1
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Marone R, Landmann E, Devaux A, Lepore R, Seyres D, Zuin J, Burgold T, Engdahl C, Capoferri G, Dell'Aglio A, Larrue C, Simonetta F, Rositzka J, Rhiel M, Andrieux G, Gallagher DN, Schröder MS, Wiederkehr A, Sinopoli A, Do Sacramento V, Haydn A, Garcia-Prat L, Divsalar C, Camus A, Xu L, Bordoli L, Schwede T, Porteus M, Tamburini J, Corn JE, Cathomen T, Cornu TI, Urlinger S, Jeker LT. Epitope-engineered human hematopoietic stem cells are shielded from CD123-targeted immunotherapy. J Exp Med 2023; 220:e20231235. [PMID: 37773046 PMCID: PMC10541312 DOI: 10.1084/jem.20231235] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [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: 07/17/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 09/30/2023] Open
Abstract
Targeted eradication of transformed or otherwise dysregulated cells using monoclonal antibodies (mAb), antibody-drug conjugates (ADC), T cell engagers (TCE), or chimeric antigen receptor (CAR) cells is very effective for hematologic diseases. Unlike the breakthrough progress achieved for B cell malignancies, there is a pressing need to find suitable antigens for myeloid malignancies. CD123, the interleukin-3 (IL-3) receptor alpha-chain, is highly expressed in various hematological malignancies, including acute myeloid leukemia (AML). However, shared CD123 expression on healthy hematopoietic stem and progenitor cells (HSPCs) bears the risk for myelotoxicity. We demonstrate that epitope-engineered HSPCs were shielded from CD123-targeted immunotherapy but remained functional, while CD123-deficient HSPCs displayed a competitive disadvantage. Transplantation of genome-edited HSPCs could enable tumor-selective targeted immunotherapy while rebuilding a fully functional hematopoietic system. We envision that this approach is broadly applicable to other targets and cells, could render hitherto undruggable targets accessible to immunotherapy, and will allow continued posttransplant therapy, for instance, to treat minimal residual disease (MRD).
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Affiliation(s)
- Romina Marone
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Basel, Switzerland
| | - Emmanuelle Landmann
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Basel, Switzerland
| | - Anna Devaux
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Basel, Switzerland
| | - Rosalba Lepore
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Basel, Switzerland
- Cimeio Therapeutics AG , Basel, Switzerland
- Ridgeline Discovery GmbH , Basel, Switzerland
| | - Denis Seyres
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Basel, Switzerland
| | - Jessica Zuin
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Basel, Switzerland
| | - Thomas Burgold
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Basel, Switzerland
| | - Corinne Engdahl
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Basel, Switzerland
| | - Giuseppina Capoferri
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Basel, Switzerland
| | - Alessandro Dell'Aglio
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Basel, Switzerland
| | - Clément Larrue
- Translational Research Centre in Onco-Hematology, Faculty of Medicine, University of Geneva, and Swiss Cancer Center Leman, Geneva, Switzerland
| | - Federico Simonetta
- Division of Hematology, Department of Oncology, Geneva University Hospitals, Geneva, Switzerland
- Department of Medicine, Translational Research Center for Onco-Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Julia Rositzka
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg , Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Manuel Rhiel
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg , Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Geoffroy Andrieux
- Institute of Medical Bioinformatics and Systems Medicine, Medical Center-University of Freiburg , Freiburg, Germany
| | - Danielle N Gallagher
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | - Markus S Schröder
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | | | | | | | - Anna Haydn
- Ridgeline Discovery GmbH , Basel, Switzerland
| | | | | | - Anna Camus
- Cimeio Therapeutics AG , Basel, Switzerland
| | - Liwen Xu
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Lorenza Bordoli
- Biozentrum, University of Basel , Basel, Switzerland
- SIB Swiss Institute of Bioinformatics , Basel, Switzerland
| | - Torsten Schwede
- Biozentrum, University of Basel , Basel, Switzerland
- SIB Swiss Institute of Bioinformatics , Basel, Switzerland
| | - Matthew Porteus
- Department of Pediatrics, School of Medicine, Stanford University, Stanford, CA, USA
| | - Jérôme Tamburini
- Department of Medicine, Translational Research Center for Onco-Hematology, Faculty of Medicine, University of Geneva, Geneva, Switzerland
| | - Jacob E Corn
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg , Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Tatjana I Cornu
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg , Freiburg, Germany
- Center for Chronic Immunodeficiency, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Stefanie Urlinger
- Cimeio Therapeutics AG , Basel, Switzerland
- Ridgeline Discovery GmbH , Basel, Switzerland
| | - Lukas T Jeker
- Department of Biomedicine, Basel University Hospital and University of Basel, Basel, Switzerland
- Transplantation Immunology and Nephrology, Basel University Hospital, Basel, Switzerland
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2
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Boontanrart MY, Mächler E, Ponta S, Nelis JC, Preiano VG, Corn JE. Engineering of the endogenous HBD promoter increases HbA2. eLife 2023; 12:e85258. [PMID: 37265399 PMCID: PMC10270685 DOI: 10.7554/elife.85258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2022] [Accepted: 05/27/2023] [Indexed: 06/03/2023] Open
Abstract
The β-hemoglobinopathies, such as sickle cell disease and β-thalassemia, are one of the most common genetic diseases worldwide and are caused by mutations affecting the structure or production of β-globin subunits in adult hemoglobin. Many gene editing efforts to treat the β-hemoglobinopathies attempt to correct β-globin mutations or increase γ-globin for fetal hemoglobin production. δ-globin, the subunit of adult hemoglobin A2, has high homology to β-globin and is already pan-cellularly expressed at low levels in adult red blood cells. However, upregulation of δ-globin is a relatively unexplored avenue to increase the amount of functional hemoglobin. Here, we use CRISPR-Cas9 to repair non-functional transcriptional elements in the endogenous promoter region of δ-globin to increase overall expression of adult hemoglobin 2 (HbA2). We find that insertion of a KLF1 site alone is insufficient to upregulate δ-globin. Instead, multiple transcription factor elements are necessary for robust upregulation of δ-globin from the endogenous locus. Promoter edited HUDEP-2 immortalized erythroid progenitor cells exhibit striking increases of HBD transcript, from less than 5% to over 20% of total β-like globins in clonal populations. Edited CD34 +hematopoietic stem and progenitors (HSPCs) differentiated to primary human erythroblasts express up to 46% HBD in clonal populations. These findings add mechanistic insight to globin gene regulation and offer a new therapeutic avenue to treat β-hemoglobinopathies.
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Affiliation(s)
| | - Elia Mächler
- Department of Biology, ETH ZurichZurichSwitzerland
| | - Simone Ponta
- Department of Biology, ETH ZurichZurichSwitzerland
| | - Jan C Nelis
- Department of Biology, ETH ZurichZurichSwitzerland
| | | | - Jacob E Corn
- Department of Biology, ETH ZurichZurichSwitzerland
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3
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Farnung J, Muhar M, Liang JR, Tolmachova KA, Benoit RM, Corn JE, Bode JW. Semisynthetic LC3 Probes for Autophagy Pathways Reveal a Noncanonical LC3 Interacting Region Motif Crucial for the Enzymatic Activity of Human ATG3. ACS Cent Sci 2023; 9:1025-1034. [PMID: 37252361 PMCID: PMC10214526 DOI: 10.1021/acscentsci.3c00009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Indexed: 05/31/2023]
Abstract
Macroautophagy is one of two major degradation systems in eukaryotic cells. Regulation and control of autophagy are often achieved through the presence of short peptide sequences called LC3 interacting regions (LIR) in autophagy-involved proteins. Using a combination of new protein-derived activity-based probes prepared from recombinant LC3 proteins, along with protein modeling and X-ray crystallography of the ATG3-LIR peptide complex, we identified a noncanonical LIR motif in the human E2 enzyme responsible for LC3 lipidation, ATG3. The LIR motif is present in the flexible region of ATG3 and adopts an uncommon β-sheet structure binding to the backside of LC3. We show that the β-sheet conformation is crucial for its interaction with LC3 and used this insight to design synthetic macrocyclic peptide-binders to ATG3. CRISPR-enabled in cellulo studies provide evidence that LIRATG3 is required for LC3 lipidation and ATG3∼LC3 thioester formation. Removal of LIRATG3 negatively impacts the rate of thioester transfer from ATG7 to ATG3.
