1
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Ancos-Pintado R, Bragado-García I, Morales ML, García-Vicente R, Arroyo-Barea A, Rodríguez-García A, Martínez-López J, Linares M, Hernández-Sánchez M. High-Throughput CRISPR Screening in Hematological Neoplasms. Cancers (Basel) 2022; 14:3612. [PMID: 35892871 PMCID: PMC9329962 DOI: 10.3390/cancers14153612] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Revised: 07/16/2022] [Accepted: 07/20/2022] [Indexed: 02/01/2023] Open
Abstract
CRISPR is becoming an indispensable tool in biological research, revolutionizing diverse fields of medical research and biotechnology. In the last few years, several CRISPR-based genome-targeting tools have been translated for the study of hematological neoplasms. However, there is a lack of reviews focused on the wide uses of this technology in hematology. Therefore, in this review, we summarize the main CRISPR-based approaches of high throughput screenings applied to this field. Here we explain several libraries and algorithms for analysis of CRISPR screens used in hematology, accompanied by the most relevant databases. Moreover, we focus on (1) the identification of novel modulator genes of drug resistance and efficacy, which could anticipate relapses in patients and (2) new therapeutic targets and synthetic lethal interactions. We also discuss the approaches to uncover novel biomarkers of malignant transformations and immune evasion mechanisms. We explain the current literature in the most common lymphoid and myeloid neoplasms using this tool. Then, we conclude with future directions, highlighting the importance of further gene candidate validation and the integration and harmonization of the data from CRISPR screening approaches.
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Affiliation(s)
- Raquel Ancos-Pintado
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Irene Bragado-García
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Luz Morales
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Roberto García-Vicente
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Andrés Arroyo-Barea
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - Alba Rodríguez-García
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
| | - Joaquín Martínez-López
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Medicine, Medicine School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain
| | - María Linares
- Department of Translational Hematology, Instituto de Investigación Hospital 12 de Octubre (imas12), Hematological Malignancies Clinical Research Unit H12O-CNIO, CIBERONC, ES 28041 Madrid, Spain; (R.A.-P.); (M.L.M.); (R.G.-V.); (A.R.-G.); (J.M.-L.); (M.L.)
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
| | - María Hernández-Sánchez
- Department of Biochemistry and Molecular Biology, Pharmacy School, Universidad Complutense de Madrid, ES 28040 Madrid, Spain; (I.B.-G.); (A.A.-B.)
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Sanchez-Gonzalez R, Koupourtidou C, Lepko T, Zambusi A, Novoselc KT, Durovic T, Aschenbroich S, Schwarz V, Breunig CT, Straka H, Huttner HB, Irmler M, Beckers J, Wurst W, Zwergal A, Schauer T, Straub T, Czopka T, Trümbach D, Götz M, Stricker SH, Ninkovic J. Innate Immune Pathways Promote Oligodendrocyte Progenitor Cell Recruitment to the Injury Site in Adult Zebrafish Brain. Cells 2022; 11:cells11030520. [PMID: 35159329 PMCID: PMC8834209 DOI: 10.3390/cells11030520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2021] [Revised: 01/18/2022] [Accepted: 01/18/2022] [Indexed: 01/13/2023] Open
Abstract
The oligodendrocyte progenitors (OPCs) are at the front of the glial reaction to the traumatic brain injury. However, regulatory pathways steering the OPC reaction as well as the role of reactive OPCs remain largely unknown. Here, we compared a long-lasting, exacerbated reaction of OPCs to the adult zebrafish brain injury with a timely restricted OPC activation to identify the specific molecular mechanisms regulating OPC reactivity and their contribution to regeneration. We demonstrated that the influx of the cerebrospinal fluid into the brain parenchyma after injury simultaneously activates the toll-like receptor 2 (Tlr2) and the chemokine receptor 3 (Cxcr3) innate immunity pathways, leading to increased OPC proliferation and thereby exacerbated glial reactivity. These pathways were critical for long-lasting OPC accumulation even after the ablation of microglia and infiltrating monocytes. Importantly, interference with the Tlr1/2 and Cxcr3 pathways after injury alleviated reactive gliosis, increased new neuron recruitment, and improved tissue restoration.
