CRISPR–Cas9-mediated generation of knockin human pluripotent stem cells lacking undesired mutations at the targeted locus, Cell Reports, 11, 10.1016/j.celrep.2015.04.007
Sadelain, 2011, Safe harbours for the integration of new DNA in the human genome, Nat Rev Cancer, 12, 51, 10.1038/nrc3179
Li, 2015, Human induced pluripotent stem Cell NEUROG2 dual knockin reporter lines generated by the CRISPR/Cas9 system, Stem Cells Dev, 24, 2925, 10.1089/scd.2015.0131
Rong, 2014, Homologous recombination in human embryonic stem cells using CRISPR/Cas9 nickase and a long DNA donor template, Protein Cell, 5, 258, 10.1007/s13238-014-0032-5
Wu, 2016, Generation and characterization of a MYF5 reporter human iPS cell line using CRISPR/Cas9 mediated homologous recombination, Sci Rep, 6, 18759, 10.1038/srep18759
Zhu, 2015, Overview of guide RNA design tools for CRISPR–Cas9 genome editing technology, Front Biol (Beijing), 10, 289, 10.1007/s11515-015-1366-y
Wang, 2014, Genetic screens in human cells using the CRISPR–Cas9 system, Science, 343, 80, 10.1126/science.1246981
Hsu, 2013, DNA targeting specificity of RNA-guided Cas9 nucleases, Nat Biotechnol, 31, 827, 10.1038/nbt.2647
Pattanayak, 2013, High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity, Nat Biotechnol, 31, 839, 10.1038/nbt.2673
Fu, 2013, High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells, Nat Biotechnol, 31, 822, 10.1038/nbt.2623
Cradick, 2013, CRISPR/Cas9 systems targeting β-globin and CCR5 genes have substantial off-target activity, Nucleic Acids Res, 41, 9584, 10.1093/nar/gkt714
Suzuki, 2014, Targeted gene correction minimally impacts whole-genome mutational load in human-disease-specific induced pluripotent stem cell clones, Cell Stem Cell, 15, 31, 10.1016/j.stem.2014.06.016
Veres, 2014, Low incidence of off-target mutations in individual CRISPR–Cas9 and TALEN targeted human stem cell clones detected by whole-genome sequencing, Cell Stem Cell, 15, 27, 10.1016/j.stem.2014.04.020
Smith, 2014, Whole-genome sequencing analysis reveals high specificity of CRISPR/Cas9 and TALEN-based genome editing in human iPSCs, Cell Stem Cell, 15, 12, 10.1016/j.stem.2014.06.011
Mali, 2013, CAS9 transcriptional activators for target specificity screening and paired nickases for cooperative genome engineering, Nat Biotechnol, 31, 833, 10.1038/nbt.2675
Wu, 2014, Genome-wide binding of the CRISPR endonuclease Cas9 in mammalian cells, Nat Biotechnol, 32, 670, 10.1038/nbt.2889
Duan, 2014, Genome-wide identification of CRISPR/Cas9 off-targets in human genome, Cell Res, 24, 1009, 10.1038/cr.2014.87
Kuscu, 2014, Genome-wide analysis reveals characteristics of off-target sites bound by the Cas9 endonuclease, Nat Biotechnol, 32, 677, 10.1038/nbt.2916
Tsai, 2014, GUIDE-seq enables genome-wide profiling of off-target cleavage by CRISPR-Cas nucleases, Nat Biotechnol, 33, 187, 10.1038/nbt.3117
Frock, 2014, Genome-wide detection of DNA double-stranded breaks induced by engineered nucleases, Nat Biotechnol, 33, 179, 10.1038/nbt.3101
Prykhozhij, 2015, CRISPR MultiTargeter: a web tool to find common and unique CRISPR single guide RNA targets in a set of similar sequences, PLoS One, 10, e0119372, 10.1371/journal.pone.0119372
Heigwer, 2014, E-CRISP: fast CRISPR target site identification, Nat Methods, 11, 122, 10.1038/nmeth.2812
Zhu, 2014, CRISPRseek: a bioconductor package to identify target-specific guide RNAs for CRISPR–Cas9 genome-editing systems, PLoS One, 9, e108424, 10.1371/journal.pone.0108424
Davis, 2015, Small molecule-triggered Cas9 protein with improved genome-editing specificity, Nat Chem Biol, 11, 316, 10.1038/nchembio.1793
Guilinger, 2014, Fusion of catalytically inactive Cas9 to FokI nuclease improves the specificity of genome modification, Nat Biotechnol, 32, 577, 10.1038/nbt.2909