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Affiliation(s)
- Jakob Farnung
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
| | - Matthias Muhar
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jin Rui Liang
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Kateryna A. Tolmachova
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
| | - Roger M. Benoit
- Laboratory
of Nanoscale Biology, Division of Biology and Chemistry, Paul Scherrer Institute, 5232 Villigen PSI, Switzerland
| | - Jacob E. Corn
- Institute
of Molecular Health Sciences, Department of Biology ETH Zürich, CH-8093 Zürich, Switzerland
| | - Jeffrey W. Bode
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences ETH Zürich, CH-8093 Zürich, Switzerland
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4
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Liang JR, Corn JE. A CRISPR view on autophagy. Trends Cell Biol 2022; 32:1008-1022. [PMID: 35581059 DOI: 10.1016/j.tcb.2022.04.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 04/05/2022] [Accepted: 04/06/2022] [Indexed: 01/21/2023]
Abstract
Autophagy is a fundamental pathway for the degradation of cytoplasmic content in response to pleiotropic extracellular and intracellular stimuli. Recent advances in the autophagy field have demonstrated that different organelles can also be specifically targeted for autophagy with broad implications on cellular and organismal health. This opens new dimensions in the autophagy field and more unanswered questions on the rationale and underlying mechanisms to degrade different organelles. Functional genomics via clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9-based screening has gained popularity in the autophagy field to understand the common and unique factors that are implicated in the signaling, recognition, and execution of different cargo-specific autophagies. We focus on recent applications of CRISPR-based screens in the autophagy field, their discoveries, and the future directions of autophagy screens.
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Affiliation(s)
- Jin Rui Liang
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zürich, Switzerland; Medical Research Council, Protein Phosphorylation & Ubiquitylation Unit, School of Life Sciences, University of Dundee, Dow Street, Dundee DD1 5EH, UK.
| | - Jacob E Corn
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zürich, Switzerland.
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5
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Siegner SM, Ugalde L, Clemens A, Garcia-Garcia L, Bueren JA, Rio P, Karasu ME, Corn JE. Adenine base editing efficiently restores the function of Fanconi anemia hematopoietic stem and progenitor cells. Nat Commun 2022; 13:6900. [PMID: 36371486 PMCID: PMC9653444 DOI: 10.1038/s41467-022-34479-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/08/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Fanconi Anemia (FA) is a debilitating genetic disorder with a wide range of severe symptoms including bone marrow failure and predisposition to cancer. CRISPR-Cas genome editing manipulates genotypes by harnessing DNA repair and has been proposed as a potential cure for FA. But FA is caused by deficiencies in DNA repair itself, preventing the use of editing strategies such as homology directed repair. Recently developed base editing (BE) systems do not rely on double stranded DNA breaks and might be used to target mutations in FA genes, but this remains to be tested. Here we develop a proof of concept therapeutic base editing strategy to address two of the most prevalent FANCA mutations in patient hematopoietic stem and progenitor cells. We find that optimizing adenine base editor construct, vector type, guide RNA format, and delivery conditions leads to very effective genetic modification in multiple FA patient backgrounds. Optimized base editing restored FANCA expression, molecular function of the FA pathway, and phenotypic resistance to crosslinking agents. ABE8e mediated editing in primary hematopoietic stem and progenitor cells from FA patients was both genotypically effective and restored FA pathway function, indicating the potential of base editing strategies for future clinical application in FA.
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Affiliation(s)
- Sebastian M. Siegner
- grid.5801.c0000 0001 2156 2780Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Laura Ugalde
- grid.5515.40000000119578126Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER) and Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Alexandra Clemens
- grid.5801.c0000 0001 2156 2780Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Laura Garcia-Garcia
- grid.5515.40000000119578126Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER) and Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Juan A. Bueren
- grid.5515.40000000119578126Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER) and Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Paula Rio
- grid.5515.40000000119578126Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER) and Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Mehmet E. Karasu
- grid.5801.c0000 0001 2156 2780Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Jacob E. Corn
- grid.5801.c0000 0001 2156 2780Department of Biology, ETH Zurich, Zurich, Switzerland
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6
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Möller L, Aird EJ, Schröder MS, Kobel L, Kissling L, van de Venn L, Corn JE. Recursive Editing improves homology-directed repair through retargeting of undesired outcomes. Nat Commun 2022; 13:4550. [PMID: 35931681 PMCID: PMC9356142 DOI: 10.1038/s41467-022-31944-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 07/11/2022] [Indexed: 12/30/2022] Open
Abstract
CRISPR-Cas induced homology-directed repair (HDR) enables the installation of a broad range of precise genomic modifications from an exogenous donor template. However, applications of HDR in human cells are often hampered by poor efficiency, stemming from a preference for error-prone end joining pathways that yield short insertions and deletions. Here, we describe Recursive Editing, an HDR improvement strategy that selectively retargets undesired indel outcomes to create additional opportunities to produce the desired HDR allele. We introduce a software tool, named REtarget, that enables the rational design of Recursive Editing experiments. Using REtarget-designed guide RNAs in single editing reactions, Recursive Editing can simultaneously boost HDR efficiencies and reduce undesired indels. We also harness REtarget to generate databases for particularly effective Recursive Editing sites across the genome, to endogenously tag proteins, and to target pathogenic mutations. Recursive Editing constitutes an easy-to-use approach without potentially deleterious cell manipulations and little added experimental burden.
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Affiliation(s)
- Lukas Möller
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Eric J Aird
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland.
| | - Markus S Schröder
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Lena Kobel
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Lucas Kissling
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Lilly van de Venn
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Jacob E Corn
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland.
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7
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Buehler M, Yi X, Ge W, Blattmann P, Rushing E, Reifenberger G, Felsberg J, Yeh C, Corn JE, Regli L, Zhang J, Cloos A, Ravi VM, Wiestler B, Heiland DH, Aebersold R, Weller M, Guo T, Weiss T. Quantitative proteomic landscapes of primary and recurrent glioblastoma reveal a protumorigeneic role for FBXO2-dependent glioma-microenvironment interactions. Neuro Oncol 2022; 25:290-302. [PMID: 35802605 PMCID: PMC9925714 DOI: 10.1093/neuonc/noac169] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Indexed: 11/14/2022] Open
Abstract
BACKGROUND Recent efforts have described the evolution of glioblastoma from initial diagnosis to post-treatment recurrence on a genomic and transcriptomic level. However, the evolution of the proteomic landscape is largely unknown. METHODS Sequential window acquisition of all theoretical fragment ion spectra mass spectrometry (SWATH-MS) was used to characterize the quantitative proteomes of two independent cohorts of paired newly diagnosed and recurrent glioblastomas. Recurrence-associated proteins were validated using immunohistochemistry and further studied in human glioma cell lines, orthotopic xenograft models, and human organotypic brain slice cultures. External spatial transcriptomic, single-cell, and bulk RNA sequencing data were analyzed to gain mechanistic insights. RESULTS Although overall proteomic changes were heterogeneous across patients, we identified BCAS1, INF2, and FBXO2 as consistently upregulated proteins at recurrence and validated these using immunohistochemistry. Knockout of FBXO2 in human glioma cells conferred a strong survival benefit in orthotopic xenograft mouse models and reduced invasive growth in organotypic brain slice cultures. In glioblastoma patient samples, FBXO2 expression was enriched in the tumor infiltration zone and FBXO2-positive cancer cells were associated with synaptic signaling processes. CONCLUSIONS These findings demonstrate a potential role of FBXO2-dependent glioma-microenvironment interactions to promote tumor growth. Furthermore, the published datasets provide a valuable resource for further studies.
