CRISPR Interference-Based Platform for Multimodal Genetic Screens in Human iPSC-Derived Neurons
Tóm tắt
Từ khóa
Tài liệu tham khảo
Adamson, 2012, A genome-wide homologous recombination screen identifies the RNA-binding protein RBMX as a component of the DNA-damage response, Nat. Cell Biol., 14, 318, 10.1038/ncb2426
Adamson, 2016, A multiplexed single-cell CRISPR screening platform enables systematic dissection of the unfolded protein response, Cell, 167, 1867, 10.1016/j.cell.2016.11.048
Cantallops, 2000, Postsynaptic CPG15 promotes synaptic maturation and presynaptic axon arbor elaboration in vivo, Nat. Neurosci., 3, 1004, 10.1038/79823
Carpenter, 2006, CellProfiler: image analysis software for identifying and quantifying cell phenotypes, Genome Biol., 7, R100, 10.1186/gb-2006-7-10-r100
Cerbini, 2015, Transcription activator-like effector nuclease (TALEN)-mediated CLYBL targeting enables enhanced transgene expression and one-step generation of dual reporter human induced pluripotent stem cell (iPSC) and neural stem cell (NSC) lines, PLoS ONE, 10, e0116032, 10.1371/journal.pone.0116032
Choi, 2014, Neuritin attenuates cognitive function impairments in tg2576 mouse model of Alzheimer’s disease, PLoS ONE, 9, e104121, 10.1371/journal.pone.0104121
Datlinger, 2017, Pooled CRISPR screening with single-cell transcriptome readout, Nat. Methods, 14, 297, 10.1038/nmeth.4177
Dixit, 2016, Perturb-Seq: dissecting molecular circuits with scalable single-cell RNA profiling of pooled genetic screens, Cell, 167, 1853, 10.1016/j.cell.2016.11.038
Eisen, 1998, Cluster analysis and display of genome-wide expression patterns, Proc. Natl. Acad. Sci. USA, 95, 14863, 10.1073/pnas.95.25.14863
Fernandopulle, 2018, Transcription factor-mediated differentiation of human iPSCs into neurons, Curr. Protoc. Cell Biol., 79, e51, 10.1002/cpcb.51
Ghosh, 2011, DLK induces developmental neuronal degeneration via selective regulation of proapoptotic JNK activity, J. Cell Biol., 194, 751, 10.1083/jcb.201103153
Gilbert, 2013, CRISPR-mediated modular RNA-guided regulation of transcription in eukaryotes, Cell, 154, 442, 10.1016/j.cell.2013.06.044
Gilbert, 2014, Genome-scale CRISPR-mediated control of gene repression and activation, Cell, 159, 647, 10.1016/j.cell.2014.09.029
Groen, 2015, UBA1: at the crossroads of ubiquitin homeostasis and neurodegeneration, Trends Mol. Med., 21, 622, 10.1016/j.molmed.2015.08.003
Haapaniemi, 2018, CRISPR-Cas9 genome editing induces a p53-mediated DNA damage response, Nat. Med., 24, 927, 10.1038/s41591-018-0049-z
Hart, 2017, Evaluation and design of genome-wide CRISPR/SpCas9 knockout screens, G3 (Bethesda), 7, 2719, 10.1534/g3.117.041277
Hester, 2011, Rapid and efficient generation of functional motor neurons from human pluripotent stem cells using gene delivered transcription factor codes, Mol. Ther., 19, 1905, 10.1038/mt.2011.135
Hill, 2018, On the design of CRISPR-based single-cell molecular screens, Nat. Methods, 15, 271, 10.1038/nmeth.4604
Horlbeck, 2016, Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation, eLife, 5, 10.7554/eLife.19760
Huntwork-Rodriguez, 2013, JNK-mediated phosphorylation of DLK suppresses its ubiquitination to promote neuronal apoptosis, J. Cell Biol., 202, 747, 10.1083/jcb.201303066
Ihry, 2018, p53 inhibits CRISPR-Cas9 engineering in human pluripotent stem cells, Nat. Med., 24, 939, 10.1038/s41591-018-0050-6
Iwamoto, 2010, A general chemical method to regulate protein stability in the mammalian central nervous system, Chem. Biol., 17, 981, 10.1016/j.chembiol.2010.07.009
