1
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Schmidt MJ, Gupta A, Bednarski C, Gehrig-Giannini S, Richter F, Pitzler C, Gamalinda M, Galonska C, Takeuchi R, Wang K, Reiss C, Dehne K, Lukason MJ, Noma A, Park-Windhol C, Allocca M, Kantardzhieva A, Sane S, Kosakowska K, Cafferty B, Tebbe J, Spencer SJ, Munzer S, Cheng CJ, Scaria A, Scharenberg AM, Cohnen A, Coco WM. Addendum to: Improved CRISPR genome editing using small highly active and specific engineered RNA-guided nucleases. Nat Commun 2023; 14:3503. [PMID: 37311765 DOI: 10.1038/s41467-023-39141-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023] Open
Affiliation(s)
| | | | | | | | | | | | | | | | | | - Kui Wang
- Casebia Therapeutics LLC, Cambridge, MA, USA
| | | | | | | | - Akiko Noma
- Casebia Therapeutics LLC, Cambridge, MA, USA
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2
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Alexander LM, Aliaga Goltsman DS, Liu J, Lin JL, Temoche-Diaz MM, Laperriere SM, Neerincx A, Bednarski C, Knyphausen P, Cohnen A, Albers J, Gonzalez-Osorio L, Fregoso Ocampo R, Oki J, Devoto AE, Castelle CJ, Lamothe RC, Cost GJ, Butterfield CN, Thomas BC, Brown CT. Novel and Engineered Type II CRISPR Systems from Uncultivated Microbes with Broad Genome Editing Capability. CRISPR J 2023; 6:261-277. [PMID: 37272861 DOI: 10.1089/crispr.2022.0090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023] Open
Abstract
Type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-Cas9 nucleases have been extensively used in biotechnology and therapeutics. However, many applications are not possible owing to the size, targetability, and potential off-target effects associated with currently known systems. In this study, we identified thousands of CRISPR type II effectors by mining an extensive, genome-resolved metagenomics database encompassing hundreds of thousands of microbial genomes. We developed a high-throughput pipeline that enabled us to predict tracrRNA sequences, to design single guide RNAs, and to demonstrate nuclease activity in vitro for 41 newly described subgroups. Active systems represent an extensive diversity of protein sequences and guide RNA structures and require diverse protospacer adjacent motifs (PAMs) that collectively expand the known targeting capability of current systems. Several nucleases showed activity levels comparable to or significantly higher than SpCas9, despite being smaller in size. In addition, top systems exhibited low levels of off-target editing in mammalian cells, and PAM-interacting domain engineered chimeras further expanded their targetability. These newly discovered nucleases are attractive enzymes for translation into many applications, including therapeutics.
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Affiliation(s)
| | | | - Jason Liu
- Metagenomi, Inc., Discovery, Emeryville, California, USA
| | - Jyun-Liang Lin
- Metagenomi, Inc., Discovery, Emeryville, California, USA
| | | | | | - Andreas Neerincx
- Bayer AG, Research & Development, Pharmaceuticals, Leverkusen, Germany
| | | | | | - Andre Cohnen
- Bayer AG, Research & Development, Pharmaceuticals, Leverkusen, Germany
| | - Justine Albers
- Metagenomi, Inc., Discovery, Emeryville, California, USA
| | | | | | - Jennifer Oki
- Metagenomi, Inc., Discovery, Emeryville, California, USA
| | - Audra E Devoto
- Metagenomi, Inc., Discovery, Emeryville, California, USA
| | | | | | - Gregory J Cost
- Metagenomi Inc., Pre-clinical, Emeryville, California, USA
| | | | - Brian C Thomas
- Metagenomi, Inc., Discovery, Emeryville, California, USA
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3
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Schmidt MJ, Gupta A, Bednarski C, Gehrig-Giannini S, Richter F, Pitzler C, Gamalinda M, Galonska C, Takeuchi R, Wang K, Reiss C, Dehne K, Lukason MJ, Noma A, Park-Windhol C, Allocca M, Kantardzhieva A, Sane S, Kosakowska K, Cafferty B, Tebbe J, Spencer SJ, Munzer S, Cheng CJ, Scaria A, Scharenberg AM, Cohnen A, Coco WM. Improved CRISPR genome editing using small highly active and specific engineered RNA-guided nucleases. Nat Commun 2021; 12:4219. [PMID: 34244505 PMCID: PMC8271026 DOI: 10.1038/s41467-021-24454-5] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2021] [Accepted: 06/14/2021] [Indexed: 12/14/2022] Open