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Affiliation(s)
| | | | - Weigang Ge
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China,Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China,Westlake Omics Biotechnology Co., Ltd., Hangzhou, Zhejiang, China
| | - Peter Blattmann
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Elisabeth Rushing
- Department of Neuropathology, University Hospital Zurich, University of Zurich, Zurich, Switzerland
| | - Guido Reifenberger
- Department of Neuropathology, Heinrich Heine University, Duesseldorf, Germany,German Cancer Consortium, partner site Essen/Düsseldorf, Duesseldorf, Germany
| | - Joerg Felsberg
- Department of Neuropathology, Heinrich Heine University, Duesseldorf, Germany,German Cancer Consortium, partner site Essen/Düsseldorf, Duesseldorf, Germany
| | - Charles Yeh
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | - Jacob E Corn
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, Zürich, Switzerland
| | - Luca Regli
- Department of Neurosurgery, Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zürich, Switzerland
| | - Junyi Zhang
- Microenvironment and Immunology Research Laboratory, Department of Neurosurgery, Medical Center, University of Freiburg, Germany,German Cancer Consortium (DKTK), partner site Freiburg, Freiburg, Germany,Translational Neuro-Oncology Research Group, Medical Center, University of Freiburg, Freiburg, Germany
| | - Ann Cloos
- Microenvironment and Immunology Research Laboratory, Department of Neurosurgery, Medical Center, University of Freiburg, Germany,German Cancer Consortium (DKTK), partner site Freiburg, Freiburg, Germany,Translational Neuro-Oncology Research Group, Medical Center, University of Freiburg, Freiburg, Germany
| | - Vidhya M Ravi
- Microenvironment and Immunology Research Laboratory, Department of Neurosurgery, Medical Center, University of Freiburg, Germany,German Cancer Consortium (DKTK), partner site Freiburg, Freiburg, Germany,Translational Neuro-Oncology Research Group, Medical Center, University of Freiburg, Freiburg, Germany,Freiburg Institute for Advanced Studies (FRIAS), University of Freiburg, Freiburg, Germany
| | - Benedikt Wiestler
- Department of Neuroradiology, Klinikum rechts der Isar, Technical University Munich, Munich, Germany
| | - Dieter Henrik Heiland
- Microenvironment and Immunology Research Laboratory, Department of Neurosurgery, Medical Center, University of Freiburg, Germany,German Cancer Consortium (DKTK), partner site Freiburg, Freiburg, Germany
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Michael Weller
- Department of Neurology and Clinical Neuroscience Center, University Hospital Zurich and University of Zurich, Zurich, Switzerland
| | - Tiannan Guo
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, Zhejiang, China,Westlake Intelligent Biomarker Discovery Lab, Westlake Laboratory of Life Sciences and Biomedicine, Hangzhou, Zhejiang, China
| | - Tobias Weiss
- Corresponding Author: Tobias Weiss, MD, PhD, Department of Neurology, University Hospital and University of Zurich, Frauenklinikstrasse 26, 8091 Zurich, Switzerland ()
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8
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Tolmachova K, Farnung J, Liang JR, Corn JE, Bode JW. Facile Preparation of UFMylation Activity-Based Probes by Chemoselective Installation of Electrophiles at the C-Terminus of Recombinant UFM1. ACS Cent Sci 2022; 8:756-762. [PMID: 35756382 PMCID: PMC9228560 DOI: 10.1021/acscentsci.2c00203] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Indexed: 05/17/2023]
Abstract
Aberrations in protein modification with ubiquitin-fold modifier (UFM1) are associated with a range of diseases, but the biological function and regulation of this post-translational modification, known as UFMylation, remain enigmatic. To provide activity-based probes for UFMylation, we have developed a new method for the installation of electrophilic warheads at the C-terminus of recombinant UFM1. A C-terminal UFM1 acyl hydrazide was readily produced by selective intein cleavage and chemoselectively acylated by a variety of carboxylic acid anhydrides at pH 3, without detriment to the folded protein or reactions at unprotected amino acid side chains. The resulting UFM1 activity-based probes show a range of tunable reactivity and high selectivity for proteins involved in UFMylation processes; structurally related E1s, E2s, and proteases associated with Ub or other Ubls were unreactive. The UFM1 probes were active both in cell lysates and in living cells. A previously inaccessible α-chloroacetyl probe was remarkably selective for covalent modification of the active-site cysteine of de-UFMylase UFSP2 in cellulo.
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Affiliation(s)
- Kateryna
A. Tolmachova
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jakob Farnung
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
| | - Jin Rui Liang
- Institute
of Molecular Health Sciences, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Jacob E. Corn
- Institute
of Molecular Health Sciences, Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Jeffrey W. Bode
- Laboratory
for Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zürich, 8093 Zürich, Switzerland
- E-mail:
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9
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Magis W, DeWitt MA, Wyman SK, Vu JT, Heo SJ, Shao SJ, Hennig F, Romero ZG, Campo-Fernandez B, Said S, McNeill MS, Rettig GR, Sun Y, Wang Y, Behlke MA, Kohn DB, Boffelli D, Walters MC, Corn JE, Martin DI. High-level correction of the sickle mutation is amplified in vivo during erythroid differentiation. iScience 2022; 25:104374. [PMID: 35633935 PMCID: PMC9130532 DOI: 10.1016/j.isci.2022.104374] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 05/03/2022] [Accepted: 05/04/2022] [Indexed: 12/21/2022] Open
Abstract
Background A point mutation in sickle cell disease (SCD) alters one amino acid in the β-globin subunit of hemoglobin, with resultant anemia and multiorgan damage that typically shortens lifespan by decades. Because SCD is caused by a single mutation, and hematopoietic stem cells (HSCs) can be harvested, manipulated, and returned to an individual, it is an attractive target for gene correction. Results An optimized Cas9 ribonucleoprotein (RNP) with an ssDNA oligonucleotide donor together generated correction of at least one β-globin allele in more than 30% of long-term engrafting human HSCs. After adopting a high-fidelity Cas9 variant, efficient correction with minimal off-target events also was observed. In vivo erythroid differentiation markedly enriches for corrected β-globin alleles, indicating that erythroblasts carrying one or more corrected alleles have a survival advantage. Significance These findings indicate that the sickle mutation can be corrected in autologous HSCs with an optimized protocol suitable for clinical translation. The gene editing protocol corrects the sickle mutation in ∼30% of engrafting cells Random assortment of engrafting stem cell clones without clonal dominance was shown Corrected erythroid cells are preferentially enriched compared with unedited cells
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10
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Heath NG, O’Geen H, Halmai NB, Corn JE, Segal DJ. Imaging Unique DNA Sequences in Individual Cells Using a CRISPR-Cas9-Based, Split Luciferase Biosensor. Front Genome Ed 2022; 4:867390. [PMID: 35403097 PMCID: PMC8990833 DOI: 10.3389/fgeed.2022.867390] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 03/09/2022] [Indexed: 11/13/2022] Open
Abstract
An extensive arsenal of biosensing tools has been developed based on the clustered regularly interspaced short palindromic repeat (CRISPR) platform, including those that detect specific DNA sequences both in vitro and in live cells. To date, DNA imaging approaches have traditionally used full fluorescent reporter-based fusion probes. Such “always-on” probes differentiate poorly between bound and unbound probe and are unable to sensitively detect unique copies of a target sequence in individual cells. Herein we describe a DNA biosensor that provides a sensitive readout for such low-copy DNA sequences through proximity-mediated reassembly of two independently optimized fragments of NanoLuc luciferase (NLuc), a small, bright luminescent reporter. Applying this “turn-on” probe in live cells, we demonstrate an application not easily achieved by fluorescent reporter-based probes, detection of individual endogenous genomic loci using standard epifluorescence microscopy. This approach could enable detection of gene edits during ex vivo editing procedures and should be a useful platform for many other live cell DNA biosensing applications.
