1
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Faber GP, Hauschner H, Atrash MK, Bilinsky L, Shav-Tal Y. Utilizing flow cytometry sorting signal width to enrich for cells positive to endogenous gene integration of fluorescent proteins. Cytometry A 2023; 103:664-669. [PMID: 37158244 DOI: 10.1002/cyto.a.24735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2023] [Revised: 04/03/2023] [Accepted: 04/24/2023] [Indexed: 05/10/2023]
Abstract
Endogenous gene knock-in using CRIPSR is becoming the standard for fluorescent tagging of endogenous proteins. Some protocols, particularly those that utilize insert cassettes that carry a fluorescent protein tag, can yield many types of cells with off-target insertions that have diffuse fluorescent signal throughout the whole cell in addition to scarce cells with on-target gene insertions that show the correct sub-cellular localization of the tagged protein. As such, when searching for cells with on-target integration using flow cytometry, the off-target fluorescent cells yield a high percentage of false positives. Here, we show that by changing the gating used to select for fluorescence during flow cytometry sorting, namely utilizing the width of the signal as opposed to the area, we can highly enrich for positively integrated cells. Reproducible gates were created to select even minuscule percentages of correct subcellular signal, and these parameters were validated by fluorescence microscopy. This method is a powerful tool to rapidly enhance the generation of cell lines with correctly integrated gene knock-ins encoding endogenous fluorescent proteins.
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Affiliation(s)
- Gabriel P Faber
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Hagit Hauschner
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | - Mohammad K Atrash
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
| | | | - Yaron Shav-Tal
- The Mina & Everard Goodman Faculty of Life Sciences & Institute of Nanotechnology, Bar-Ilan University, Ramat Gan, Israel
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2
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Faber GP, Hauschner H, Atrash MK, Bilinsky L, Shav-Tal Y. Utilizing flow cytometry sorting signal width to enrich for cells positive to endogenous gene integration of fluorescent proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.21.533670. [PMID: 36993529 PMCID: PMC10055236 DOI: 10.1101/2023.03.21.533670] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/25/2023]
Abstract
Endogenous gene knock-in using CRIPSR is becoming the standard for fluorescent tagging of endogenous proteins. Some protocols, particularly those that utilize insert cassettes that carry a fluorescent protein tag, can yield many types of cells with off-target insertions that have diffuse fluorescent signal throughout the whole cell in addition to scarce cells with on-target gene insertions that show the correct sub-cellular localization of the tagged protein. As such, when searching for cells with on-target integration using flow cytometry, the off-target fluorescent cells yield a high percentage of false positives. Here, we show that by changing the gating used to select for fluorescence during flow cytometry sorting, namely utilizing the width of the signal as opposed to the area, we can highly enrich for positively integrated cells. Reproducible gates were created to select for even minuscule percentages of correct subcellular signal, and these parameters were validated by fluorescence microscopy. This method is a powerful tool to rapidly enhance the generation of cell-lines with correctly integrated gene knock-ins encoding endogenous fluorescent proteins.
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3
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Ambrosi G, Voloshanenko O, Eckert AF, Kranz D, Nienhaus GU, Boutros M. Allele-specific endogenous tagging and quantitative analysis of β-catenin in colorectal cancer cells. eLife 2022; 11:64498. [PMID: 35014953 PMCID: PMC8752093 DOI: 10.7554/elife.64498] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 12/16/2021] [Indexed: 12/16/2022] Open
Abstract
Wnt signaling plays important roles in development, homeostasis, and tumorigenesis. Mutations in β-catenin that activate Wnt signaling have been found in colorectal and hepatocellular carcinomas. However, the dynamics of wild-type and mutant forms of β-catenin are not fully understood. Here, we genome-engineered fluorescently tagged alleles of endogenous β-catenin in a colorectal cancer cell line. Wild-type and oncogenic mutant alleles were tagged with different fluorescent proteins, enabling the analysis of both variants in the same cell. We analyzed the properties of both β-catenin alleles using immunoprecipitation, immunofluorescence, and fluorescence correlation spectroscopy approaches, revealing distinctly different biophysical properties. In addition, activation of Wnt signaling by treatment with a GSK3β inhibitor or a truncating APC mutation modulated the wild-type allele to mimic the properties of the mutant β-catenin allele. The one-step tagging strategy demonstrates how genome engineering can be employed for the parallel functional analysis of different genetic variants.