Tsai, 2014, Dimeric CRISPR RNA-guided FokI nucleases for highly specific genome editing, Nat Biotechnol, 32, 569, 10.1038/nbt.2908
Kleinstiver, 2016, High-fidelity CRISPR–Cas9 nucleases with no detectable genome-wide off-target effects, Nature, 529, 490, 10.1038/nature16526
Slaymaker, 2016, Rationally engineered Cas9 nucleases with improved specificity, Science, 351, 84, 10.1126/science.aad5227
Hou, 2013, Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis, Proc Natl Acad Sci, 110, 15644, 10.1073/pnas.1313587110
Zetsche, 2015, Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system, Cell, 163, 759, 10.1016/j.cell.2015.09.038
Kim, 2016, Genome-wide analysis reveals specificities of Cpf1 endonucleases in human cells, Nat Biotechnol, 34, 863, 10.1038/nbt.3609
Kleinstiver, 2016, Genome-wide specificities of CRISPR-Cas Cpf1 nucleases in human cells, Nat Biotechnol, 34, 869, 10.1038/nbt.3620
Kleinstiver, 2015, Engineered CRISPR–Cas9 nucleases with altered PAM specificities, Nature, 523, 481, 10.1038/nature14592
Kleinstiver, 2015, Broadening the targeting range of Staphylococcus aureus CRISPR–Cas9 by modifying PAM recognition, Nat Biotechnol, 33, 1293, 10.1038/nbt.3404
Kumar, 2001, Systematic determination of the packaging limit of lentiviral vectors, Hum Gene Ther, 12, 1893, 10.1089/104303401753153947
Naldini, 1998, Lentiviruses as gene transfer agents for delivery to non-dividing cells, Curr Opin Biotechnol, 9, 457, 10.1016/S0958-1669(98)80029-3
Miyoshi, 1998, Development of a self-inactivating lentivirus vector, J Virol, 72, 8150, 10.1128/JVI.72.10.8150-8157.1998
Philippe, 2006, Lentiviral vectors with a defective integrase allow efficient and sustained transgene expression in vitro and in vivo, Proc Natl Acad Sci U S A, 103, 17684, 10.1073/pnas.0606197103
Chirmule, 1999, Immune responses to adenovirus and adeno-associated virus in humans, Gene Ther, 6, 1574, 10.1038/sj.gt.3300994
Dong, 2010, Characterization of genome integrity for oversized recombinant AAV vector, Mol Ther, 18, 87, 10.1038/mt.2009.258
Wu, 2010, Effect of genome size on AAV vector packaging, Mol Ther, 18, 80, 10.1038/mt.2009.255
Gori, 2015, Delivery and specificity of CRISPR/Cas9 genome editing technologies for human gene therapy, Hum Gene Ther, 26, 443, 10.1089/hum.2015.074
Skipper, 2015, Delivering the goods for genome engineering and editing, Hum Gene Ther, 26, 486, 10.1089/hum.2015.063
Li, 2015, Challenges in CRISPR/CAS9 delivery: potential roles of nonviral vectors, Hum Gene Ther, 26, 452, 10.1089/hum.2015.069
Liang, 2015, Rapid and highly efficient mammalian cell engineering via Cas9 protein transfection, J Biotechnol, 208, 44, 10.1016/j.jbiotec.2015.04.024
Branda, 2004, Talking about a revolution: the impact of site-specific recombinases on genetic analyses in mice, Dev Cell, 6, 7, 10.1016/S1534-5807(03)00399-X
Li, 2013, piggyBac transposase tools for genome engineering, Proc Natl Acad Sci U S A, 110, 2279, 10.1073/pnas.1305987110
Yusa, 2011, Targeted gene correction of α1-antitrypsin deficiency in induced pluripotent stem cells, Nature, 478, 391, 10.1038/nature10424
Mei, 2010, Combinatorial development of biomaterials for clonal growth of human pluripotent stem cells, Nat Mater, 9, 768, 10.1038/nmat2812
Zhu, 2015, A CRISPR/Cas-mediated selection-free knockin strategy in human embryonic stem cells, Stem Cell Reports, 4, 1103, 10.1016/j.stemcr.2015.04.016
Hatada, 2015, Low-dose irradiation enhances gene targeting in human pluripotent stem cells, Stem Cells Transl Med, 4, 998, 10.5966/sctm.2015-0050
He, 2016, Knock-in of large reporter genes in human cells via CRISPR/Cas9-induced homology-dependent and independent DNA repair, Nucleic Acids Res, 44, 10.1093/nar/gkw064