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Affiliation(s)
- Nicholas G. Heath
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Henriette O’Geen
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Nicole B. Halmai
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
| | - Jacob E. Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- Department of Biology, ETH, Zürich, Switzerland
| | - David J. Segal
- Genome Center and Department of Biochemistry and Molecular Medicine, University of California, Davis, Davis, CA, United States
- Integrative Genetics and Genomics, University of California, Davis, Davis, CA, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, United States
- *Correspondence: David J. Segal,
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11
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Ravi NS, Wienert B, Wyman SK, Bell HW, George A, Mahalingam G, Vu JT, Prasad K, Bandlamudi BP, Devaraju N, Rajendiran V, Syedbasha N, Pai AA, Nakamura Y, Kurita R, Narayanasamy M, Balasubramanian P, Thangavel S, Marepally S, Velayudhan SR, Srivastava A, DeWitt MA, Crossley M, Corn JE, Mohankumar KM. Identification of novel HPFH-like mutations by CRISPR base editing that elevate the expression of fetal hemoglobin. eLife 2022; 11:65421. [PMID: 35147495 PMCID: PMC8865852 DOI: 10.7554/elife.65421] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [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: 12/03/2020] [Accepted: 02/11/2022] [Indexed: 11/29/2022] Open
Abstract
Naturally occurring point mutations in the HBG promoter switch hemoglobin synthesis from defective adult beta-globin to fetal gamma-globin in sickle cell patients with hereditary persistence of fetal hemoglobin (HPFH) and ameliorate the clinical severity. Inspired by this natural phenomenon, we tiled the highly homologous HBG proximal promoters using adenine and cytosine base editors that avoid the generation of large deletions and identified novel regulatory regions including a cluster at the –123 region. Base editing at –123 and –124 bp of HBG promoter induced fetal hemoglobin (HbF) to a higher level than disruption of well-known BCL11A binding site in erythroblasts derived from human CD34+ hematopoietic stem and progenitor cells (HSPC). We further demonstrated in vitro that the introduction of –123T > C and –124T > C HPFH-like mutations drives gamma-globin expression by creating a de novo binding site for KLF1. Overall, our findings shed light on so far unknown regulatory elements within the HBG promoter and identified additional targets for therapeutic upregulation of fetal hemoglobin.
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Affiliation(s)
- Nithin Sam Ravi
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Beeke Wienert
- Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, United States
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Henry William Bell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia
| | - Anila George
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | | | - Jonathan T Vu
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Kirti Prasad
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | | | | | - Vignesh Rajendiran
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Nazar Syedbasha
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Aswin Anand Pai
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Ibaraki, Japan
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute Blood Service Headquarters, Japanese Red Cross Society, Japan, Tokyo, Japan
| | | | | | | | - Srujan Marepally
- Centre for Stem Cell Research, Christian Medical College, Vellore, India
| | - Shaji R Velayudhan
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Alok Srivastava
- Department of Haematology, Christian Medical College & Hospital, Vellore, India
| | - Mark A DeWitt
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, United States
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Kensington, Australia
| | - Jacob E Corn
- Department of Biology, ETH Zurich, Zurich, Switzerland
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12
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Riepe C, Zelin E, Frankino PA, Meacham ZA, Fernandez S, Ingolia NT, Corn JE. Double stranded DNA breaks and genome editing trigger loss of ribosomal protein RPS27A. FEBS J 2021; 289:3101-3114. [PMID: 34914197 PMCID: PMC9295824 DOI: 10.1111/febs.16321] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [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: 05/26/2021] [Revised: 11/09/2021] [Accepted: 12/14/2021] [Indexed: 11/03/2022]
Abstract
DNA damage activates a robust transcriptional stress response, but much less is known about how DNA damage impacts translation. The advent of genome editing with Cas9 has intensified interest in understanding cellular responses to DNA damage. Here, we find that DNA double-strand breaks (DSBs), including those induced by Cas9, trigger the loss of ribosomal protein RPS27A from ribosomes via p53-independent proteasomal degradation. Comparisons of Cas9 and dCas9 ribosome profiling and mRNA-seq experiments reveal a global translational response to DSBs that precedes changes in transcript abundance. Our results demonstrate that even a single double-strand break can lead to altered translational output and ribosome remodeling, suggesting caution in interpreting cellular phenotypes measured immediately after genome editing.
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Affiliation(s)
- Celeste Riepe
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Elena Zelin
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Phillip A Frankino
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Zuriah A Meacham
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Samantha Fernandez
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Nicholas T Ingolia
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA.,Department of Biology, ETH, Zürich, Switzerland
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13
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Boontanrart MY, Schröder MS, Stehli GM, Banović M, Wyman SK, Lew RJ, Bordi M, Gowen BG, DeWitt MA, Corn JE. ATF4 Regulates MYB to Increase γ-Globin in Response to Loss of β-Globin. Cell Rep 2021; 32:107993. [PMID: 32755585 DOI: 10.1016/j.celrep.2020.107993] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2020] [Revised: 05/20/2020] [Accepted: 07/14/2020] [Indexed: 12/26/2022] Open
Abstract
β-Hemoglobinopathies can trigger rapid production of red blood cells in a process known as stress erythropoiesis. Cellular stress prompts differentiating erythroid precursors to express high levels of fetal γ-globin. However, the mechanisms underlying γ-globin production during cellular stress are still poorly defined. Here, we use CRISPR-Cas genome editing to model the stress caused by reduced levels of adult β-globin. We find that decreased β-globin is sufficient to induce robust re-expression of γ-globin, and RNA sequencing (RNA-seq) of differentiating isogenic erythroid precursors implicates ATF4 as a causal regulator of this response. ATF4 binds within the HBS1L-MYB intergenic enhancer and regulates expression of MYB, a known γ-globin regulator. Overall, the reduction of ATF4 upon β-globin knockout decreases the levels of MYB and BCL11A. Identification of ATF4 as a key regulator of globin compensation adds mechanistic insight to the poorly understood phenomenon of stress-induced globin compensation and could inform strategies to treat hemoglobinopathies.
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Affiliation(s)
- Mandy Y Boontanrart
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | | | | | - Marija Banović
- Department of Biology, ETH Zurich, Zurich 8092, Switzerland
| | - Stacia K Wyman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Rachel J Lew
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matteo Bordi
- Department of Biology, ETH Zurich, Zurich 8092, Switzerland
| | - Benjamin G Gowen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Mark A DeWitt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zurich, Zurich 8092, Switzerland; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
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14
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Baik R, Wyman SK, Kabir S, Corn JE. Genome editing to model and reverse a prevalent mutation associated with myeloproliferative neoplasms. PLoS One 2021; 16:e0247858. [PMID: 33661998 PMCID: PMC7932127 DOI: 10.1371/journal.pone.0247858] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 12/22/2020] [Accepted: 02/15/2021] [Indexed: 12/26/2022] Open
Abstract
Myeloproliferative neoplasms (MPNs) cause the over-production of blood cells such as erythrocytes (polycythemia vera) or platelets (essential thrombocytosis). JAK2 V617F is the most prevalent somatic mutation in many MPNs, but previous modeling of this mutation in mice relied on transgenic overexpression and resulted in diverse phenotypes that were in some cases attributed to expression level. CRISPR-Cas9 engineering offers new possibilities to model and potentially cure genetically encoded disorders via precise modification of the endogenous locus in primary cells. Here we develop "scarless" Cas9-based reagents to create and reverse the JAK2 V617F mutation in an immortalized human erythroid progenitor cell line (HUDEP-2), CD34+ adult human hematopoietic stem and progenitor cells (HSPCs), and immunophenotypic long-term hematopoietic stem cells (LT-HSCs). We find no overt in vitro increase in proliferation associated with an endogenous JAK2 V617F allele, but co-culture with wild type cells unmasks a competitive growth advantage provided by the mutation. Acquisition of the V617F allele also promotes terminal differentiation of erythroid progenitors, even in the absence of hematopoietic cytokine signaling. Taken together, these data are consistent with the gradually progressive manifestation of MPNs and reveals that endogenously acquired JAK2 V617F mutations may yield more subtle phenotypes as compared to transgenic overexpression models.
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Affiliation(s)
- Ron Baik
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
- New York University School of Medicine, New York, NY, United States of America
| | - Stacia K. Wyman
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
| | - Shaheen Kabir
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA, United States of America
- * E-mail: (JEC); (SK)
| | - Jacob E. Corn
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States of America
- * E-mail: (JEC); (SK)
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15
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Siegner SM, Karasu ME, Schröder MS, Kontarakis Z, Corn JE. PnB Designer: a web application to design prime and base editor guide RNAs for animals and plants. BMC Bioinformatics 2021; 22:101. [PMID: 33653259 PMCID: PMC7923538 DOI: 10.1186/s12859-021-04034-6] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 02/16/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND The rapid expansion of the CRISPR toolbox through tagging effector domains to either enzymatically inactive Cas9 (dCas9) or Cas9 nickase (nCas9) has led to several promising new gene editing strategies. Recent additions include CRISPR cytosine or adenine base editors (CBEs and ABEs) and the CRISPR prime editors (PEs), in which a deaminase or reverse transcriptase are fused to nCas9, respectively. These tools hold great promise to model and correct disease-causing mutations in animal and plant models. But so far, no widely-available tools exist to automate the design of both BE and PE reagents. RESULTS We developed PnB Designer, a web-based application for the design of pegRNAs for PEs and guide RNAs for BEs. PnB Designer makes it easy to design targeting guide RNAs for single or multiple targets on a variant or reference genome from organisms spanning multiple kingdoms. With PnB Designer, we designed pegRNAs to model all known disease causing mutations available in ClinVar. Additionally, PnB Designer can be used to design guide RNAs to install or revert a SNV, scanning the genome with one CBE and seven different ABE PAM variants and returning the best BE to use. PnB Designer is publicly accessible at http://fgcz-shiny.uzh.ch/PnBDesigner/ CONCLUSION: With PnB Designer we created a user-friendly design tool for CRISPR PE and BE reagents, which should simplify choosing editing strategy and avoiding design complications.