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Affiliation(s)
- Giulia Ambrosi
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, Heidelberg, Germany
| | - Oksana Voloshanenko
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, Heidelberg, Germany
| | - Antonia F Eckert
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - Dominique Kranz
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, Heidelberg, Germany
| | - G Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology, Karlsruhe, Germany.,Institute of Nanotechnology, Karlsruhe Institute of Technology, Karlsruhe, Germany.,Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Karlsruhe, Germany.,Department of Physics, University of Illinois at Urbana-Champaign, Urbana, United States
| | - Michael Boutros
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and Heidelberg University, BioQuant and Medical Faculty Mannheim, Heidelberg, Germany
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4
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Snijders KE, Fehér A, Táncos Z, Bock I, Téglási A, van den Berk L, Niemeijer M, Bouwman P, Le Dévédec SE, Moné MJ, Van Rossom R, Kumar M, Wilmes A, Jennings P, Verfaillie CM, Kobolák J, Ter Braak B, Dinnyés A, van de Water B. Fluorescent tagging of endogenous Heme oxygenase-1 in human induced pluripotent stem cells for high content imaging of oxidative stress in various differentiated lineages. Arch Toxicol 2021; 95:3285-3302. [PMID: 34480604 PMCID: PMC8448683 DOI: 10.1007/s00204-021-03127-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2021] [Accepted: 07/27/2021] [Indexed: 12/28/2022]
Abstract
Tagging of endogenous stress response genes can provide valuable in vitro models for chemical safety assessment. Here, we present the generation and application of a fluorescent human induced pluripotent stem cell (hiPSC) reporter line for Heme oxygenase-1 (HMOX1), which is considered a sensitive and reliable biomarker for the oxidative stress response. CRISPR/Cas9 technology was used to insert an enhanced green fluorescent protein (eGFP) at the C-terminal end of the endogenous HMOX1 gene. Individual clones were selected and extensively characterized to confirm precise editing and retained stem cell properties. Bardoxolone-methyl (CDDO-Me) induced oxidative stress caused similarly increased expression of both the wild-type and eGFP-tagged HMOX1 at the mRNA and protein level. Fluorescently tagged hiPSC-derived proximal tubule-like, hepatocyte-like, cardiomyocyte-like and neuron-like progenies were treated with CDDO-Me (5.62–1000 nM) or diethyl maleate (5.62–1000 µM) for 24 h and 72 h. Multi-lineage oxidative stress responses were assessed through transcriptomics analysis, and HMOX1-eGFP reporter expression was carefully monitored using live-cell confocal imaging. We found that eGFP intensity increased in a dose-dependent manner with dynamics varying amongst lineages and stressors. Point of departure modelling further captured the specific lineage sensitivities towards oxidative stress. We anticipate that the newly developed HMOX1 hiPSC reporter will become a valuable tool in understanding and quantifying critical target organ cell-specific oxidative stress responses induced by (newly developed) chemical entities.
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Affiliation(s)
- Kirsten E Snijders
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | | | | | | | | | - Linda van den Berk
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Marije Niemeijer
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Peter Bouwman
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Sylvia E Le Dévédec
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Martijn J Moné
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - Rob Van Rossom
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Manoj Kumar
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | - Anja Wilmes
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Amsterdam, The Netherlands
| | - Paul Jennings
- Division of Molecular and Computational Toxicology, Amsterdam Institute for Molecules, Medicines and Systems, Amsterdam, The Netherlands
| | - Catherine M Verfaillie
- Department of Development and Regeneration, Stem Cell Institute, KU Leuven, Leuven, Belgium
| | | | - Bas Ter Braak
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands
| | - András Dinnyés
- BioTalentum Ltd., 2100, Gödöllő, Hungary. .,Department of Physiology and Animal Health, Institute of Physiology and Animal Health, Hungarian University of Agriculture and Life Sciences, 2100, Gödöllő, Hungary.
| | - Bob van de Water
- Division of Drug Discovery and Safety, Leiden Academic Centre for Drug Research, Leiden University, Einsteinweg 55, 2333 CC, Leiden, The Netherlands.
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5
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Fueller J, Herbst K, Meurer M, Gubicza K, Kurtulmus B, Knopf JD, Kirrmaier D, Buchmuller BC, Pereira G, Lemberg MK, Knop M. CRISPR-Cas12a-assisted PCR tagging of mammalian genes. J Cell Biol 2020; 219:e201910210. [PMID: 32406907 PMCID: PMC7265327 DOI: 10.1083/jcb.201910210] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2019] [Revised: 02/10/2020] [Accepted: 03/26/2020] [Indexed: 12/20/2022] Open
Abstract
Here we describe a time-efficient strategy for endogenous C-terminal gene tagging in mammalian tissue culture cells. An online platform is used to design two long gene-specific oligonucleotides for PCR with generic template cassettes to create linear dsDNA donors, termed PCR cassettes. PCR cassettes encode the tag (e.g., GFP), a Cas12a CRISPR RNA for cleavage of the target locus, and short homology arms for directed integration via homologous recombination. The integrated tag is coupled to a generic terminator shielding the tagged gene from the co-inserted auxiliary sequences. Co-transfection of PCR cassettes with a Cas12a-encoding plasmid leads to robust endogenous expression of tagged genes, with tagging efficiency of up to 20% without selection, and up to 60% when selection markers are used. We used target-enrichment sequencing to investigate all potential sources of artifacts. Our work outlines a quick strategy particularly suitable for exploratory studies using endogenous expression of fluorescent protein-tagged genes.
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Affiliation(s)
- Julia Fueller
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Konrad Herbst
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Matthias Meurer
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Krisztina Gubicza
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Bahtiyar Kurtulmus
- Center for Organismal Studies, University of Heidelberg and DKFZ, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Julia D. Knopf
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Daniel Kirrmaier
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
- Cell Morphogenesis and Signal Transduction, DKFZ-ZMBH Alliance and DKFZ, Heidelberg, Germany
| | - Benjamin C. Buchmuller
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Gislene Pereira
- Center for Organismal Studies, University of Heidelberg and DKFZ, DKFZ-ZMBH Alliance, Heidelberg, Germany
| | - Marius K. Lemberg
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
| | - Michael Knop
- Zentrum für Molekulare Biologie der Universität Heidelberg (ZMBH), German Cancer Research Center (DKFZ)-ZMBH Alliance, Heidelberg, Germany
- Cell Morphogenesis and Signal Transduction, DKFZ-ZMBH Alliance and DKFZ, Heidelberg, Germany
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6
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Lundberg E, Borner GHH. Spatial proteomics: a powerful discovery tool for cell biology. Nat Rev Mol Cell Biol 2020; 20:285-302. [PMID: 30659282 DOI: 10.1038/s41580-018-0094-y] [Citation(s) in RCA: 278] [Impact Index Per Article: 69.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Protein subcellular localization is tightly controlled and intimately linked to protein function in health and disease. Capturing the spatial proteome - that is, the localizations of proteins and their dynamics at the subcellular level - is therefore essential for a complete understanding of cell biology. Owing to substantial advances in microscopy, mass spectrometry and machine learning applications for data analysis, the field is now mature for proteome-wide investigations of spatial cellular regulation. Studies of the human proteome have begun to reveal a complex architecture, including single-cell variations, dynamic protein translocations, changing interaction networks and proteins localizing to multiple compartments. Furthermore, several studies have successfully harnessed the power of comparative spatial proteomics as a discovery tool to unravel disease mechanisms. We are at the beginning of an era in which spatial proteomics finally integrates with cell biology and medical research, thereby paving the way for unbiased systems-level insights into cellular processes. Here, we discuss current methods for spatial proteomics using imaging or mass spectrometry and specifically highlight global comparative applications. The aim of this Review is to survey the state of the field and also to encourage more cell biologists to apply spatial proteomics approaches.