Abstract
Streptococcus pyogenes (Spy) Cas9 has potential as a component of gene therapeutics for incurable diseases. One of its limitations is its large size, which impedes its formulation and delivery in therapeutic applications. Smaller Cas9s are an alternative, but lack robust activity or specificity and frequently recognize longer PAMs. Here, we investigated four uncharacterized, smaller Cas9s and found three employing a "GG" dinucleotide PAM similar to SpyCas9. Protein engineering generated synthetic RNA-guided nucleases (sRGNs) with editing efficiencies and specificities exceeding even SpyCas9 in vitro and in human cell lines on disease-relevant targets. sRGN mRNA lipid nanoparticles displayed manufacturing advantages and high in vivo editing efficiency in the mouse liver. Finally, sRGNs, but not SpyCas9, could be packaged into all-in-one AAV particles with a gRNA and effected robust in vivo editing of non-human primate (NHP) retina photoreceptors. Human gene therapy efforts are expected to benefit from these improved alternatives to existing CRISPR nucleases.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | - Kui Wang
- Casebia Therapeutics LLC, Cambridge, MA, USA
| | | | | | | | - Akiko Noma
- Casebia Therapeutics LLC, Cambridge, MA, USA
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4
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Craig-Mueller N, Hammad R, Elling R, Alzubi J, Timm B, Kolter J, Knelangen N, Bednarski C, Gläser B, Ammann S, Ivics Z, Fischer J, Speckmann C, Schwarz K, Lachmann N, Ehl S, Moritz T, Henneke P, Cathomen T. Modeling MyD88 Deficiency In Vitro Provides New Insights in Its Function. Front Immunol 2021; 11:608802. [PMID: 33424861 PMCID: PMC7786022 DOI: 10.3389/fimmu.2020.608802] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2020] [Accepted: 11/18/2020] [Indexed: 11/24/2022] Open
Abstract
Inherited defects in MyD88 and IRAK4, two regulators in Toll-like receptor (TLR) signaling, are clinically highly relevant, but still incompletely understood. MyD88- and IRAK4-deficient patients are exceedingly susceptible to a narrow spectrum of pathogens, with ∼50% lethality in the first years of life. To better understand the underlying molecular and cellular characteristics that determine disease progression, we aimed at modeling the cellular response to pathogens in vitro. To this end, we determined the immunophenotype of monocytes and macrophages derived from MyD88- and IRAK4-deficient patients. We recognized that macrophages derived from both patients were particularly poorly activated by streptococci, indicating that both signaling intermediates are essential for the immune response to facultative pathogens. To characterize this defect in more detail, we generated induced pluripotent stem cells (iPSCs) of fibroblasts derived from an MyD88-deficient patient. The underlying genetic defect was corrected using Sleeping Beauty transposon vectors encoding either the long (L) or the short (S) MYD88 isoform, respectively. Macrophages derived from these iPSC lines (iMacs) expressed typical macrophage markers, stably produced either MyD88 isoform, and showed robust phagocytic activity. Notably, iMacs expressing MyD88-L, but not MyD88-S, exhibited similar responses to external stimuli, including cytokine release patterns, as compared to genetically normal iMacs. Thus, the two MyD88 isoforms assume distinct functions in signaling. In conclusion, iPSC technology, in combination with efficient myeloid differentiation protocols, provides a valuable and inexhaustible source of macrophages, which can be used for disease modeling. Moreover, iPSC-derived macrophages may eventually aid in stabilizing MyD88-deficient patients during pyogenic infections.