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Affiliation(s)
- Rosario Sanchez-Gonzalez
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Department Biology II, University of Munich, 80539 München, Germany;
| | - Christina Koupourtidou
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Tjasa Lepko
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Alessandro Zambusi
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Klara Tereza Novoselc
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Tamara Durovic
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Sven Aschenbroich
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Veronika Schwarz
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Graduate School Systemic Neurosciences, LMU, 80539 Munich, Germany
| | - Christopher T. Breunig
- Reprogramming and Regeneration, Biomedical Center (BMC), Physiological Genomics, Faculty of Medicine, LMU Munich, 80539 München, Germany; (C.T.B.); (S.H.S.)
- Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany
| | - Hans Straka
- Department Biology II, University of Munich, 80539 München, Germany;
| | - Hagen B. Huttner
- Department of Neurology, Justus-Liebig-University Giessen, Klinikstrasse 33, 35392 Giessen, Germany;
| | - Martin Irmler
- Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (M.I.); (J.B.)
| | - Johannes Beckers
- Institute of Experimental Genetics, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (M.I.); (J.B.)
- German Center for Diabetes Research (DZD e.V.), 85764 Neuherberg, Germany
- Chair of Experimental Genetics, School of Life Sciences Weihenstephan, Technical University Munich, 80333 München, Germany
| | - Wolfgang Wurst
- Institute of Developmental Genetics, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (W.W.); (D.T.)
- Munich Cluster for Systems Neurology SYNERGY, LMU, 80539 Munich, Germany
- Chair of Developmental Genetics c/o Helmholtz Zentrum München, School of Life Sciences Weihenstephan, Technical University Munich, 80333 München, Germany
- German Center for Neurodegenerative Diseases (DZNE), Site Munich, 80539 Munich, Germany
| | - Andreas Zwergal
- Department of Neurology, Ludwig-Maximilians University, Campus Grosshadern, 81377 Munich, Germany;
| | - Tamas Schauer
- Biomedical Center (BMC), Bioinformatic Core Facility, Faculty of Medicine, LMU Munich, 80539 München, Germany; (T.S.); (T.S.)
| | - Tobias Straub
- Biomedical Center (BMC), Bioinformatic Core Facility, Faculty of Medicine, LMU Munich, 80539 München, Germany; (T.S.); (T.S.)
| | - Tim Czopka
- Centre for Clinical Brain Sciences, University of Edinburgh, Edinburgh EH8 9YL, UK;
| | - Dietrich Trümbach
- Institute of Developmental Genetics, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (W.W.); (D.T.)
| | - Magdalena Götz
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Munich Cluster for Systems Neurology SYNERGY, LMU, 80539 Munich, Germany
- Biomedical Center (BMC), Division of Physiological Genomics, Faculty of Medicine, LMU Munich, 80539 München, Germany
| | - Stefan H. Stricker
- Reprogramming and Regeneration, Biomedical Center (BMC), Physiological Genomics, Faculty of Medicine, LMU Munich, 80539 München, Germany; (C.T.B.); (S.H.S.)
- Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany
| | - Jovica Ninkovic
- Institute of Stem Cell Research, Helmholtz Center Munich, 85764 Oberschleißheim, Germany; (R.S.-G.); (C.K.); (T.L.); (A.Z.); (K.T.N.); (T.D.); (S.A.); (V.S.); (M.G.)
- Biomedical Center (BMC), Division of Cell Biology and Anatomy, Faculty of Medicine, LMU Munich, 80539 München, Germany
- Munich Cluster for Systems Neurology SYNERGY, LMU, 80539 Munich, Germany
- Correspondence:
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3
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Yates JD, Russell RC, Barton NJ, Yost HJ, Hill J. A simple and rapid method for enzymatic synthesis of CRISPR-Cas9 sgRNA libraries. Nucleic Acids Res 2021; 49:e131. [PMID: 34554233 PMCID: PMC8682767 DOI: 10.1093/nar/gkab838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Revised: 09/03/2021] [Accepted: 09/09/2021] [Indexed: 11/14/2022] Open
Abstract
CRISPR-Cas9 sgRNA libraries have transformed functional genetic screening and have enabled several innovative methods that rely on simultaneously targeting numerous genetic loci. Such libraries could be used in a vast number of biological systems and in the development of new technologies, but library generation is hindered by the cost, time, and sequence data required for sgRNA library synthesis. Here, we describe a rapid enzymatic method for generating robust, variant-matched libraries from any source of cDNA in under 3 h. This method, which we have named SLALOM, utilizes a custom sgRNA scaffold sequence and a novel method for detaching oligonucleotides from solid supports by a strand displacing polymerase. With this method, we constructed libraries targeting the E. coli genome and the transcriptome of developing zebrafish hearts, demonstrating its ability to expand the reach of CRISPR technology and facilitate methods requiring custom libraries.