Jackson, 2003, Expression profiling reveals off-target gene regulation by RNAi, Nat. Biotechnol., 21, 635, 10.1038/nbt831
Javaherian, 2005, Coordinated motor neuron axon growth and neuromuscular synaptogenesis are promoted by CPG15 in vivo, Neuron, 45, 505, 10.1016/j.neuron.2004.12.051
Kaelin, 2012, Molecular biology. Use and abuse of RNAi to study mammalian gene function, Science, 337, 421, 10.1126/science.1225787
Kampmann, 2017, A CRISPR approach to neurodegenerative diseases, Trends Mol. Med., 23, 483, 10.1016/j.molmed.2017.04.003
Kampmann, 2018, CRISPRi and CRISPRa screens in mammalian cells for precision biology and medicine, ACS Chem. Biol., 13, 406, 10.1021/acschembio.7b00657
Kampmann, 2013, Integrated platform for genome-wide screening and construction of high-density genetic interaction maps in mammalian cells, Proc. Natl. Acad. Sci. USA, 110, E2317, 10.1073/pnas.1307002110
Kampmann, 2014, Functional genomics platform for pooled screening and generation of mammalian genetic interaction maps, Nat. Protoc., 9, 1825, 10.1038/nprot.2014.103
Koike-Yusa, 2014, Genome-wide recessive genetic screening in mammalian cells with a lentiviral CRISPR-guide RNA library, Nat. Biotechnol., 32, 267, 10.1038/nbt.2800
Langmead, 2009, Ultrafast and memory-efficient alignment of short DNA sequences to the human genome, Genome Biol., 10, R25, 10.1186/gb-2009-10-3-r25
Larhammar, 2017, Dual leucine zipper kinase-dependent PERK activation contributes to neuronal degeneration following insult, eLife, 6, 10.7554/eLife.20725
Li, 2014, MAGeCK enables robust identification of essential genes from genome-scale CRISPR/Cas9 knockout screens, Genome Biol., 15, 554, 10.1186/s13059-014-0554-4
Li, 2016, Protein prenylation constitutes an endogenous brake on axonal growth, Cell Rep., 16, 545, 10.1016/j.celrep.2016.06.013
Liu, 2018, CRISPR activation screens systematically identify factors that drive neuronal fate and reprogramming, Cell Stem Cell, 23, 758, 10.1016/j.stem.2018.09.003
Luo, 2014, Stable enhanced green fluorescent protein expression after differentiation and transplantation of reporter human induced pluripotent stem cells generated by AAVS1 transcription activator-like effector nucleases, Stem Cells Transl. Med., 3, 821, 10.5966/sctm.2013-0212
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
McCarthy, 2017, Scater: pre-processing, quality control, normalization and visualization of single-cell RNA-seq data in R, Bioinformatics, 33, 1179, 10.1093/bioinformatics/btw777
Miller, 2009, A dual leucine kinase-dependent axon self-destruction program promotes Wallerian degeneration, Nat. Neurosci., 12, 387, 10.1038/nn.2290
Miyaoka, 2014, Isolation of single-base genome-edited human iPS cells without antibiotic selection, Nat. Methods, 11, 291, 10.1038/nmeth.2840
Mootha, 2003, PGC-1alpha-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes, Nat. Genet., 34, 267, 10.1038/ng1180
Naeve, 1997, Neuritin: a gene induced by neural activity and neurotrophins that promotes neuritogenesis, Proc. Natl. Acad. Sci. USA, 94, 2648, 10.1073/pnas.94.6.2648
Nieland, 2014, High content image analysis identifies novel regulators of synaptogenesis in a high-throughput RNAi screen of primary neurons, PLoS ONE, 9, e91744, 10.1371/journal.pone.0091744
Okita, 2013, An efficient nonviral method to generate integration-free human-induced pluripotent stem cells from cord blood and peripheral blood cells, Stem Cells, 31, 458, 10.1002/stem.1293