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Affiliation(s)
- Nils Craig-Mueller
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,MD Program, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Ruba Hammad
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,PhD Program, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Roland Elling
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Freiburg, Germany
| | - Jamal Alzubi
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany
| | - Barbara Timm
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany
| | - Julia Kolter
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany
| | - Nele Knelangen
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany
| | - Christien Bednarski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany
| | - Birgitta Gläser
- Institute of Human Genetics, Medical Center-University of Freiburg, Freiburg, Germany
| | - Sandra Ammann
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul-Ehrlich Institute, Langen, Germany
| | - Judith Fischer
- Institute of Human Genetics, Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Carsten Speckmann
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,Center for Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Klaus Schwarz
- Institute for Clinical Transfusion Medicine and Immunogenetics Ulm, German Red Cross Blood Service Baden-Württemberg-Hessen, and Institute for Transfusion Medicine, University of Ulm, Ulm, Germany
| | - Nico Lachmann
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster for Regenerative and Translational Medicine, Hannover, Germany
| | - Stephan Ehl
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Thomas Moritz
- Institute of Experimental Hematology, Hannover Medical School, Hannover, Germany.,REBIRTH Cluster for Regenerative and Translational Medicine, Hannover, Germany
| | - Philipp Henneke
- Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,Institute for Immunodeficiency, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Pediatrics and Adolescent Medicine, Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center-University of Freiburg, Freiburg, Germany.,Center for Chronic Immunodeficiency (CCI), Medical Center-University of Freiburg, Freiburg, Germany.,Faculty of Medicine, University of Freiburg, Freiburg, Germany
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5
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Junge N, Yuan Q, Vu TH, Krooss S, Bednarski C, Balakrishnan A, Cathomen T, Manns MP, Baumann U, Sharma AD, Ott M. Homologous recombination mediates stable Fah gene integration and phenotypic correction in tyrosinaemia mouse-model. World J Hepatol 2018; 10:277-286. [PMID: 29527263 PMCID: PMC5838446 DOI: 10.4254/wjh.v10.i2.277] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/07/2017] [Revised: 02/01/2018] [Accepted: 03/01/2018] [Indexed: 02/06/2023] Open
Abstract
AIM To stably correct tyrosinaemia in proliferating livers of fumarylacetoacetate-hydrolase knockout (Fah-/-) mice by homologous-recombination-mediated targeted addition of the Fah gene.
METHODS C57BL/6 Fah∆exon5 mice served as an animal model for human tyrosinaemia type 1 in our study. The vector was created by amplifying human Fah cDNA including the TTR promoter from a lentivirus plasmid as described. The Fah expression cassette was flanked by homologous arms (620 bp and 749 bp long) of the Rosa26 gene locus. Mice were injected with 2.1 × 108 VP of this vector (rAAV8-ROSA26.HAL-TTR.Fah-ROSA26.HAR) via the tail vein. Mice in the control group were injected with 2.1 × 108 VP of a similar vector but missing the homologous arms (rAAV8-TTR.Fah). Primary hepatocytes from Fah-/- recipient mice, treated with our vectors, were isolated and 1 × 106 hepatocytes were transplanted into secondary Fah-/- recipient mice by injection into the spleen. Upon either vector application or hepatocyte transplantation NTBC treatment was stopped in recipient mice.