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Affiliation(s)
- Emma Lundberg
- Science for Life Laboratory, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH - Royal Institute of Technology, Stockholm, Sweden. .,Department of Genetics, Stanford University, Stanford, CA, USA. .,Chan Zuckerberg Biohub, San Francisco, CA, USA.
| | - Georg H H Borner
- Max Planck Institute of Biochemistry, Department of Proteomics and Signal Transduction, Martinsried, Germany.
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7
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Simultaneous co-localized super-resolution fluorescence microscopy and atomic force microscopy: combined SIM and AFM platform for the life sciences. Sci Rep 2020; 10:1122. [PMID: 31980680 PMCID: PMC6981207 DOI: 10.1038/s41598-020-57885-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2019] [Accepted: 01/07/2020] [Indexed: 01/05/2023] Open
Abstract
Correlating data from different microscopy techniques holds the potential to discover new facets of signaling events in cellular biology. Here we report for the first time a hardware set-up capable of achieving simultaneous co-localized imaging of spatially correlated far-field super-resolution fluorescence microscopy and atomic force microscopy, a feat only obtained until now by fluorescence microscopy set-ups with spatial resolution restricted by the Abbe diffraction limit. We detail system integration and demonstrate system performance using sub-resolution fluorescent beads and applied to a test sample consisting of human bone osteosarcoma epithelial cells, with plasma membrane transporter 1 (MCT1) tagged with an enhanced green fluorescent protein (EGFP) at the N-terminal.
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8
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Akamatsu M, Vasan R, Serwas D, Ferrin MA, Rangamani P, Drubin DG. Principles of self-organization and load adaptation by the actin cytoskeleton during clathrin-mediated endocytosis. eLife 2020; 9:49840. [PMID: 31951196 PMCID: PMC7041948 DOI: 10.7554/elife.49840] [Citation(s) in RCA: 89] [Impact Index Per Article: 22.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2019] [Accepted: 01/16/2020] [Indexed: 12/20/2022] Open
Abstract
Force generation by actin assembly shapes cellular membranes. An experimentally constrained multiscale model shows that a minimal branched actin network is sufficient to internalize endocytic pits against membrane tension. Around 200 activated Arp2/3 complexes are required for robust internalization. A newly developed molecule-counting method determined that ~200 Arp2/3 complexes assemble at sites of clathrin-mediated endocytosis in human cells. Simulations predict that actin self-organizes into a radial branched array with growing ends oriented toward the base of the pit. Long actin filaments bend between attachment sites in the coat and the base of the pit. Elastic energy stored in bent filaments, whose presence was confirmed by cryo-electron tomography, contributes to endocytic internalization. Elevated membrane tension directs more growing filaments toward the base of the pit, increasing actin nucleation and bending for increased force production. Thus, spatially constrained actin filament assembly utilizes an adaptive mechanism enabling endocytosis under varying physical constraints. The outer membrane of a cell is a tight but elastic barrier that controls what enters or leaves the cell. Large molecules typically cannot cross this membrane unaided. Instead, to enter the cell, they must be packaged into a pocket of the membrane that is then pulled inside. This process, called endocytosis, shuttles material into a cell hundreds of times a minute. Endocytosis relies on molecular machines that assemble and disassemble at the membrane as required. One component, a protein called actin, self-assembles near the membrane into long filaments with many repeated subunits. These filaments grow against the membrane, pulling it inwards. But it was not clear how actin filaments organize in such a way that allows them to pull on the membrane with enough force – and without a template to follow. Akamatsu et al. set about identifying how actin operates during endocytosis by using computer simulations that were informed by measurements made in living cells. The simulations included information about the location of actin and other essential molecules, along with the details of how these molecules work individually and together. Akamatsu et al. also developed a method to count the numbers of molecules of a key protein at individual sites of endocytosis. High-resolution imaging was then used to create 3D pictures of actin and endocytosis in action in human cells grown in the laboratory. The analysis showed the way actin filaments arrange themselves depends on the starting positions of a few key molecules that connect to actin. Imaging confirmed that, like a pole-vaulting pole, the flexible actin filaments bend to store energy and then release it to pull the membrane inwards during endocytosis. Finally, the simulations predicted that the collection of filaments adapts its shape and size in response to the resistance of the elastic membrane. This makes the system opportunistic and adaptable to the unpredictable environment within cells.