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Affiliation(s)
- Joshua D Yates
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Robert C Russell
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - Nathaniel J Barton
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
| | - H Joseph Yost
- Molecular Medicine Program and Department of Neurobiology, University of Utah, Salt Lake City, UT, USA
| | - Jonathon T Hill
- Department of Cell Biology and Physiology, Brigham Young University, Provo, UT, USA
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4
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Iyer VS, Jiang L, Shen Y, Boddul SV, Panda SK, Kasza Z, Schmierer B, Wermeling F. Designing custom CRISPR libraries for hypothesis-driven drug target discovery. Comput Struct Biotechnol J 2020; 18:2237-2246. [PMID: 32952937 PMCID: PMC7479249 DOI: 10.1016/j.csbj.2020.08.009] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2020] [Revised: 07/24/2020] [Accepted: 08/09/2020] [Indexed: 12/20/2022] Open
Abstract
Over the last decade Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) has been developed into a potent molecular biology tool used to rapidly modify genes or their expression in a multitude of ways. In parallel, CRISPR-based screening approaches have been developed as powerful discovery platforms for dissecting the genetic basis of cellular behavior, as well as for drug target discovery. CRISPR screens can be designed in numerous ways. Here, we give a brief background to CRISPR screens and discuss the pros and cons of different design approaches, including unbiased genome-wide screens that target all known genes, as well as hypothesis-driven custom screens in which selected subsets of genes are targeted (Fig. 1). We provide several suggestions for how a custom screen can be designed, which could broadly serve as inspiration for any experiment that includes candidate gene selection. Finally, we discuss how results from CRISPR screens could be translated into drug development, as well as future trends we foresee in the rapidly evolving CRISPR screen field.
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Affiliation(s)
- Vaishnavi Srinivasan Iyer
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore
| | - Long Jiang
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Yunbing Shen
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Sanjaykumar V Boddul
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Sudeepta Kumar Panda
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden.,Structural Genomics Consortium, Department of Medicine, Karolinska University Hospital and Karolinska Institutet, Stockholm, Sweden
| | - Zsolt Kasza
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
| | - Bernhard Schmierer
- High Throughput Genome Engineering, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden.,Science for Life Laboratory, Stockholm, Sweden
| | - Fredrik Wermeling
- Center for Molecular Medicine, Division of Rheumatology, Department of Medicine, Solna, Karolinska Institutet and Karolinska University Hospital, Stockholm, Sweden
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5
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Breunig CT, Köferle A, Neuner AM, Wiesbeck MF, Baumann V, Stricker SH. CRISPR Tools for Physiology and Cell State Changes: Potential of Transcriptional Engineering and Epigenome Editing. Physiol Rev 2020; 101:177-211. [PMID: 32525760 DOI: 10.1152/physrev.00034.2019] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Given the large amount of genome-wide data that have been collected during the last decades, a good understanding of how and why cells change during development, homeostasis, and disease might be expected. Unfortunately, the opposite is true; triggers that cause cellular state changes remain elusive, and the underlying molecular mechanisms are poorly understood. Although genes with the potential to influence cell states are known, the historic dependency on methods that manipulate gene expression outside the endogenous chromatin context has prevented us from understanding how cells organize, interpret, and protect cellular programs. Fortunately, recent methodological innovations are now providing options to answer these outstanding questions, by allowing to target and manipulate individual genomic and epigenomic loci. In particular, three experimental approaches are now feasible due to DNA targeting tools, namely, activation and/or repression of master transcription factors in their endogenous chromatin context; targeting transcription factors to endogenous, alternative, or inaccessible sites; and finally, functional manipulation of the chromatin context. In this article, we discuss the molecular basis of DNA targeting tools and review the potential of these new technologies before we summarize how these have already been used for the manipulation of cellular states and hypothesize about future applications.