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Affiliation(s)
| | | | | | - Zacharias Kontarakis
- Department of Biology, ETH Zurich, Zurich, Switzerland
- Genome Engineering and Measurement Lab, ETH Zurich, Zurich, Switzerland
| | - Jacob E Corn
- Department of Biology, ETH Zurich, Zurich, Switzerland.
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16
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Zhang Y, Prach LM, O'Brien TE, DiMaio F, Prigozhin DM, Corn JE, Alber T, Siegel JB, Tantillo DJ. Crystal Structure and Mechanistic Molecular Modeling Studies of Mycobacterium tuberculosis Diterpene Cyclase Rv3377c. Biochemistry 2020; 59:4507-4515. [PMID: 33182997 DOI: 10.1021/acs.biochem.0c00762] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Terpenes make up the largest class of natural products, with extensive chemical and structural diversity. Diterpenes, mostly isolated from plants and rarely prokaryotes, exhibit a variety of important biological activities and valuable applications, including providing antitumor and antibiotic pharmaceuticals. These natural products are constructed by terpene synthases, a class of enzymes that catalyze one of the most complex chemical reactions in biology: converting simple acyclic oligo-isoprenyl diphosphate substrates to complex polycyclic products via carbocation intermediates. Here we obtained the second ever crystal structure of a class II diterpene synthase from bacteria, tuberculosinol pyrophosphate synthase (i.e., Halimadienyl diphosphate synthase, MtHPS, or Rv3377c) from Mycobacterium tuberculosis (Mtb). This enzyme transforms (E,E,E)-geranylgeranyl diphosphate into tuberculosinol pyrophosphate (Halimadienyl diphosphate). Rv3377c is part of the Mtb diterpene pathway along with Rv3378c, which converts tuberculosinol pyrophosphate to 1-tuberculosinyl adenosine (1-TbAd). This pathway was shown to exist only in virulent Mycobacterium species, but not in closely related avirulent species, and was proposed to be involved in phagolysosome maturation arrest. To gain further insight into the reaction pathway and the mechanistically relevant enzyme substrate binding orientation, electronic structure calculation and docking studies of reaction intermediates were carried out. Results reveal a plausible binding mode of the substrate that can provide the information to guide future drug design and anti-infective therapies of this biosynthetic pathway.
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Affiliation(s)
- Yue Zhang
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Lisa M Prach
- Department of Molecular and Cell Biology, University of California, Berkeley, California 94720, United States
| | - Terrence E O'Brien
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
| | - Frank DiMaio
- Department of Biochemistry, University of Washington, Seattle, Washington 98195, United States
| | - Daniil M Prigozhin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Jacob E Corn
- Department of Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Tom Alber
- Department of Molecular & Cell Biology and QB3 Institute, University of California, Berkeley, California 94720, United States
| | - Justin B Siegel
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States.,Department of Biochemistry and Molecular Medicine, University of California-Davis, Davis, California 95616, United States.,Genome Center, University of California-Davis, Davis, California 95616, United States
| | - Dean J Tantillo
- Department of Chemistry, University of California-Davis, Davis, California 95616, United States
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17
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Shin JJ, Schröder MS, Caiado F, Wyman SK, Bray NL, Bordi M, Dewitt MA, Vu JT, Kim WT, Hockemeyer D, Manz MG, Corn JE. Controlled Cycling and Quiescence Enables Efficient HDR in Engraftment-Enriched Adult Hematopoietic Stem and Progenitor Cells. Cell Rep 2020; 32:108093. [PMID: 32877675 PMCID: PMC7487781 DOI: 10.1016/j.celrep.2020.108093] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Revised: 07/07/2020] [Accepted: 08/07/2020] [Indexed: 12/12/2022] Open
Abstract
Genome editing often takes the form of either error-prone sequence disruption by non-homologous end joining (NHEJ) or sequence replacement by homology-directed repair (HDR). Although NHEJ is generally effective, HDR is often difficult in primary cells. Here, we use a combination of immunophenotyping, next-generation sequencing, and single-cell RNA sequencing to investigate and reprogram genome editing outcomes in subpopulations of adult hematopoietic stem and progenitor cells. We find that although quiescent stem-enriched cells mostly use NHEJ, non-quiescent cells with the same immunophenotype use both NHEJ and HDR. Inducing quiescence before editing results in a loss of HDR in all cell subtypes. We develop a strategy of controlled cycling and quiescence that yields a 6-fold increase in the HDR/NHEJ ratio in quiescent stem cells ex vivo and in vivo. Our results highlight the tension between editing and cellular physiology and suggest strategies to manipulate quiescent cells for research and therapeutic genome editing.
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Affiliation(s)
- Jiyung J Shin
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | | | - Francisco Caiado
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Nicolas L Bray
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Matteo Bordi
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Mark A Dewitt
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Jonathan T Vu
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Won-Tae Kim
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Dirk Hockemeyer
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA
| | - Markus G Manz
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, 8091 Zurich, Switzerland
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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18
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Wang AS, Chen LC, Wu RA, Hao Y, McSwiggen DT, Heckert AB, Richardson CD, Gowen BG, Kazane KR, Vu JT, Wyman SK, Shin JJ, Darzacq X, Walter JC, Corn JE. The Histone Chaperone FACT Induces Cas9 Multi-turnover Behavior and Modifies Genome Manipulation in Human Cells. Mol Cell 2020; 79:221-233.e5. [PMID: 32603710 PMCID: PMC7398558 DOI: 10.1016/j.molcel.2020.06.014] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 02/26/2020] [Accepted: 06/05/2020] [Indexed: 12/23/2022]
Abstract
Cas9 is a prokaryotic RNA-guided DNA endonuclease that binds substrates tightly in vitro but turns over rapidly when used to manipulate genomes in eukaryotic cells. Little is known about the factors responsible for dislodging Cas9 or how they influence genome engineering. Unbiased detection through proximity labeling of transient protein interactions in cell-free Xenopus laevis egg extract identified the dimeric histone chaperone facilitates chromatin transcription (FACT) as an interactor of substrate-bound Cas9. FACT is both necessary and sufficient to displace dCas9, and FACT immunodepletion converts Cas9's activity from multi-turnover to single turnover. In human cells, FACT depletion extends dCas9 residence times, delays genome editing, and alters the balance between indel formation and homology-directed repair. FACT knockdown also increases epigenetic marking by dCas9-based transcriptional effectors with a concomitant enhancement of transcriptional modulation. FACT thus shapes the intrinsic cellular response to Cas9-based genome manipulation most likely by determining Cas9 residence times.
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Affiliation(s)
- Alan S Wang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Leo C Chen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - R Alex Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Yvonne Hao
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - David T McSwiggen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute of Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Alec B Heckert
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute of Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Christopher D Richardson
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Benjamin G Gowen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Katelynn R Kazane
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jonathan T Vu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Stacia K Wyman
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jiyung J Shin
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; California Institute of Regenerative Medicine Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Johannes C Walter
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA; Howard Hughes Medical Institute, Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA 02115, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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19
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Rose JC, Popp NA, Richardson CD, Stephany JJ, Mathieu J, Wei CT, Corn JE, Maly DJ, Fowler DM. Suppression of unwanted CRISPR-Cas9 editing by co-administration of catalytically inactivating truncated guide RNAs. Nat Commun 2020; 11:2697. [PMID: 32483117 PMCID: PMC7264211 DOI: 10.1038/s41467-020-16542-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
CRISPR-Cas9 nucleases are powerful genome engineering tools, but unwanted cleavage at off-target and previously edited sites remains a major concern. Numerous strategies to reduce unwanted cleavage have been devised, but all are imperfect. Here, we report that off-target sites can be shielded from the active Cas9•single guide RNA (sgRNA) complex through the co-administration of dead-RNAs (dRNAs), truncated guide RNAs that direct Cas9 binding but not cleavage. dRNAs can effectively suppress a wide-range of off-targets with minimal optimization while preserving on-target editing, and they can be multiplexed to suppress several off-targets simultaneously. dRNAs can be combined with high-specificity Cas9 variants, which often do not eliminate all unwanted editing. Moreover, dRNAs can prevent cleavage of homology-directed repair (HDR)-corrected sites, facilitating scarless editing by eliminating the need for blocking mutations. Thus, we enable precise genome editing by establishing a flexible approach for suppressing unwanted editing of both off-targets and HDR-corrected sites.