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Affiliation(s)
- Matthew Akamatsu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Ritvik Vasan
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, United States
| | - Daniel Serwas
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Michael A Ferrin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Padmini Rangamani
- Department of Mechanical and Aerospace Engineering, University of California, San Diego, La Jolla, United States
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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9
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Roberts B, Hendershott MC, Arakaki J, Gerbin KA, Malik H, Nelson A, Gehring J, Hookway C, Ludmann SA, Yang R, Haupt A, Grancharova T, Valencia V, Fuqua MA, Tucker A, Rafelski SM, Gunawardane RN. Fluorescent Gene Tagging of Transcriptionally Silent Genes in hiPSCs. Stem Cell Reports 2019; 12:1145-1158. [PMID: 30956114 PMCID: PMC6522946 DOI: 10.1016/j.stemcr.2019.03.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Revised: 03/04/2019] [Accepted: 03/05/2019] [Indexed: 12/27/2022] Open
Abstract
We describe a multistep method for endogenous tagging of transcriptionally silent genes in human induced pluripotent stem cells (hiPSCs). A monomeric EGFP (mEGFP) fusion tag and a constitutively expressed mCherry fluorescence selection cassette were delivered in tandem via homology-directed repair to five genes not expressed in hiPSCs but important for cardiomyocyte sarcomere function: TTN, MYL7, MYL2, TNNI1, and ACTN2. CRISPR/Cas9 was used to deliver the selection cassette and subsequently mediate its excision via microhomology-mediated end-joining and non-homologous end-joining. Most excised clones were effectively tagged, and all properly tagged clones expressed the mEGFP fusion protein upon differentiation into cardiomyocytes, allowing live visualization of these cardiac proteins at the sarcomere. This methodology provides a broadly applicable strategy for endogenously tagging transcriptionally silent genes in hiPSCs, potentially enabling their systematic and dynamic study during differentiation and morphogenesis.
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Affiliation(s)
- Brock Roberts
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | - Joy Arakaki
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | - Haseeb Malik
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | - Jamie Gehring
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | | | - Ruian Yang
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | - Amanda Haupt
- Allen Institute for Cell Science, Seattle, WA 98109, USA
| | | | | | | | - Andrew Tucker
- Allen Institute for Cell Science, Seattle, WA 98109, USA
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10
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Mann BJ, Wadsworth P. Distribution of Eg5 and TPX2 in mitosis: Insight from CRISPR tagged cells. Cytoskeleton (Hoboken) 2018; 75:508-521. [DOI: 10.1002/cm.21486] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 07/11/2018] [Accepted: 07/30/2018] [Indexed: 11/07/2022]
Affiliation(s)
- B. J. Mann
- Department of Biology, Program in Molecular and Cellular Biology University of Massachusetts Amherst Massachusetts
| | - P. Wadsworth
- Department of Biology, Program in Molecular and Cellular Biology University of Massachusetts Amherst Massachusetts
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11
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Schöneberg J, Dambournet D, Liu TL, Forster R, Hockemeyer D, Betzig E, Drubin DG. 4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell-derived intestinal organoids. Mol Biol Cell 2018; 29:2959-2968. [PMID: 30188768 PMCID: PMC6329908 DOI: 10.1091/mbc.e18-06-0375] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
New methods in stem cell 3D organoid tissue culture, advanced imaging, and big data image analytics now allow tissue-scale 4D cell biology, but currently available analytical pipelines are inadequate for handing and analyzing the resulting gigabytes and terabytes of high-content imaging data. We expressed fluorescent protein fusions of clathrin and dynamin2 at endogenous levels in genome-edited human embryonic stem cells, which were differentiated into hESC-derived intestinal epithelial organoids. Lattice light-sheet imaging with adaptive optics (AO-LLSM) allowed us to image large volumes of these organoids (70 × 60 × 40 µm xyz) at 5.7 s/frame. We developed an open-source data analysis package termed pyLattice to process the resulting large (∼60 Gb) movie data sets and to track clathrin-mediated endocytosis (CME) events. CME tracks could be recorded from ∼35 cells at a time, resulting in ∼4000 processed tracks per movie. On the basis of their localization in the organoid, we classified CME tracks into apical, lateral, and basal events and found that CME dynamics is similar for all three classes, despite reported differences in membrane tension. pyLattice coupled with AO-LLSM makes possible quantitative high temporal and spatial resolution analysis of subcellular events within tissues.
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Affiliation(s)
| | - Daphné Dambournet
- Department of Molecular and Cell Biology, Berkeley, Berkeley, CA 94720
| | - Tsung-Li Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | - Ryan Forster
- Department of Molecular and Cell Biology, Berkeley, Berkeley, CA 94720
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, Berkeley, Berkeley, CA 94720
| | - Eric Betzig
- Department of Molecular and Cell Biology, Berkeley, Berkeley, CA 94720.,Department of Physics, University of California, Berkeley, Berkeley, CA 94720.,Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147
| | - David G Drubin
- Department of Molecular and Cell Biology, Berkeley, Berkeley, CA 94720
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12
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Haupt A, Grancharova T, Arakaki J, Fuqua MA, Roberts B, Gunawardane RN. Endogenous Protein Tagging in Human Induced Pluripotent Stem Cells Using CRISPR/Cas9. J Vis Exp 2018:58130. [PMID: 30199041 PMCID: PMC6231893 DOI: 10.3791/58130] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
A protocol is presented for generating human induced pluripotent stem cells (hiPSCs) that express endogenous proteins fused to in-frame N- or C-terminal fluorescent tags. The prokaryotic CRISPR/Cas9 system (clustered regularly interspaced short palindromic repeats/CRISPR-associated 9) may be used to introduce large exogenous sequences into genomic loci via homology directed repair (HDR). To achieve the desired knock-in, this protocol employs the ribonucleoprotein (RNP)-based approach where wild type Streptococcus pyogenes Cas9 protein, synthetic 2-part guide RNA (gRNA), and a donor template plasmid are delivered to the cells via electroporation. Putatively edited cells expressing the fluorescently tagged proteins are enriched by fluorescence activated cell sorting (FACS). Clonal lines are then generated and can be analyzed for precise editing outcomes. By introducing the fluorescent tag at the genomic locus of the gene of interest, the resulting subcellular localization and dynamics of the fusion protein can be studied under endogenous regulatory control, a key improvement over conventional overexpression systems. The use of hiPSCs as a model system for gene tagging provides the opportunity to study the tagged proteins in diploid, nontransformed cells. Since hiPSCs can be differentiated into multiple cell types, this approach provides the opportunity to create and study tagged proteins in a variety of isogenic cellular contexts.