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Affiliation(s)
- Christopher T Breunig
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Anna Köferle
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Andrea M Neuner
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Maximilian F Wiesbeck
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Valentin Baumann
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
| | - Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian- Universität, BioMedical Center, Planegg-Martinsried, Germany; and Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, BioMedical Center, Planegg-Martinsried, Germany
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6
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Baumann V, Wiesbeck M, Breunig CT, Braun JM, Köferle A, Ninkovic J, Götz M, Stricker SH. Targeted removal of epigenetic barriers during transcriptional reprogramming. Nat Commun 2019; 10:2119. [PMID: 31073172 PMCID: PMC6509258 DOI: 10.1038/s41467-019-10146-8] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2018] [Accepted: 04/23/2019] [Indexed: 02/07/2023] Open
Abstract
Master transcription factors have the ability to direct and reverse cellular identities, and consequently their genes must be subject to particular transcriptional control. However, it is unclear which molecular processes are responsible for impeding their activation and safeguarding cellular identities. Here we show that the targeting of dCas9-VP64 to the promoter of the master transcription factor Sox1 results in strong transcript and protein up-regulation in neural progenitor cells (NPCs). This gene activation restores lost neuronal differentiation potential, which substantiates the role of Sox1 as a master transcription factor. However, despite efficient transactivator binding, major proportions of progenitor cells are unresponsive to the transactivating stimulus. By combining the transactivation domain with epigenome editing we find that among a series of euchromatic processes, the removal of DNA methylation (by dCas9-Tet1) has the highest potential to increase the proportion of cells activating foreign master transcription factors and thus breaking down cell identity barriers.
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Affiliation(s)
- Valentin Baumann
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universitaet, BioMedical Center, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University, 82152, Planegg-Martinsried, Germany
| | - Maximilian Wiesbeck
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universitaet, BioMedical Center, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
| | - Christopher T Breunig
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universitaet, BioMedical Center, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
| | - Julia M Braun
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universitaet, BioMedical Center, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
| | - Anna Köferle
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universitaet, BioMedical Center, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
| | - Jovica Ninkovic
- Neurogenesis and Regeneration, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
- BioMedizinisches Centrum, Ludwig-Maximilian-Universität, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
| | - Magdalena Götz
- BioMedizinisches Centrum, Ludwig-Maximilian-Universität, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany
- Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany
| | - Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universitaet, BioMedical Center, Grosshaderner Strasse 9, 82152, Planegg-Martinsried, Germany.
- BioMedizinisches Centrum, Ludwig-Maximilian-Universität, Großhaderner Str. 9, 82152, Planegg-Martinsried, Germany.
- Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Grosshaderner Strasse 9, Planegg-Martinsried, 82152, Germany.
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7
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Anton T, Karg E, Bultmann S. Applications of the CRISPR/Cas system beyond gene editing. Biol Methods Protoc 2018; 3:bpy002. [PMID: 32161796 PMCID: PMC6994046 DOI: 10.1093/biomethods/bpy002] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2017] [Revised: 02/28/2018] [Accepted: 04/03/2018] [Indexed: 12/26/2022] Open
Abstract
Since the discovery of the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas) as a tool for gene editing a plethora of locus-specific as well as genome-wide approaches have been developed that allow efficient and reproducible manipulation of genomic sequences. However, the seemingly unbound potential of CRISPR/Cas does not stop with its utilization as a site-directed nuclease. Mutations in its catalytic centers render Cas9 (dCas9) a universal recruitment platform that can be utilized to control transcription, visualize DNA sequences, investigate in situ proteome compositions and manipulate epigenetic modifications at user-defined genomic loci. In this review, we give a comprehensive introduction and overview of the development, improvement and application of recent dCas9-based approaches.