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Affiliation(s)
- John C Rose
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA.
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Nicholas A Popp
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Christopher D Richardson
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Jason J Stephany
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA
| | - Julie Mathieu
- Department of Comparative Medicine, Institute for Stem Cell and Regenerative Medicine, University of Washington, Seattle, WA, 98109, USA
| | - Cindy T Wei
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA
| | - Jacob E Corn
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA, 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
- Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Dustin J Maly
- Department of Chemistry, University of Washington, Seattle, WA, 98195, USA.
- Department of Biochemistry, University of Washington, Seattle, WA, 98195, USA.
| | - Douglas M Fowler
- Department of Genome Sciences, University of Washington, Seattle, WA, 98195, USA.
- Department of Bioengineering, University of Washington, Seattle, WA, 98195, USA.
- Genetic Networks Program, Canadian Institute for Advanced Research, Toronto, ON, Canada.
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20
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Wienert B, Nguyen DN, Guenther A, Feng SJ, Locke MN, Wyman SK, Shin J, Kazane KR, Gregory GL, Carter MAM, Wright F, Conklin BR, Marson A, Richardson CD, Corn JE. Timed inhibition of CDC7 increases CRISPR-Cas9 mediated templated repair. Nat Commun 2020; 11:2109. [PMID: 32355159 PMCID: PMC7193628 DOI: 10.1038/s41467-020-15845-1] [Citation(s) in RCA: 69] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/12/2020] [Indexed: 12/11/2022] Open
Abstract
Repair of double strand DNA breaks (DSBs) can result in gene disruption or gene modification via homology directed repair (HDR) from donor DNA. Altering cellular responses to DSBs may rebalance editing outcomes towards HDR and away from other repair outcomes. Here, we utilize a pooled CRISPR screen to define host cell involvement in HDR between a Cas9 DSB and a plasmid double stranded donor DNA (dsDonor). We find that the Fanconi Anemia (FA) pathway is required for dsDonor HDR and that other genes act to repress HDR. Small molecule inhibition of one of these repressors, CDC7, by XL413 and other inhibitors increases the efficiency of HDR by up to 3.5 fold in many contexts, including primary T cells. XL413 stimulates HDR during a reversible slowing of S-phase that is unexplored for Cas9-induced HDR. We anticipate that XL413 and other such rationally developed inhibitors will be useful tools for gene modification.
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Affiliation(s)
- Beeke Wienert
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA
- Gladstone Institutes, San Francisco, CA, 94158, USA
| | - David N Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA
- Diabetes Center, University of California, San Francisco, CA, 94143, USA
- Department of Medicine, University of California, San Francisco, CA, 94143, USA
| | - Alexis Guenther
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA
| | - Sharon J Feng
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA
| | - Melissa N Locke
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA
| | - Jiyung Shin
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zurich, Switzerland
| | - Katelynn R Kazane
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA
| | | | | | - Francis Wright
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA
| | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA, 94158, USA
- Departments of Medicine, Ophthalmology, and Pharmacology, University of California, San Francisco, CA, 94143, USA
| | - Alex Marson
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA
- Department of Microbiology and Immunology, University of California, San Francisco, CA, 94143, USA
- Diabetes Center, University of California, San Francisco, CA, 94143, USA
- Department of Medicine, University of California, San Francisco, CA, 94143, USA
- Parker Institute for Cancer Immunotherapy, San Francisco, CA, 94129, USA
- Chan Zuckerberg Biohub, San Francisco, CA, 94158, USA
| | - Chris D Richardson
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA.
- Department of Molecular, Cellular, and Developmental Biology, University of California, Santa Barbara, CA, 93106, USA.
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, CA, 94703, USA.
- Department of Molecular and Cell Biology, University of California, Berkeley, CA, 94703, USA.
- Department of Biology, Institute of Molecular Health Sciences, ETH Zürich, 8093, Zurich, Switzerland.
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21
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Wienert B, Wyman SK, Yeh CD, Conklin BR, Corn JE. CRISPR off-target detection with DISCOVER-seq. Nat Protoc 2020; 15:1775-1799. [PMID: 32313254 DOI: 10.1038/s41596-020-0309-5] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Accepted: 02/06/2020] [Indexed: 11/09/2022]
Abstract
DISCOVER-seq (discovery of in situ Cas off-targets and verification by sequencing) is a broadly applicable approach for unbiased CRISPR-Cas off-target identification in cells and tissues. It leverages the recruitment of DNA repair factors to double-strand breaks (DSBs) after genome editing with CRISPR nucleases. Here, we describe a detailed experimental protocol and analysis pipeline with which to perform DISCOVER-seq. The principle of this method is to track the precise recruitment of MRE11 to DSBs by chromatin immunoprecipitation followed by next-generation sequencing. A customized open-source bioinformatics pipeline, BLENDER (blunt end finder), then identifies off-target sequences genome wide. DISCOVER-seq is capable of finding and measuring off-targets in primary cells and in situ. The two main advantages of DISCOVER-seq are (i) low false-positive rates because DNA repair enzyme binding is required for genome edits to occur and (ii) its applicability to a wide variety of systems, including patient-derived cells and animal models. The whole protocol, including the analysis, can be completed within 2 weeks.
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Affiliation(s)
- Beeke Wienert
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA. .,Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, USA.
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Charles D Yeh
- Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Bruce R Conklin
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA.,Institute of Data Science and Biotechnology, Gladstone Institutes, San Francisco, California, USA.,Departments of Medicine, Ophthalmology & Pharmacology, University of California, San Francisco, San Francisco, California, USA
| | - Jacob E Corn
- Department of Biology, ETH Zurich, Zurich, Switzerland.
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22
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Liang JR, Lingeman E, Luong T, Ahmed S, Muhar M, Nguyen T, Olzmann JA, Corn JE. A Genome-wide ER-phagy Screen Highlights Key Roles of Mitochondrial Metabolism and ER-Resident UFMylation. Cell 2020; 180:1160-1177.e20. [PMID: 32160526 DOI: 10.1016/j.cell.2020.02.017] [Citation(s) in RCA: 138] [Impact Index Per Article: 34.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Revised: 11/04/2019] [Accepted: 02/07/2020] [Indexed: 12/13/2022]
Abstract
Selective autophagy of organelles is critical for cellular differentiation, homeostasis, and organismal health. Autophagy of the ER (ER-phagy) is implicated in human neuropathy but is poorly understood beyond a few autophagosomal receptors and remodelers. By using an ER-phagy reporter and genome-wide CRISPRi screening, we identified 200 high-confidence human ER-phagy factors. Two pathways were unexpectedly required for ER-phagy. First, reduced mitochondrial metabolism represses ER-phagy, which is opposite of general autophagy and is independent of AMPK. Second, ER-localized UFMylation is required for ER-phagy to repress the unfolded protein response via IRE1α. The UFL1 ligase is brought to the ER surface by DDRGK1 to UFMylate RPN1 and RPL26 and preferentially targets ER sheets for degradation, analogous to PINK1-Parkin regulation during mitophagy. Our data provide insight into the cellular logic of ER-phagy, reveal parallels between organelle autophagies, and provide an entry point to the relatively unexplored process of degrading the ER network.
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Affiliation(s)
- Jin Rui Liang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Emily Lingeman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Thao Luong
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Saba Ahmed
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Matthias Muhar
- Department of Biology, ETH Zürich, 8093 Zürich, Switzerland
| | - Truc Nguyen
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - James A Olzmann
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, San Francisco, CA 94158, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biology, ETH Zürich, 8093 Zürich, Switzerland.