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13
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Nomura W. Development of Toolboxes for Precision Genome/Epigenome Editing and Imaging of Epigenetics. CHEM REC 2018; 18:1717-1726. [PMID: 30066981 DOI: 10.1002/tcr.201800036] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2018] [Accepted: 07/17/2018] [Indexed: 12/17/2022]
Abstract
Zinc finger (ZF) proteins are composed of repeated ββα modules and coordinate a zinc ion. ZF domains recognizing specific DNA target sequences can be substituted for the binding domains of various DNA-modifying enzymes to create designer nucleases, recombinases, and methyltransferases with programmable sequence specificity. Enzymatic genome editing and modification can be applied to many fields of basic research and medicine. The recent development of new platforms using transcription activator-like effector (TALE) proteins or the CRISPR-Cas9 system has expanded the range of possibilities for genome-editing technologies. In addition, these DNA binding domains can also be utilized to build a toolbox for epigenetic controls by fusing them with protein- or DNA-modifying enzymes. Here, our research on epigenome editing including the development of artificial zinc finger recombinase (ZFR), split DNA methyltransferase, and fluorescence imaging of histone proteins by ZIP tag-probe system is introduced. Advances in the ZF, TALE, and CRISPR-Cas9 platforms have paved the way for the next generation of genome/epigenome engineering approaches.
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Affiliation(s)
- Wataru Nomura
- Institute of Biomaterials and Bioenginerring, Tokyo Medical and Dental University, 2-3-10 Kandasurugadai, Chiyoda-ku, Tokyo, 101-0062, Japan
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14
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Ponrathnam T, Mishra RK. From chromosomes to genomes: new insights with emerging techniques. THE NUCLEUS 2018. [DOI: 10.1007/s13237-018-0242-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
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15
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Dambournet D, Sochacki KA, Cheng AT, Akamatsu M, Taraska JW, Hockemeyer D, Drubin DG. Genome-edited human stem cells expressing fluorescently labeled endocytic markers allow quantitative analysis of clathrin-mediated endocytosis during differentiation. J Cell Biol 2018; 217:3301-3311. [PMID: 29980624 PMCID: PMC6123002 DOI: 10.1083/jcb.201710084] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Revised: 11/05/2017] [Accepted: 06/04/2018] [Indexed: 12/11/2022] Open
Abstract
We developed a general approach for investigation of how cellular processes become adapted for specific cell types during differentiation. Previous studies reported substantial differences in the morphology and dynamics of clathrin-mediated endocytosis (CME) sites. However, associating specific CME properties with distinct differentiated cell types and determining how these properties are developmentally specified during differentiation have been elusive. Using genome-edited human embryonic stem cells, and isogenic fibroblasts and neuronal progenitor cells derived from them, we established by live-cell imaging and platinum replica transmission electron microscopy that CME site dynamics and ultrastructure on the plasma membrane are precisely reprogrammed during differentiation. Expression levels for the endocytic adaptor protein AP2μ2 were found to underlie dramatic changes in CME dynamics and structure. Additionally, CME dependency on actin assembly and phosphoinositide-3 kinase activity are distinct for each cell type. Collectively, our results demonstrate that key CME properties are reprogrammed during differentiation at least in part through AP2μ2 expression regulation.
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Affiliation(s)
- Daphné Dambournet
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Kem A Sochacki
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | | | - Matthew Akamatsu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Justin W Taraska
- National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, MD
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
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16
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Koch B, Nijmeijer B, Kueblbeck M, Cai Y, Walther N, Ellenberg J. Generation and validation of homozygous fluorescent knock-in cells using CRISPR-Cas9 genome editing. Nat Protoc 2018; 13:1465-1487. [PMID: 29844520 PMCID: PMC6556379 DOI: 10.1038/nprot.2018.042] [Citation(s) in RCA: 68] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Gene tagging with fluorescent proteins is essential for investigations of the dynamic properties of cellular proteins. CRISPR-Cas9 technology is a powerful tool for inserting fluorescent markers into all alleles of the gene of interest (GOI) and allows functionality and physiological expression of the fusion protein. It is essential to evaluate such genome-edited cell lines carefully in order to preclude off-target effects caused by (i) incorrect insertion of the fluorescent protein, (ii) perturbation of the fusion protein by the fluorescent proteins or (iii) nonspecific genomic DNA damage by CRISPR-Cas9. In this protocol, we provide a step-by-step description of our systematic pipeline to generate and validate homozygous fluorescent knock-in cell lines.We have used the paired Cas9D10A nickase approach to efficiently insert tags into specific genomic loci via homology-directed repair (HDR) with minimal off-target effects. It is time-consuming and costly to perform whole-genome sequencing of each cell clone to check for spontaneous genetic variations occurring in mammalian cell lines. Therefore, we have developed an efficient validation pipeline of the generated cell lines consisting of junction PCR, Southern blotting analysis, Sanger sequencing, microscopy, western blotting analysis and live-cell imaging for cell-cycle dynamics. This protocol takes between 6 and 9 weeks. With this protocol, up to 70% of the targeted genes can be tagged homozygously with fluorescent proteins, thus resulting in physiological levels and phenotypically functional expression of the fusion proteins.