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Affiliation(s)
- Tobias Anton
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152 Martinsried, Germany
| | - Elisabeth Karg
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152 Martinsried, Germany
| | - Sebastian Bultmann
- Department of Biology II and Center for Integrated Protein Science Munich (CIPSM), LMU Munich, 82152 Martinsried, Germany
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Breunig CT, Durovic T, Neuner AM, Baumann V, Wiesbeck MF, Köferle A, Götz M, Ninkovic J, Stricker SH. One step generation of customizable gRNA vectors for multiplex CRISPR approaches through string assembly gRNA cloning (STAgR). PLoS One 2018; 13:e0196015. [PMID: 29702666 PMCID: PMC5922533 DOI: 10.1371/journal.pone.0196015] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2018] [Accepted: 04/04/2018] [Indexed: 11/25/2022] Open
Abstract
Novel applications based on the bacterial CRISPR system make genetic, genomic, transcriptional and epigenomic engineering widely accessible for the first time. A significant advantage of CRISPR over previous methods is its tremendous adaptability due to its bipartite nature. Cas9 or its engineered variants define the molecular effect, while short gRNAs determine the targeting sites. A majority of CRISPR approaches depend on the simultaneous delivery of multiple gRNAs into single cells, either as an essential precondition, to increase responsive cell populations or to enhance phenotypic outcomes. Despite these requirements, methods allowing the efficient generation and delivery of multiple gRNA expression units into single cells are still sparse. Here we present STAgR (String assembly gRNA cloning), a single step gRNA multiplexing system, that obtains its advantages by employing the N20 targeting sequences as necessary homologies for Gibson assembly. We show that STAgR allows reliable and cost-effective generation of vectors with high numbers of gRNAs enabling multiplexed CRISPR approaches. Moreover, STAgR is easily customizable, as vector backbones as well as gRNA structures, numbers and promoters can be freely chosen and combined. Finally, we demonstrate STAgR's widespread functionality, its efficiency in multi-targeting approaches, using it for both, genome and transcriptome editing, as well as applying it in vitro and in vivo.
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Affiliation(s)
- Christopher T. Breunig
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, BioMedical Center, Planegg-Martinsried, Germany
- Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Planegg-Martinsried, Germany
| | - Tamara Durovic
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University, Munich, Germany
- Neurogenesis and Regeneration, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Neuherberg, Germany
| | - Andrea M. Neuner
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, BioMedical Center, Planegg-Martinsried, Germany
| | - Valentin Baumann
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, BioMedical Center, Planegg-Martinsried, Germany
- Graduate School of Systemic Neurosciences, Ludwig-Maximilians-University, Munich, Germany
| | - Maximilian F. Wiesbeck
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, BioMedical Center, Planegg-Martinsried, Germany
| | - Anna Köferle
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, BioMedical Center, Planegg-Martinsried, Germany
| | - Magdalena Götz
- Neural stem cells, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Neuherberg, Germany
- Physiological Genomics, BioMedical Center, Ludwig-Maximilian-Universität, Planegg-Martinsried, Germany
| | - Jovica Ninkovic
- Neurogenesis and Regeneration, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Neuherberg, Germany
- Physiological Genomics, BioMedical Center, Ludwig-Maximilian-Universität, Planegg-Martinsried, Germany
| | - Stefan H. Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, BioMedical Center, Planegg-Martinsried, Germany
- Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health, Planegg-Martinsried, Germany
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Loucari CC, Patsali P, van Dijk TB, Stephanou C, Papasavva P, Zanti M, Kurita R, Nakamura Y, Christou S, Sitarou M, Philipsen S, Lederer CW, Kleanthous M. Rapid and Sensitive Assessment of Globin Chains for Gene and Cell Therapy of Hemoglobinopathies. Hum Gene Ther Methods 2018; 29:60-74. [PMID: 29325430 PMCID: PMC5806072 DOI: 10.1089/hgtb.2017.190] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2017] [Accepted: 01/09/2018] [Indexed: 02/06/2023] Open
Abstract
The β-hemoglobinopathies sickle cell anemia and β-thalassemia are the focus of many gene-therapy studies. A key disease parameter is the abundance of globin chains because it indicates the level of anemia, likely toxicity of excess or aberrant globins, and therapeutic potential of induced or exogenous β-like globins. Reversed-phase high-performance liquid chromatography (HPLC) allows versatile and inexpensive globin quantification, but commonly applied protocols suffer from long run times, high sample requirements, or inability to separate murine from human β-globin chains. The latter point is problematic for in vivo studies with gene-addition vectors in murine disease models and mouse/human chimeras. This study demonstrates HPLC-based measurements of globin expression (1) after differentiation of the commonly applied human umbilical cord blood-derived erythroid progenitor-2 cell line, (2) in erythroid progeny of CD34+ cells for the analysis of clustered regularly interspaced short palindromic repeats/Cas9-mediated disruption of the globin regulator BCL11A, and (3) of transgenic mice holding the human β-globin locus. At run times of 8 min for separation of murine and human β-globin chains as well as of human γ-globin chains, and with routine measurement of globin-chain ratios for 12 nL of blood (tested for down to 0.75 nL) or of 300,000 in vitro differentiated cells, the methods presented here and any variant-specific adaptations thereof will greatly facilitate evaluation of novel therapy applications for β-hemoglobinopathies.