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23
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Luteijn RD, Zaver SA, Gowen BG, Wyman SK, Garelis NE, Onia L, McWhirter SM, Katibah GE, Corn JE, Woodward JJ, Raulet DH. Author Correction: SLC19A1 transports immunoreactive cyclic dinucleotides. Nature 2020; 579:E12. [PMID: 32144410 DOI: 10.1038/s41586-020-2064-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Rutger D Luteijn
- Department of Molecular and Cell Biology, and Cancer Research Laboratory, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA
| | - Shivam A Zaver
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - Benjamin G Gowen
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA
| | - Nick E Garelis
- Department of Molecular and Cell Biology, and Cancer Research Laboratory, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA
| | - Liberty Onia
- Department of Molecular and Cell Biology, and Cancer Research Laboratory, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA
| | | | | | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, USA.,Institute of Molecular Health Sciences, Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Joshua J Woodward
- Department of Microbiology, University of Washington, Seattle, WA, USA
| | - David H Raulet
- Department of Molecular and Cell Biology, and Cancer Research Laboratory, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, USA.
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24
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Luteijn RD, Zaver SA, Gowen BG, Wyman S, Garelis N, Onia L, McWhirter SM, Katibah GE, Corn JE, Woodward JJ, Raulet DH. SLC19A1 transports immunoreactive cyclic dinucleotides. Nature 2019; 573:434-438. [PMID: 31511694 PMCID: PMC6785039 DOI: 10.1038/s41586-019-1553-0] [Citation(s) in RCA: 202] [Impact Index Per Article: 40.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Accepted: 08/08/2019] [Indexed: 01/05/2023]
Abstract
The accumulation of DNA in the cytosol serves as a key immunostimulatory signal associated with infections, cancer and genomic damage1,2. Cytosolic DNA triggers immune responses by activating the cyclic GMP-AMP synthase (cGAS)-stimulator of interferon genes (STING) pathway3. The binding of DNA to cGAS activates its enzymatic activity, leading to the synthesis of a second messenger, cyclic guanosine monophosphate-adenosine monophosphate (2'3'-cGAMP)4-7. This cyclic dinucleotide (CDN) activates STING8, which in turn activates the transcription factors interferon regulatory factor 3 (IRF3) and nuclear factor κ-light-chain-enhancer of activated B cells (NF-κB), promoting the transcription of genes encoding type I interferons and other cytokines and mediators that stimulate a broader immune response. Exogenous 2'3'-cGAMP produced by malignant cells9 and other CDNs, including those produced by bacteria10-12 and synthetic CDNs used in cancer immunotherapy13,14, must traverse the cell membrane to activate STING in target cells. How these charged CDNs pass through the lipid bilayer is unknown. Here we used a genome-wide CRISPR-interference screen to identify the reduced folate carrier SLC19A1, a folate-organic phosphate antiporter, as the major transporter of CDNs. Depleting SLC19A1 in human cells inhibits CDN uptake and functional responses, and overexpressing SLC19A1 increases both uptake and functional responses. In human cell lines and primary cells ex vivo, CDN uptake is inhibited by folates as well as two medications approved for treatment of inflammatory diseases, sulfasalazine and the antifolate methotrexate. The identification of SLC19A1 as the major transporter of CDNs into cells has implications for the immunotherapeutic treatment of cancer13, host responsiveness to CDN-producing pathogenic microorganisms11 and-potentially-for some inflammatory diseases.
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Affiliation(s)
- Rutger D. Luteijn
- Department of Molecular and Cell Biology, and Cancer Research Laboratory, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA
| | - Shivam A. Zaver
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - Benjamin G. Gowen
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA, 94720, USA,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Stacia Wyman
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA, 94720, USA,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Nick Garelis
- Department of Molecular and Cell Biology, and Cancer Research Laboratory, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA
| | - Liberty Onia
- Department of Molecular and Cell Biology, and Cancer Research Laboratory, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA
| | | | | | - Jacob E. Corn
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA, 94720, USA,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA, 94720, USA
| | - Joshua J. Woodward
- Department of Microbiology, University of Washington, Seattle, WA, 98195, USA
| | - David H. Raulet
- Department of Molecular and Cell Biology, and Cancer Research Laboratory, Division of Immunology and Pathogenesis, University of California, Berkeley, CA, 94720, USA,correspondence: , tel: 510-642-9521
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25
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Kabir S, Cidado J, Andersen C, Dick C, Lin PC, Mitros T, Ma H, Baik SH, Belmonte MA, Drew L, Corn JE. The CUL5 ubiquitin ligase complex mediates resistance to CDK9 and MCL1 inhibitors in lung cancer cells. eLife 2019; 8:44288. [PMID: 31294695 PMCID: PMC6701926 DOI: 10.7554/elife.44288] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [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: 12/15/2018] [Accepted: 07/05/2019] [Indexed: 12/22/2022] Open
Abstract
Overexpression of anti-apoptotic proteins MCL1 and Bcl-xL are frequently observed in many cancers. Inhibitors targeting MCL1 are in clinical development, however numerous cancer models are intrinsically resistant to this approach. To discover mechanisms underlying resistance to MCL1 inhibition, we performed multiple flow-cytometry based genome-wide CRISPR screens interrogating two drugs that directly (MCL1i) or indirectly (CDK9i) target MCL1. Remarkably, both screens identified three components (CUL5, RNF7 and UBE2F) of a cullin-RING ubiquitin ligase complex (CRL5) that resensitized cells to MCL1 inhibition. We find that levels of the BH3-only pro-apoptotic proteins Bim and Noxa are proteasomally regulated by the CRL5 complex. Accumulation of Noxa caused by depletion of CRL5 components was responsible for re-sensitization to CDK9 inhibitor, but not MCL1 inhibitor. Discovery of a novel role of CRL5 in apoptosis and resistance to multiple types of anticancer agents suggests the potential to improve combination treatments.
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Affiliation(s)
- Shaheen Kabir
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States.,Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, San Francisco, United States
| | - Justin Cidado
- Bioscience Oncology, IMED Biotech Unit, AstraZeneca, Waltham, United States
| | - Courtney Andersen
- Bioscience Oncology, IMED Biotech Unit, AstraZeneca, Waltham, United States
| | - Cortni Dick
- Bioscience Oncology, IMED Biotech Unit, AstraZeneca, Waltham, United States
| | - Pei-Chun Lin
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Therese Mitros
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Hong Ma
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Seung Hyun Baik
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Matthew A Belmonte
- Bioscience Oncology, IMED Biotech Unit, AstraZeneca, Waltham, United States
| | - Lisa Drew
- Bioscience Oncology, IMED Biotech Unit, AstraZeneca, Waltham, United States
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
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26
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Shin J, Corn JE. E Pluribus Unum ("Out of Many, One"): CRISPR Modeling of Myeloid Expansion. Cell Stem Cell 2019; 21:415-416. [PMID: 28985519 DOI: 10.1016/j.stem.2017.09.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
In this issue of Cell Stem Cell, Tothova et al. (2017) demonstrate a promising way to model the complex genetics of clonal hematopoiesis and myeloid disorders using CRISPR-Cas9 genome editing in human hematopoietic stem and progenitor cells. Their approach opens the door to genotype-specific pharmacologic testing.
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Affiliation(s)
- Jiyung Shin
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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27
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Wienert B, Wyman SK, Richardson CD, Yeh CD, Akcakaya P, Porritt MJ, Morlock M, Vu JT, Kazane KR, Watry HL, Judge LM, Conklin BR, Maresca M, Corn JE. Unbiased detection of CRISPR off-targets in vivo using DISCOVER-Seq. Science 2019; 364:286-289. [PMID: 31000663 PMCID: PMC6589096 DOI: 10.1126/science.aav9023] [Citation(s) in RCA: 199] [Impact Index Per Article: 39.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 02/23/2019] [Indexed: 12/12/2022]
Abstract
CRISPR-Cas genome editing induces targeted DNA damage but can also affect off-target sites. Current off-target discovery methods work using purified DNA or specific cellular models but are incapable of direct detection in vivo. We developed DISCOVER-Seq (discovery of in situ Cas off-targets and verification by sequencing), a universally applicable approach for unbiased off-target identification that leverages the recruitment of DNA repair factors in cells and organisms. Tracking the precise recruitment of MRE11 uncovers the molecular nature of Cas activity in cells with single-base resolution. DISCOVER-Seq works with multiple guide RNA formats and types of Cas enzymes, allowing characterization of new editing tools. Off-targets can be identified in cell lines and patient-derived induced pluripotent stem cells and during adenoviral editing of mice, paving the way for in situ off-target discovery within individual patient genotypes during therapeutic genome editing.