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Affiliation(s)
- Birgit Koch
- EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
- current address: Max Planck Insitute for Medical Research, Jahnstraße 29, 69120 Heidelberg, Germany
| | | | | | - Yin Cai
- EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
- current address: Roche SIS, Maybachstr. 30, 71332 Waiblingen, Germany
| | - Nike Walther
- EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
| | - Jan Ellenberg
- EMBL, Meyerhofstrasse 1, D-69117 Heidelberg, Germany
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17
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Liu TL, Upadhyayula S, Milkie DE, Singh V, Wang K, Swinburne IA, Mosaliganti KR, Collins ZM, Hiscock TW, Shea J, Kohrman AQ, Medwig TN, Dambournet D, Forster R, Cunniff B, Ruan Y, Yashiro H, Scholpp S, Meyerowitz EM, Hockemeyer D, Drubin DG, Martin BL, Matus DQ, Koyama M, Megason SG, Kirchhausen T, Betzig E. Observing the cell in its native state: Imaging subcellular dynamics in multicellular organisms. Science 2018; 360:eaaq1392. [PMID: 29674564 PMCID: PMC6040645 DOI: 10.1126/science.aaq1392] [Citation(s) in RCA: 315] [Impact Index Per Article: 52.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 02/19/2018] [Indexed: 01/10/2023]
Abstract
True physiological imaging of subcellular dynamics requires studying cells within their parent organisms, where all the environmental cues that drive gene expression, and hence the phenotypes that we actually observe, are present. A complete understanding also requires volumetric imaging of the cell and its surroundings at high spatiotemporal resolution, without inducing undue stress on either. We combined lattice light-sheet microscopy with adaptive optics to achieve, across large multicellular volumes, noninvasive aberration-free imaging of subcellular processes, including endocytosis, organelle remodeling during mitosis, and the migration of axons, immune cells, and metastatic cancer cells in vivo. The technology reveals the phenotypic diversity within cells across different organisms and developmental stages and may offer insights into how cells harness their intrinsic variability to adapt to different physiological environments.
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Affiliation(s)
- Tsung-Li Liu
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Srigokul Upadhyayula
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Daniel E Milkie
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ved Singh
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Kai Wang
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Ian A Swinburne
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Kishore R Mosaliganti
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Zach M Collins
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Tom W Hiscock
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Jamien Shea
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Abraham Q Kohrman
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Taylor N Medwig
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Daphne Dambournet
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Ryan Forster
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Brian Cunniff
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Yuan Ruan
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Hanako Yashiro
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Steffen Scholpp
- Living Systems Institute, College of Life and Environmental Sciences, University of Exeter, Exeter EX4 4QD, UK
- Institute of Toxicology and Genetics, Karlsruhe Institute of Technology, 76021 Karlsruhe, Germany
| | - Elliot M Meyerowitz
- Howard Hughes Medical Institute and Division of Biology and Biological Engineering, California Institute of Technology, Pasadena, CA 91125, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Benjamin L Martin
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - David Q Matus
- Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, NY 11794-5215, USA
| | - Minoru Koyama
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
| | - Sean G Megason
- Department of Systems Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Tom Kirchhausen
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA
- Department of Cell Biology, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, 200 Longwood Avenue, Boston, MA 02115, USA
- Department of Pediatrics, Harvard Medical School, 200 Longwood Avenue, Boston, MA 02115, USA
| | - Eric Betzig
- Janelia Research Campus, Howard Hughes Medical Institute, Ashburn, VA 20147, USA.
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18
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Drubin DG, Hyman AA. Stem cells: the new "model organism". Mol Biol Cell 2017; 28:1409-1411. [PMID: 28559439 PMCID: PMC5449140 DOI: 10.1091/mbc.e17-03-0183] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2017] [Accepted: 04/04/2017] [Indexed: 01/15/2023] Open
Abstract
Human tissue culture cells have long been a staple of molecular and cell biology research. However, although these cells are derived from humans, they have often lost considerable aspects of natural physiological function. Here we argue that combined advances in genome editing, stem cell production, and organoid derivation from stem cells represent a revolution in cell biology. These advances have important ramifications for the study of basic cell biology mechanisms, as well as for the ways in which discoveries in mechanisms are translated into understanding of disease.
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Affiliation(s)
- David G Drubin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720-3202
| | - Anthony A Hyman
- Max Planck Institute of Molecular Cell Biology and Genetics, 01307 Dresden, Germany
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19
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Risk associated with off-target plant genome editing and methods for its limitation. Emerg Top Life Sci 2017; 1:231-240. [PMID: 33525760 PMCID: PMC7288994 DOI: 10.1042/etls20170037] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/13/2017] [Accepted: 09/19/2017] [Indexed: 12/26/2022]
Abstract
Assessment for potential adverse effects of plant genome editing logically focuses on the specific characteristics of the derived phenotype and its release environment. Genome-edited crops, depending on the editing objective, can be classified as either indistinguishable from crops developed through conventional plant breeding or as crops which are transgenic. Therefore, existing regulatory regimes and risk assessment procedures accommodate genome-edited crops. The ability for regulators and the public to accept a product focus in the evaluation of genome-edited crops will depend on research which clarifies the precision of the genome-editing process and evaluates unanticipated off-target edits from the process. Interpretation of genome-wide effects of genome editing should adhere to existing frameworks for comparative risk assessment where the nature and degree of effects are considered relative to a baseline of genome-wide mutations as found in crop varieties developed through conventional breeding methods. Research addressing current uncertainties regarding unintended changes from plant genome editing, and adopting procedures that clearly avoid the potential for gene drive initiation, will help to clarify anticipated public and regulatory questions regarding risk of crops derived through genome editing.