RESULTS Here, we report successful HR-mediated genome editing by integration of a Fah gene expression cassette into the “safe harbour locus” Rosa26 by recombinant AAV8. Both groups of mice showed long-term survival, weight gain and FAH positive clusters as determined by immunohistochemistry analysis of liver sections in the absence of NTBC treatment. In the group of C57BL/6 Fah∆exon5 mice, which have been transplanted with hepatocytes from a mouse injected with rAAV8-ROSA26.HAL-TTR.Fah-ROSA26.HAR 156 d before, 6 out of 6 mice showed long-term survival, weight gain and FAH positive clusters without need for NTBC treatment. In contrast only 1 out 5 mice, who received hepatocytes from rAAV8-TTR.Fah treated mice, survived and showed few and smaller FAH positive clusters. These results demonstrate that homologous recombination-mediated Fah gene transfer corrects the phenotype in a mouse model of human tyrosinaemia type 1 (Fah-/- mice) and is long lasting in a proliferating state of the liver as shown by withdrawal of NTBC treatment and serial transplantation of isolated hepatocytes from primary Fah-/- recipient mice into secondary Fah-/- recipient mice. This long term therapeutic efficacy is clearly superior to our control mice treated with episomal rAAV8 gene therapy approach.
CONCLUSION HR-mediated rAAV8 gene therapy provides targeted transgene integration and phenotypic correction in Fah-/- mice with superior long-term efficacy compared to episomal rAAV8 therapy in proliferating livers.
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Affiliation(s)
- Norman Junge
- Department of Pediatric Gastroenterology and Hepatology, Hannover Medical School, Hannover 30625, Germany
| | - Qinggong Yuan
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover 30625, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover 30625, Germany
| | - Thu Huong Vu
- Department of Pediatric Gastroenterology and Hepatology, Hannover Medical School, Hannover 30625, Germany
| | - Simon Krooss
- TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover 30625, Germany
| | - Christien Bednarski
- Medical Center, University of Freiburg, Institute for Cell and Gene Therapy, Freiburg 79108, Germany
| | - Asha Balakrishnan
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover 30625, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover 30625, Germany
| | - Toni Cathomen
- Medical Center, University of Freiburg, Institute for Cell and Gene Therapy, Freiburg 79108, Germany
| | - Michael P Manns
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover 30625, Germany
| | - Ulrich Baumann
- Department of Pediatric Gastroenterology and Hepatology, Hannover Medical School, Hannover 30625, Germany
| | - Amar Deep Sharma
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover 30625, Germany
- Research Group MicroRNA in Liver Regeneration, Cluster of Excellence REBIRTH, Hannover Medical School, Hannover 30625, Germany
| | - Michael Ott
- Department of Gastroenterology, Hepatology and Endocrinology, Hannover Medical School, Hannover 30625, Germany
- TWINCORE, Centre for Experimental and Clinical Infection Research, Hannover 30625, Germany
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6
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Merkert S, Bednarski C, Göhring G, Cathomen T, Martin U. Generation of a gene-corrected isogenic control iPSC line from cystic fibrosis patient-specific iPSCs homozygous for p.Phe508del mutation mediated by TALENs and ssODN. Stem Cell Res 2017; 23:95-97. [PMID: 28925369 DOI: 10.1016/j.scr.2017.07.010] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Revised: 06/13/2017] [Accepted: 07/07/2017] [Indexed: 01/12/2023] Open
Abstract
Cystic fibrosis (CF) is a monogenetic disease caused by mutations in the cystic fibrosis transmembrane conductance regulator (CFTR) gene, which affects multiple organs. Human induced pluripotent stem cells (iPSCs) derived from CF patients and the generation of isogeneic gene-corrected control cell lines enable disease modelling, drug discovery or toxicological studies and therefore the development of CF patient-specific therapies. We have previously generated a hiPSC line from a CF patient homozygous for the p.Phe508del mutation. Here we used TALENs and single-stranded oligonucleotides to correct the mutated triplet in our CF-iPSC line.