Xie, 2014, Seamless gene correction of β-thalassemia mutations in patient-specific iPSCs using CRISPR/Cas9 and piggyBac, Genome Res, 24, 1526, 10.1101/gr.173427.114
Li, 2015, Precise correction of the dystrophin gene in duchenne muscular dystrophy patient induced pluripotent stem cells by TALEN and CRISPR–Cas9, Stem Cell Reports, 4, 143, 10.1016/j.stemcr.2014.10.013
Firth, 2015, Functional gene correction for cystic fibrosis in lung epithelial cells generated from patient iPSCs, Cell Reports, 12, 10.1016/j.celrep.2015.07.062
Chen, 2016, Effects of genetic correction on the differentiation of hair cell-like cells from iPSCs with MYO15A mutation, Cell Death Differ, 23, 1347, 10.1038/cdd.2016.16
Ye, 2014, Seamless modification of wild-type induced pluripotent stem cells to the natural CCR5Δ32 mutation confers resistance to HIV infection, Proc Natl Acad Sci, 111, 9591, 10.1073/pnas.1407473111
Ding, 2013, Enhanced efficiency of human pluripotent stem cell genome editing through replacing TALENs with CRISPRs, Cell Stem Cell, 12, 393, 10.1016/j.stem.2013.03.006
Chen, 2015, Engineering human stem cell lines with inducible gene knockout using CRISPR/Cas9, Cell Stem Cell, 17, 233, 10.1016/j.stem.2015.06.001
Byrne, 2015, Multi-kilobase homozygous targeted gene replacement in human induced pluripotent stem cells, Nucleic Acids Res, 43, 10.1093/nar/gku1246
Sanjana, 2016, Genome-scale CRISPR pooled screens, Anal Biochem
Shalem, 2014, Genome-scale CRISPR–Cas9 knockout screening in human cells, Science, 343, 84, 10.1126/science.1247005
Korkmaz, 2016, Functional genetic screens for enhancer elements in the human genome using CRISPR–Cas9, Nat Biotechnol, 34, 192, 10.1038/nbt.3450
Shi, 2015, Discovery of cancer drug targets by CRISPR–Cas9 screening of protein domains, Nat Biotechnol, 33, 661, 10.1038/nbt.3235
Wang, 2015, Identification and characterization of essential genes in the human genome, Science, 350, 1096, 10.1126/science.aac7041
Hart, 2015, High-resolution CRISPR screens reveal fitness genes and genotype-specific cancer liabilities, Cell, 163, 1515, 10.1016/j.cell.2015.11.015
Zhou, 2014, High-throughput screening of a CRISPR/Cas9 library for functional genomics in human cells, Nature, 509, 487, 10.1038/nature13166
Parnas, 2015, A genome-wide CRISPR screen in primary immune cells to dissect regulatory networks, Cell, 162, 675, 10.1016/j.cell.2015.06.059
Qi, 2013, Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression, Cell, 152, 1173, 10.1016/j.cell.2013.02.022
Gilbert, 2013, CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes, Cell, 154, 442, 10.1016/j.cell.2013.06.044
Konermann, 2014, Genome-scale transcriptional activation by an engineered CRISPR–Cas9 complex, Nature, 517, 583, 10.1038/nature14136
Hilton, 2015, Epigenome editing by a CRISPR–Cas9-based acetyltransferase activates genes from promoters and enhancers, Nat Biotechnol, 33, 510, 10.1038/nbt.3199
Thakore, 2015, Highly specific epigenome editing by CRISPR–Cas9 repressors for silencing of distal regulatory elements, Nat Methods, 12, 1143, 10.1038/nmeth.3630
Mandegar, 2016, CRISPR interference efficiently induces specific and reversible gene silencing in human iPSCs, Cell Stem Cell, 18, 541, 10.1016/j.stem.2016.01.022
Vora, 2016, Next stop for the CRISPR revolution: RNA-guided epigenetic regulators, FEBS J, 283, 3181, 10.1111/febs.13768
Chakraborty, 2014, A CRISPR/Cas9-based system for reprogramming cell lineage specification, Stem Cell Reports, 3, 940, 10.1016/j.stemcr.2014.09.013
Black, 2016, Targeted epigenetic remodeling of endogenous loci by CRISPR/Cas9-based transcriptional activators directly converts fibroblasts to neuronal cells, Cell Stem Cell, 19, 406, 10.1016/j.stem.2016.07.001
Cheng, 2013, Multiplexed activation of endogenous genes by CRISPR-on, an RNA-guided transcriptional activator system, Cell Res, 23, 1163, 10.1038/cr.2013.122