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20
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Roberts B, Haupt A, Tucker A, Grancharova T, Arakaki J, Fuqua MA, Nelson A, Hookway C, Ludmann SA, Mueller IA, Yang R, Horwitz R, Rafelski SM, Gunawardane RN. Systematic gene tagging using CRISPR/Cas9 in human stem cells to illuminate cell organization. Mol Biol Cell 2017; 28:2854-2874. [PMID: 28814507 PMCID: PMC5638588 DOI: 10.1091/mbc.e17-03-0209] [Citation(s) in RCA: 151] [Impact Index Per Article: 21.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 08/09/2017] [Accepted: 08/10/2017] [Indexed: 12/12/2022] Open
Abstract
The generation of a collection of human induced pluripotent stem cell (hiPSC) lines expressing endogenously GFP-tagged proteins using CRISPR/Cas9 methods is described. The methods used and the genomic and cell biological data validating the GFP-tagged hiPSC lines are also presented. We present a CRISPR/Cas9 genome-editing strategy to systematically tag endogenous proteins with fluorescent tags in human induced pluripotent stem cells (hiPSC). To date, we have generated multiple hiPSC lines with monoallelic green fluorescent protein tags labeling 10 proteins representing major cellular structures. The tagged proteins include alpha tubulin, beta actin, desmoplakin, fibrillarin, nuclear lamin B1, nonmuscle myosin heavy chain IIB, paxillin, Sec61 beta, tight junction protein ZO1, and Tom20. Our genome-editing methodology using Cas9/crRNA ribonuclear protein and donor plasmid coelectroporation, followed by fluorescence-based enrichment of edited cells, typically resulted in <0.1–4% homology-directed repair (HDR). Twenty-five percent of clones generated from each edited population were precisely edited. Furthermore, 92% (36/39) of expanded clonal lines displayed robust morphology, genomic stability, expression and localization of the tagged protein to the appropriate subcellular structure, pluripotency-marker expression, and multilineage differentiation. It is our conclusion that, if cell lines are confirmed to harbor an appropriate gene edit, pluripotency, differentiation potential, and genomic stability are typically maintained during the clonal line–generation process. The data described here reveal general trends that emerged from this systematic gene-tagging approach. Final clonal lines corresponding to each of the 10 cellular structures are now available to the research community.
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Affiliation(s)
| | - Amanda Haupt
- Allen Institute for Cell Science, Seattle, WA 98109
| | | | | | - Joy Arakaki
- Allen Institute for Cell Science, Seattle, WA 98109
| | | | | | | | | | | | - Ruian Yang
- Allen Institute for Cell Science, Seattle, WA 98109
| | - Rick Horwitz
- Allen Institute for Cell Science, Seattle, WA 98109
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21
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Abstract
With the introduction of precision genome editing using CRISPR-Cas9 technology, we have entered a new era of genetic engineering and gene therapy. With RNA-guided endonucleases, such as Cas9, it is possible to engineer DNA double strand breaks (DSB) at specific genomic loci. DSB repair by the error-prone non-homologous end-joining (NHEJ) pathway can disrupt a target gene by generating insertions and deletions. Alternatively, Cas9-mediated DSBs can be repaired by homology-directed repair (HDR) using an homologous DNA repair template, thus allowing precise gene editing by incorporating genetic changes into the repair template. HDR can introduce gene sequences for protein epitope tags, delete genes, make point mutations, or alter enhancer and promoter activities. In anticipation of adapting this technology for gene therapy in human somatic cells, much focus has been placed on increasing the fidelity of CRISPR-Cas9 and increasing HDR efficiency to improve precision genome editing. In this review, we will discuss applications of CRISPR technology for gene inactivation and genome editing with a focus on approaches to enhancing CRISPR-Cas9-mediated HDR for the generation of cell and animal models, and conclude with a discussion of recent advances and challenges towards the application of this technology for gene therapy in humans.
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Affiliation(s)
- Jayme Salsman
- a Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
| | - Graham Dellaire
- a Department of Pathology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- b Department of Biochemistry & Molecular Biology, Dalhousie University, Halifax, NS B3H 4R2, Canada
- c Beatrice Hunter Cancer Research Institute, Halifax, NS B3H 4R2, Canada
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22
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Ehrke-Schulz E, Schiwon M, Hagedorn C, Ehrhardt A. Establishment of the CRISPR/Cas9 System for Targeted Gene Disruption and Gene Tagging. Methods Mol Biol 2017; 1654:165-176. [PMID: 28986789 DOI: 10.1007/978-1-4939-7231-9_11] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/10/2023]
Abstract
CRISPR/Cas9 RNA-guided nucleases refashioned in vivo gene editing approaches for specific gene disruption, gene correction, or gene addition. Moreover, chimeric Cas9 proteins can be applied to direct fused cis-acting effector protein domains, enzymes, or fluorescent markers to DNA to target sequences to regulate gene expression, to introduce epigenetic changes, or to fluorescently label DNA sequences of interest. Here we show how to design guide RNAs for specific DNA targeting. We provide a protocol to customize the CRISPR/Cas9 machinery encoded on commercially available plasmids and present how to test the targeting efficiency of Cas9 with a target-specific gRNA by testing mutation induction efficiency. To exemplify related applications we provide a guideline of how to apply the CRISPR/Cas9 technology for gene labeling.
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Affiliation(s)
- Eric Ehrke-Schulz
- Faculty of Health, School of Medicine, Center for Biomedical Research and Education ZBAF, Witten/Herdecke University, Stockumer Straße 10, Witten, 58453, Germany
| | - Maren Schiwon
- Faculty of Health, School of Medicine, Center for Biomedical Research and Education ZBAF, Witten/Herdecke University, Stockumer Straße 10, Witten, 58453, Germany
| | - Claudia Hagedorn
- Faculty of Health, School of Medicine, Center for Biomedical Research and Education ZBAF, Witten/Herdecke University, Witten, Germany
| | - Anja Ehrhardt
- Faculty of Health, School of Medicine, Center for Biomedical Research and Education ZBAF, Witten/Herdecke University, Stockumer Straße 10, Witten, 58453, Germany.