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Affiliation(s)
- Sylvia Merkert
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany; REBIRTH-Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Germany
| | - Christien Bednarski
- Institute for Cell and Gene Therapy and Center for Chronic Immunodeficiency, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Gudrun Göhring
- Department of Human Genetics, Hannover Medical School, 30625 Hannover, Germany
| | - Toni Cathomen
- Institute for Cell and Gene Therapy and Center for Chronic Immunodeficiency, University Medical Center Freiburg, 79106 Freiburg, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiothoracic, Transplantation and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany; REBIRTH-Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany; Biomedical Research in Endstage and Obstructive Lung Disease (BREATH), Member of the German Center for Lung Research (DZL), Germany.
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7
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Bednarski C, Tomczak K, vom Hövel B, Weber WM, Cathomen T. Targeted Integration of a Super-Exon into the CFTR Locus Leads to Functional Correction of a Cystic Fibrosis Cell Line Model. PLoS One 2016; 11:e0161072. [PMID: 27526025 PMCID: PMC4985144 DOI: 10.1371/journal.pone.0161072] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 07/29/2016] [Indexed: 01/04/2023] Open
Abstract
In vitro disease models have enabled insights into the pathophysiology of human disease as well as the functional evaluation of new therapies, such as novel genome engineering strategies. In the context of cystic fibrosis (CF), various cellular disease models have been established in recent years, including organoids based on induced pluripotent stem cell technology that allowed for functional readouts of CFTR activity. Yet, many of these in vitro CF models require complex and expensive culturing protocols that are difficult to implement and may not be amenable for high throughput screens. Here, we show that a simple cellular CF disease model based on the bronchial epithelial ΔF508 cell line CFBE41o- can be used to validate functional CFTR correction. We used an engineered nuclease to target the integration of a super-exon, encompassing the sequences of CFTR exons 11 to 27, into exon 11 and re-activated endogenous CFTR expression by treating CFBE41o- cells with a demethylating agent. We demonstrate that the integration of this super-exon resulted in expression of a corrected mRNA from the endogenous CFTR promoter and used short-circuit current measurements in Ussing chambers to corroborate restored ion transport of the repaired CFTR channels. In conclusion, this study proves that the targeted integration of a large super-exon in CFTR exon 11 leads to functional correction of CFTR, suggesting that this strategy can be used to functionally correct all CFTR mutations located downstream of the 5' end of exon 11.
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Affiliation(s)
- Christien Bednarski
- Institute for Cell and Gene Therapy, Medical Center–University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center–University of Freiburg, Freiburg, Germany
| | - Katja Tomczak
- Institute of Animal Physiology, Westphalian Wilhelms-University, Muenster, Germany
| | - Beate vom Hövel
- Institute for Cell and Gene Therapy, Medical Center–University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center–University of Freiburg, Freiburg, Germany
| | - Wolf-Michael Weber
- Institute of Animal Physiology, Westphalian Wilhelms-University, Muenster, Germany
| | - Toni Cathomen
- Institute for Cell and Gene Therapy, Medical Center–University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency, Medical Center–University of Freiburg, Freiburg, Germany
- Faculty of Medicine, University of Freiburg, Freiburg, Germany
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8
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Merkert S, Wunderlich S, Bednarski C, Haase A, Dreyer AK, Schwanke K, Cathomen T, Martin U. Generation of CF-patient derived iPS cells and efficient footprintless designer nuclease-based gene targeting. Pneumologie 2014. [DOI: 10.1055/s-0034-1376851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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9
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Haller R, Ulrich S, Weinreich S, Merkert S, Bednarski C, Mauritz C, Martin U. Modeling Cystic Fibrosis in vitro: A new possible platform for patient customised drug screening and ex-vivo gene therapy? Pneumologie 2014. [DOI: 10.1055/s-0034-1376824] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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10
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Merkert S, Wunderlich S, Bednarski C, Beier J, Haase A, Dreyer AK, Schwanke K, Meyer J, Göhring G, Cathomen T, Martin U. Efficient designer nuclease-based homologous recombination enables direct PCR screening for footprintless targeted human pluripotent stem cells. Stem Cell Reports 2014; 2:107-18. [PMID: 24678453 PMCID: PMC3966116 DOI: 10.1016/j.stemcr.2013.12.003] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2013] [Revised: 12/03/2013] [Accepted: 12/04/2013] [Indexed: 12/13/2022] Open
Abstract