Balboa, 2015, Conditionally stabilized dCas9 activator for controlling gene expression in human cell reprogramming and differentiation, Stem Cell Reports, 5, 448, 10.1016/j.stemcr.2015.08.001
Chavez, 2015, Highly efficient Cas9-mediated transcriptional programming, Nat Methods, 12, 326, 10.1038/nmeth.3312
Kearns, 2014, Cas9 effector-mediated regulation of transcription and differentiation in human pluripotent stem cells, Development, 141, 219, 10.1242/dev.103341
Nishizawa, 2016, Epigenetic variation between human induced pluripotent stem cell lines is an indicator of differentiation capacity cell stem cell epigenetic variation between human induced pluripotent stem cell lines is an indicator of differentiation capacity, Cell Stem Cell, 19, 341, 10.1016/j.stem.2016.06.019
Kim, 2010, Epigenetic memory in induced pluripotent stem cells, Nature, 467, 285, 10.1038/nature09342
Chen, 2013, Dynamic imaging of genomic loci in living human cells by an optimized CRISPR/Cas system, Cell, 155, 1479, 10.1016/j.cell.2013.12.001
Ma, 2016, Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow, Nat Biotechnol, 34, 528, 10.1038/nbt.3526
Nishida, 2016, Targeted nucleotide editing using hybrid prokaryotic and vertebrate adaptive immune systems, Science, 102, 553
Komor, 2016, Programmable editing of a target base in genomic DNA without double-stranded DNA cleavage, Nature, 533, 420, 10.1038/nature17946
Avior, 2016, Pluripotent stem cells in disease modelling and drug discovery, Nat Rev Mol Cell Biol, 17, 170, 10.1038/nrm.2015.27
Zhang, 2013, Rapid single-step induction of functional neurons from human pluripotent stem cells, Neuron, 78, 785, 10.1016/j.neuron.2013.05.029
Clevers, 2016, Modeling development and disease with organoids, Cell, 165, 1586, 10.1016/j.cell.2016.05.082
Yin, 2016, Engineering stem cell organoids, Cell Stem Cell, 18, 25, 10.1016/j.stem.2015.12.005
Gjorevski, 2016, Designer matrices for intestinal stem cell and organoid culture, Nature, 539, 560, 10.1038/nature20168
Ranga, 2016, Neural tube morphogenesis in synthetic 3D microenvironments, Proc Natl Acad Sci U S A, 113, E6831, 10.1073/pnas.1603529113
Takebe, 2013, Vascularized and functional human liver from an iPSC-derived organ bud transplant, Nature, 499, 481, 10.1038/nature12271
Takebe, 2015, Vascularized and complex organ buds from diverse tissues via mesenchymal cell-driven condensation, Cell Stem Cell, 16, 556, 10.1016/j.stem.2015.03.004
Polstein, 2015, A light-inducible CRISPR–Cas9 system for control of endogenous gene activation, Nat Chem Biol, 11, 198, 10.1038/nchembio.1753
Nihongaki, 2015, CRISPR–Cas9-based photoactivatable transcription system, Chem Biol, 22, 169, 10.1016/j.chembiol.2014.12.011
Trappmann, 2012, Extracellular-matrix tethering regulates stem-cell fate, Nat Mater, 11, 642, 10.1038/nmat3339
Yang, 2014, Mechanical memory and dosing influence stem cell fate, Nat Mater, 13, 645, 10.1038/nmat3889
Zhang, 2016, Biodegradable scaffold with built-in vasculature for organ-on-a-chip engineering and direct surgical anastomosis, Nat Mater, 1, 1
Kolesky, 2016, Three-dimensional bioprinting of thick vascularized tissues, Proc Natl Acad Sci U S A, 113, 3179, 10.1073/pnas.1521342113
Kang, 2016, A 3D bioprinting system to produce human-scale tissue constructs with structural integrity, Nat Biotechnol, 34, 312, 10.1038/nbt.3413
Maruyama, 2015, Increasing the efficiency of precise genome editing with CRISPR–Cas9 by inhibition of nonhomologous end joining, Nat Biotechnol, 33, 538, 10.1038/nbt.3190
Chu, 2015, Increasing the efficiency of homology-directed repair for CRISPR–Cas9-induced precise gene editing in mammalian cells, Nat Biotechnol, 33, 543, 10.1038/nbt.3198