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23
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Santos DP, Kiskinis E, Eggan K, Merkle FT. Comprehensive Protocols for CRISPR/Cas9-based Gene Editing in Human Pluripotent Stem Cells. CURRENT PROTOCOLS IN STEM CELL BIOLOGY 2016; 38:5B.6.1-5B.6.60. [PMID: 27532820 PMCID: PMC4988528 DOI: 10.1002/cpsc.15] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome editing of human pluripotent stem cells (hPSCs) with the CRISPR/Cas9 system has the potential to revolutionize hPSC-based disease modeling, drug screening, and transplantation therapy. Here, we aim to provide a single resource to enable groups, even those with limited experience with hPSC culture or the CRISPR/Cas9 system, to successfully perform genome editing. The methods are presented in detail and are supported by a theoretical framework to allow for the incorporation of inevitable improvements in the rapidly evolving gene-editing field. We describe protocols to generate hPSC lines with gene-specific knock-outs, small targeted mutations, or knock-in reporters. © 2016 by John Wiley & Sons, Inc.
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Affiliation(s)
- David P. Santos
- The Ken & Ruth Davee Department of Neurology & Clinical Neurological Sciences, Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Evangelos Kiskinis
- The Ken & Ruth Davee Department of Neurology & Clinical Neurological Sciences, Department of Physiology, Feinberg School of Medicine, Northwestern University, Chicago, IL, 60611, USA
| | - Kevin Eggan
- Department of Stem Cell and Regenerative Biology, and Harvard Stem Cell Institute, Harvard University, Cambridge, MA 02138, USA
- Stanley Center for Psychiatric Research, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA
| | - Florian T. Merkle
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Wellcome Trust-MRC Institute of Metabolic Science, and Wellcome Trust-MRC Cambridge Stem Cell Institute, University of Cambridge, Cambridge CB2 0QQ, UK
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24
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Hong SH, Cortesio CL, Drubin DG. Machine-Learning-Based Analysis in Genome-Edited Cells Reveals the Efficiency of Clathrin-Mediated Endocytosis. Cell Rep 2015; 12:2121-30. [PMID: 26387943 DOI: 10.1016/j.celrep.2015.08.048] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2015] [Revised: 06/05/2015] [Accepted: 08/17/2015] [Indexed: 12/30/2022] Open
Abstract
Cells internalize various molecules through clathrin-mediated endocytosis (CME). Previous live-cell imaging studies suggested that CME is inefficient, with about half of the events terminated. These CME efficiency estimates may have been confounded by overexpression of fluorescently tagged proteins and inability to filter out false CME sites. Here, we employed genome editing and machine learning to identify and analyze authentic CME sites. We examined CME dynamics in cells that express fluorescent fusions of two defining CME proteins, AP2 and clathrin. Support vector machine classifiers were built to identify and analyze authentic CME sites. From inception until disappearance, authentic CME sites contain both AP2 and clathrin, have the same degree of limited mobility, continue to accumulate AP2 and clathrin over lifetimes >∼20 s, and almost always form vesicles as assessed by dynamin2 recruitment. Sites that contain only clathrin or AP2 show distinct dynamics, suggesting they are not part of the CME pathway.
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Affiliation(s)
- Sun Hae Hong
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - Christa L Cortesio
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA
| | - David G Drubin
- Department of Molecular and Cell Biology, University of California-Berkeley, Berkeley, CA 94720, USA.
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25
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Fortian A, Dionne LK, Hong SH, Kim W, Gygi SP, Watkins SC, Sorkin A. Endocytosis of Ubiquitylation-Deficient EGFR Mutants via Clathrin-Coated Pits is Mediated by Ubiquitylation. Traffic 2015; 16:1137-54. [PMID: 26251007 DOI: 10.1111/tra.12314] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2015] [Revised: 08/03/2015] [Accepted: 08/03/2015] [Indexed: 12/11/2022]
Abstract
Signaling by epidermal growth factor receptor (EGFR) is controlled by endocytosis. However, mechanisms of EGFR endocytosis remain poorly understood. Here, we found that the EGFR mutant lacking known ubiquitylation, acetylation and clathrin adaptor AP-2-binding sites (21KRΔAP2) was internalized at relatively high rates via the clathrin-dependent pathway in human duodenal adenocarcinoma HuTu-80 cells. RNA interference analysis revealed that this residual internalization is strongly inhibited by depletion of Grb2 and the E2 ubiquitin-conjugating enzyme UbcH5b/c, and partially affected by depletion of the E3 ubiquitin ligase Cbl and ubiquitin-binding adaptors, indicating that an ubiquitylation process is involved. Several new ubiquitin conjugation sites were identified by mass spectrometry in the 21KRΔAP2 mutant, suggesting that cryptic ubiquitylation may mediate endocytosis of this mutant. Total internal reflection fluorescence microscopy imaging of HuTu-80 cells transfected with labeled ubiquitin adaptor epsin1 demonstrated that the ubiquitylation-deficient EGFR mutant was endocytosed through a limited population of epsin-enriched clathrin-coated pits (CCPs), although with a prolonged CCP lifetime. Native EGFR was recruited with the same efficiency into CCPs containing either AP-2 or epsin1 that were tagged with fluorescent proteins by genome editing of MDA-MD-231 cells. We propose that two redundant mechanisms, ubiquitylation and interaction with AP-2, contribute to EGFR endocytosis via CCPs in a stochastic fashion.
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Affiliation(s)
- Arola Fortian
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA,, USA
| | - Lai K Dionne
- Department of Pharmacology, University of Colorado Anschutz Medical Center, Aurora, CO,, USA
| | - Sun H Hong
- Department of Molecular and Cell Biology, University of California at Berkeley, Berkeley, CA,, USA
| | - Woong Kim
- Department of Cell Biology, University of Harvard School of Medicine, Boston, MA,, USA
| | - Steven P Gygi
- Department of Cell Biology, University of Harvard School of Medicine, Boston, MA,, USA
| | - Simon C Watkins
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA,, USA
| | - Alexander Sorkin
- Department of Cell Biology, University of Pittsburgh School of Medicine, Pittsburgh, PA,, USA
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