Genetic engineering of human induced pluripotent stem cells (hiPSCs) via customized designer nucleases has been shown to be significantly more efficient than conventional gene targeting, but still typically depends on the introduction of additional genetic selection elements. In our study, we demonstrate the efficient nonviral and selection-independent gene targeting in human pluripotent stem cells (hPSCs). Our high efficiencies of up to 1.6% of gene-targeted hiPSCs, accompanied by a low background of randomly inserted transgenes, eliminated the need for antibiotic or fluorescence-activated cell sorting selection, and allowed the use of short donor oligonucleotides for footprintless gene editing. Gene-targeted hiPSC clones were established simply by direct PCR screening. This optimized approach allows targeted transgene integration into safe harbor sites for more predictable and robust expression and enables the straightforward generation of disease-corrected, patient-derived iPSC lines for research purposes and, ultimately, for future clinical applications. Footprintless gene editing in hiPSCs using ssODNs without any preselection Targeted clone isolation simply via PCR screening Targeted reporter integration into safe harbor locus AAVS1 with up to 1.6% efficiency hiPSC reporter assay for gene editing via customized designer nucleases
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Affiliation(s)
- Sylvia Merkert
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplant and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany ; REBIRTH-Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
| | - Stephanie Wunderlich
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplant and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany ; REBIRTH-Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
| | - Christien Bednarski
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, 79106 Freiburg, Germany ; Center for Chronic Immunodeficiency, University Medical Center Freiburg, 79106 Freiburg, Germany ; Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Jennifer Beier
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplant and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany ; REBIRTH-Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
| | - Alexandra Haase
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplant and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany ; REBIRTH-Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
| | - Anne-Kathrin Dreyer
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Kristin Schwanke
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplant and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany ; REBIRTH-Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
| | - Johann Meyer
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Gudrun Göhring
- Institute of Cell and Molecular Pathology, Hannover Medical School, 30625 Hannover, Germany
| | - Toni Cathomen
- Institute for Cell and Gene Therapy, University Medical Center Freiburg, 79106 Freiburg, Germany ; Center for Chronic Immunodeficiency, University Medical Center Freiburg, 79106 Freiburg, Germany ; Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
| | - Ulrich Martin
- Leibniz Research Laboratories for Biotechnology and Artificial Organs (LEBAO), Department of Cardiac, Thoracic, Transplant and Vascular Surgery, Hannover Medical School, 30625 Hannover, Germany ; REBIRTH-Cluster of Excellence, Hannover Medical School, 30625 Hannover, Germany
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Händel EM, Gellhaus K, Khan K, Bednarski C, Cornu TI, Müller-Lerch F, Kotin RM, Heilbronn R, Cathomen T. Versatile and efficient genome editing in human cells by combining zinc-finger nucleases with adeno-associated viral vectors. Hum Gene Ther 2012; 23:321-9. [PMID: 21980922 PMCID: PMC3300077 DOI: 10.1089/hum.2011.140] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2011] [Accepted: 10/05/2011] [Indexed: 11/13/2022] Open
Abstract
Zinc-finger nucleases (ZFNs) have become a valuable tool for targeted genome engineering. Based on the enzyme's ability to create a site-specific DNA double-strand break, ZFNs promote genome editing by activating the cellular DNA damage response, including homology-directed repair (HDR) and nonhomologous end-joining. The goal of this study was (i) to demonstrate the versatility of combining the ZFN technology with a vector platform based on adeno-associated virus (AAV), and (ii) to assess the toxicity evoked by this platform. To this end, human cell lines that harbor enhanced green fluorescence protein (EGFP) reporters were generated to easily quantify the frequencies of gene deletion, gene disruption, and gene correction. We demonstrated that ZFN-encoding AAV expression vectors can be employed to induce large chromosomal deletions or to disrupt genes in up to 32% of transduced cells. In combination with AAV vectors that served as HDR donors, the AAV-ZFN platform was utilized to correct a mutation in EGFP in up to 6% of cells. Genome editing on the DNA level was confirmed by genotyping. Although cell cycle profiling revealed a modest G2/M arrest at high AAV-ZFN vector doses, platform-induced apoptosis could not be detected. In conclusion, the combined AAV-ZFN vector technology is a useful tool to edit the human genome with high efficiency. Because AAV vectors can transduce many cell types relevant for gene therapy, the ex vivo and in vivo delivery of ZFNs via AAV vectors will be of great interest for the treatment of inherited disorders.