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Affiliation(s)
- Constantinos C. Loucari
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Petros Patsali
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Thamar B. van Dijk
- Erasmus University Medical Center, Department of Cell Biology, Rotterdam, The Netherlands
| | - Coralea Stephanou
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Panayiota Papasavva
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Maria Zanti
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Ryo Kurita
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | | | | | - Sjaak Philipsen
- Erasmus University Medical Center, Department of Cell Biology, Rotterdam, The Netherlands
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassaemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
- Cyprus School of Molecular Medicine, Nicosia, Cyprus
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Andersen GB, Tost J. A Summary of the Biological Processes, Disease-Associated Changes, and Clinical Applications of DNA Methylation. Methods Mol Biol 2018; 1708:3-30. [PMID: 29224136 DOI: 10.1007/978-1-4939-7481-8_1] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
DNA methylation at cytosines followed by guanines, CpGs, forms one of the multiple layers of epigenetic mechanisms controlling and modulating gene expression through chromatin structure. It closely interacts with histone modifications and chromatin remodeling complexes to form the local genomic and higher-order chromatin landscape. DNA methylation is essential for proper mammalian development, crucial for imprinting and plays a role in maintaining genomic stability. DNA methylation patterns are susceptible to change in response to environmental stimuli such as diet or toxins, whereby the epigenome seems to be most vulnerable during early life. Changes of DNA methylation levels and patterns have been widely studied in several diseases, especially cancer, where interest has focused on biomarkers for early detection of cancer development, accurate diagnosis, and response to treatment, but have also been shown to occur in many other complex diseases. Recent advances in epigenome engineering technologies allow now for the large-scale assessment of the functional relevance of DNA methylation. As a stable nucleic acid-based modification that is technically easy to handle and which can be analyzed with great reproducibility and accuracy by different laboratories, DNA methylation is a promising biomarker for many applications.
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Affiliation(s)
- Gitte Brinch Andersen
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France
| | - Jörg Tost
- Laboratory for Epigenetics & Environment, Centre National de Recherche en Génomique Humaine, CEA-Institut de Biologie Francois Jacob, Bâtiment G2, 2 rue Gaston Crémieux, 91000, Evry, France.
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Abstract
The popularity of the CRISPR/Cas9 system for both genome and epigenome engineering stems from its simplicity and adaptability. An effector (the Cas9 nuclease or a nuclease-dead dCas9 fusion protein) is targeted to a specific site in the genome by a small synthetic RNA known as the guide RNA, or gRNA. The bipartite nature of the CRISPR system enables its use in screening approaches since plasmid libraries containing expression cassettes of thousands of individual gRNAs can be used to interrogate many different sites in a single experiment. To date, gRNA sequences for the construction of libraries have been almost exclusively generated by oligonucleotide synthesis, which limits the achievable complexity of sequences in the library and is relatively cost-intensive. Here, a detailed protocol for CORALINA (comprehensive gRNA library generation through controlled nuclease activity), a simple and cost-effective method for the generation of highly complex gRNA libraries based on enzymatic digestion of input DNA, is described. Since CORALINA libraries can be generated from any source of DNA, plenty of options for customization exist, enabling a large variety of CRISPR-based screens.
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Affiliation(s)
- Anna Köferle
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, BioMedical Center
| | - Stefan H Stricker
- MCN Junior Research Group, Munich Center for Neurosciences, Ludwig-Maximilian-Universität, BioMedical Center; Epigenetic Engineering, Institute of Stem Cell Research, Helmholtz Zentrum, German Research Center for Environmental Health;
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Rodger EJ, Chatterjee A. The epigenomic basis of common diseases. Clin Epigenetics 2017; 9:5. [PMID: 28149333 PMCID: PMC5270348 DOI: 10.1186/s13148-017-0313-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 01/13/2017] [Indexed: 12/24/2022] Open
Abstract
A report of the 6th Epigenomics of Common Diseases Conference held at the Wellcome Genome Campus in Hinxton, Cambridge, UK, on 1-4 November 2016.
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Affiliation(s)
- Euan J. Rodger
- Department of Pathology, Dunedin School of Medicine, University of Otago, Hanover Street, P.O. Box 56, Dunedin, 9054 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
| | - Aniruddha Chatterjee
- Department of Pathology, Dunedin School of Medicine, University of Otago, Hanover Street, P.O. Box 56, Dunedin, 9054 New Zealand
- Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand
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