Pozniak, 2013, Dual leucine zipper kinase is required for excitotoxicity-induced neuronal degeneration, J. Exp. Med., 210, 2553, 10.1084/jem.20122832
Robinson, 2010, edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, 26, 139, 10.1093/bioinformatics/btp616
Rosenbluh, 2017, Complementary information derived from CRISPR Cas9 mediated gene deletion and suppression, Nat. Commun., 8, 15403, 10.1038/ncomms15403
Saldanha, 2004, Java Treeview--extensible visualization of microarray data, Bioinformatics, 20, 3246, 10.1093/bioinformatics/bth349
Schindelin, 2012, Fiji: an open-source platform for biological-image analysis, Nat. Methods, 9, 676, 10.1038/nmeth.2019
Schiroli, 2019, Precise gene editing preserves hematopoietic stem cell function following transient p53-mediated DNA damage response, Cell Stem Cell, 24, 551, 10.1016/j.stem.2019.02.019
Sergushichev, 2016, An algorithm for fast preranked gene set enrichment analysis using cumulative statistic calculation, bioRxiv
Shalem, 2014, Genome-scale CRISPR-Cas9 knockout screening in human cells, Science, 343, 84, 10.1126/science.1247005
Sharma, 2013, High-throughput genetic screen for synaptogenic factors: identification of LRP6 as critical for excitatory synapse development, Cell Rep., 5, 1330, 10.1016/j.celrep.2013.11.008
Shi, 2018, Haploinsufficiency leads to neurodegeneration in C9ORF72 ALS/FTD human induced motor neurons, Nat. Med., 24, 313, 10.1038/nm.4490
Subramanian, 2005, Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles, Proc. Natl. Acad. Sci. USA, 102, 15545, 10.1073/pnas.0506580102
Tsunemoto, 2018, Diverse reprogramming codes for neuronal identity, Nature, 557, 375, 10.1038/s41586-018-0103-5
Valakh, 2015, Cytoskeletal disruption activates the DLK/JNK pathway, which promotes axonal regeneration and mimics a preconditioning injury, Neurobiol. Dis., 77, 13, 10.1016/j.nbd.2015.02.014
Wang, 2014, Genetic screens in human cells using the CRISPR-Cas9 system, Science, 343, 80, 10.1126/science.1246981
Wang, 2017, Scalable production of iPSC-derived human neurons to identify tau-lowering compounds by high-content screening, Stem Cell Reports, 9, 1221, 10.1016/j.stemcr.2017.08.019
Watkins, 2013, DLK initiates a transcriptional program that couples apoptotic and regenerative responses to axonal injury, Proc. Natl. Acad. Sci. USA, 110, 4039, 10.1073/pnas.1211074110
Welsbie, 2013, Functional genomic screening identifies dual leucine zipper kinase as a key mediator of retinal ganglion cell death, Proc. Natl. Acad. Sci. USA, 110, 4045, 10.1073/pnas.1211284110
Willsey, 2018, The Psychiatric Cell Map Initiative: a convergent systems biological approach to illuminating key molecular pathways in neuropsychiatric disorders, Cell, 174, 505, 10.1016/j.cell.2018.06.016
Yang, 2017, Generation of pure GABAergic neurons by transcription factor programming, Nat. Methods, 14, 621, 10.1038/nmeth.4291
Yao, 2016, Neuritin up-regulates Kv4.2 α-subunit of potassium channel expression and affects neuronal excitability by regulating the calcium-calcineurin-NFATc4 signaling pathway, J. Biol. Chem., 291, 17369, 10.1074/jbc.M115.708883
Zhang, 2005, WebGestalt: an integrated system for exploring gene sets in various biological contexts, Nucleic Acids Res., 33, W741, 10.1093/nar/gki475
Zhang, 2013, Rapid single-step induction of functional neurons from human pluripotent stem cells, Neuron, 78, 785, 10.1016/j.neuron.2013.05.029