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Affiliation(s)
- Eva-Maria Händel
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
- Institute of Virology, Campus Benjamin Franklin, Charité Medical School, 12203 Berlin, Germany
| | - Katharina Gellhaus
- Institute of Virology, Campus Benjamin Franklin, Charité Medical School, 12203 Berlin, Germany
| | - Kafaitullah Khan
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
- Institute of Virology, Campus Benjamin Franklin, Charité Medical School, 12203 Berlin, Germany
| | - Christien Bednarski
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
- Institute of Virology, Campus Benjamin Franklin, Charité Medical School, 12203 Berlin, Germany
| | - Tatjana I. Cornu
- Institute of Virology, Campus Benjamin Franklin, Charité Medical School, 12203 Berlin, Germany
| | - Felix Müller-Lerch
- Institute of Virology, Campus Benjamin Franklin, Charité Medical School, 12203 Berlin, Germany
| | - Robert M. Kotin
- Molecular Virology and Gene Delivery Section, Laboratory of Biochemical Genetics, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland 20892
| | - Regine Heilbronn
- Institute of Virology, Campus Benjamin Franklin, Charité Medical School, 12203 Berlin, Germany
| | - Toni Cathomen
- Institute of Experimental Hematology, Hannover Medical School, 30625 Hannover, Germany
- Institute of Virology, Campus Benjamin Franklin, Charité Medical School, 12203 Berlin, Germany
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Rosário M, Franke R, Bednarski C, Birchmeier W. The neurite outgrowth multiadaptor RhoGAP, NOMA-GAP, regulates neurite extension through SHP2 and Cdc42. ACTA ACUST UNITED AC 2007; 178:503-16. [PMID: 17664338 PMCID: PMC2064841 DOI: 10.1083/jcb.200609146] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Neuronal differentiation involves the formation and extension of neuronal processes. We have identified a novel regulator of neurite formation and extension, the neurite outgrowth multiadaptor, NOMA-GAP, which belongs to a new family of multiadaptor proteins with RhoGAP activity. We show that NOMA-GAP is essential for NGF-stimulated neuronal differentiation and for the regulation of the ERK5 MAP kinase and the Cdc42 signaling pathways downstream of NGF. NOMA-GAP binds directly to the NGF receptor, TrkA, and becomes tyrosine phosphorylated upon receptor activation, thus enabling recruitment and activation of the tyrosine phosphatase SHP2. Recruitment of SHP2 is required for the stimulation of neuronal process extension and for sustained activation of ERK5 downstream of NOMA-GAP. In addition, we show that NOMA-GAP promotes neurite outgrowth by tempering activation of the Cdc42/PAK signaling pathway in response to NGF. NOMA-GAP, through its dual function as a multiadaptor and RhoGAP protein, thus plays an essential role downstream of NGF in promoting neurite outgrowth and extension.
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Affiliation(s)
- Marta Rosário
- Max Delbrück Center for Molecular Medicine, Berlin, Germany.
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