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Affiliation(s)
- Beeke Wienert
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Stacia K Wyman
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
| | - Christopher D Richardson
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Charles D Yeh
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Pinar Akcakaya
- Discovery Biology, AstraZeneca, 43150 Gothenburg, Sweden
| | | | | | - Jonathan T Vu
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
| | - Katelynn R Kazane
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Hannah L Watry
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA
- Gladstone Institutes, San Francisco, CA 94158, USA
| | - Luke M Judge
- Gladstone Institutes, San Francisco, CA 94158, USA
- Department of Pediatrics, University of California San Francisco, San Francisco, CA 94143, USA
| | - Bruce R Conklin
- Gladstone Institutes, San Francisco, CA 94158, USA
- Departments of Medicine, Ophthalmology, and Pharmacology, University of California San Francisco, San Francisco, California 94143, USA
| | | | - Jacob E Corn
- Innovative Genomics Institute, University of California Berkeley, Berkeley, CA 94704, USA.
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, CA 94720, USA
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28
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Chung JE, Magis W, Vu J, Heo SJ, Wartiovaara K, Walters MC, Kurita R, Nakamura Y, Boffelli D, Martin DIK, Corn JE, DeWitt MA. CRISPR-Cas9 interrogation of a putative fetal globin repressor in human erythroid cells. PLoS One 2019; 14:e0208237. [PMID: 30645582 PMCID: PMC6333401 DOI: 10.1371/journal.pone.0208237] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2018] [Accepted: 11/14/2018] [Indexed: 01/14/2023] Open
Abstract
Sickle Cell Disease and ß-thalassemia, which are caused by defective or deficient adult ß-globin (HBB) respectively, are the most common serious genetic blood diseases in the world. Persistent expression of the fetal ß-like globin, also known as 𝛾-globin, can ameliorate both disorders by serving in place of the adult ß-globin as a part of the fetal hemoglobin tetramer (HbF). Here we use CRISPR-Cas9 gene editing to explore a potential 𝛾-globin silencer region upstream of the δ-globin gene identified by comparison of naturally-occurring deletion mutations associated with up-regulated 𝛾-globin. We find that deletion of a 1.7 kb consensus element or select 350 bp sub-regions from bulk populations of cells increases levels of HbF. Screening of individual sgRNAs in one sub-region revealed three single guides that caused increases in 𝛾-globin expression. Deletion of the 1.7 kb region in HUDEP-2 clonal sublines, and in colonies derived from CD34+ hematopoietic stem/progenitor cells (HSPCs), does not cause significant up-regulation of 𝛾-globin. These data suggest that the 1.7 kb region is not an autonomous 𝛾-globin silencer, and thus by itself is not a suitable therapeutic target for gene editing treatment of ß-hemoglobinopathies.
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Affiliation(s)
- Jennifer E Chung
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America
| | - Wendy Magis
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America
| | - Jonathan Vu
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America
| | - Seok-Jin Heo
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America
| | - Kirmo Wartiovaara
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America.,Research Programs Unit, Molecular Neurology and Biomedicum Stem Cell Centre, Faculty of Medicine, University of Helsinki, Helsinki, Finland.,Clinical Genetics, HUSLAB, Helsinki University Central Hospital, Helsinki, Finland
| | - Mark C Walters
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America.,Blood and Marrow Transplant Program, Division of Hematology, UCSF Benioff Children's Hospital, Oakland, CA, United States of America
| | - Ryo Kurita
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Center, Tsukuba, Ibaraki, Japan.,Faculty of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America
| | - David I K Martin
- Children's Hospital Oakland Research Institute, UCSF Benioff Children's Hospital, Oakland, CA, United States of America
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America.,Department of Molecular and Cellular Biology, University of California, Berkeley, CA, United States of America
| | - Mark A DeWitt
- Innovative Genomics Institute, University of California, Berkeley, CA, United States of America
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Lomova A, Clark DN, Campo-Fernandez B, Flores-Bjurström C, Kaufman ML, Fitz-Gibbon S, Wang X, Miyahira EY, Brown D, DeWitt MA, Corn JE, Hollis RP, Romero Z, Kohn DB. Improving Gene Editing Outcomes in Human Hematopoietic Stem and Progenitor Cells by Temporal Control of DNA Repair. Stem Cells 2018; 37:284-294. [PMID: 30372555 DOI: 10.1002/stem.2935] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2018] [Accepted: 10/02/2018] [Indexed: 12/14/2022]
Abstract
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated system (Cas9)-mediated gene editing of human hematopoietic stem cells (hHSCs) is a promising strategy for the treatment of genetic blood diseases through site-specific correction of identified causal mutations. However, clinical translation is hindered by low ratio of precise gene modification using the corrective donor template (homology-directed repair, HDR) to gene disruption (nonhomologous end joining, NHEJ) in hHSCs. By using a modified version of Cas9 with reduced nuclease activity in G1 phase of cell cycle when HDR cannot occur, and transiently increasing the proportion of cells in HDR-preferred phases (S/G2), we achieved a four-fold improvement in HDR/NHEJ ratio over the control condition in vitro, and a significant improvement after xenotransplantation of edited hHSCs into immunodeficient mice. This strategy for improving gene editing outcomes in hHSCs has important implications for the field of gene therapy, and can be applied to diseases where increased HDR/NHEJ ratio is critical for therapeutic success. Stem Cells 2019;37:284-294.
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Affiliation(s)
- Anastasia Lomova
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, California, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Danielle N Clark
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Beatriz Campo-Fernandez
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Carmen Flores-Bjurström
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Michael L Kaufman
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Sorel Fitz-Gibbon
- Institute of Genomics and Proteomics, UCLA, Los Angeles, California, USA
| | - Xiaoyan Wang
- Department of General Internal Medicine and Health Services Research, UCLA, Los Angeles, California, USA
| | - Eric Y Miyahira
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Devin Brown
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Mark A DeWitt
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
| | - Roger P Hollis
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Zulema Romero
- Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA
| | - Donald B Kohn
- Department of Molecular and Medical Pharmacology, University of California Los Angeles (UCLA), Los Angeles, California, USA.,Department of Microbiology, Immunology and Molecular Genetics, UCLA, Los Angeles, California, USA.,Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, UCLA, Los Angeles, California, USA
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30
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31
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Liang JR, Lingeman E, Ahmed S, Corn JE. Atlastins remodel the endoplasmic reticulum for selective autophagy. J Cell Biol 2018; 217:3354-3367. [PMID: 30143524 PMCID: PMC6168278 DOI: 10.1083/jcb.201804185] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 06/15/2018] [Accepted: 07/11/2018] [Indexed: 12/19/2022] Open
Abstract
Specific receptors are required for the autophagic degradation of endoplasmic reticulum (ER), known as ER-phagy. However, little is known about how the ER is remodeled and separated for packaging into autophagosomes. We developed two ER-phagy-specific reporter systems and found that Atlastins are key positive effectors and also targets of ER-phagy. Atlastins are ER-resident GTPases involved in ER membrane morphology, and Atlastin-depleted cells have decreased ER-phagy under starvation conditions. Atlastin's role in ER-phagy requires a functional GTPase domain and proper ER localization, both of which are also involved in ER architecture. The three Atlastin family members functionally compensate for one another during ER-phagy and may form heteromeric complexes with one another. We further find that Atlastins act downstream of the FAM134B ER-phagy receptor, such that depletion of Atlastins represses ER-autophagy induced by the overexpression of FAM134B. We propose that during ER-phagy, Atlastins remodel ER membrane to separate pieces of FAM134B-marked ER for efficient autophagosomal engulfment.
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Affiliation(s)
- Jin Rui Liang
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Emily Lingeman
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Saba Ahmed
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA .,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA
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Abstract
Fast-moving, competitive fields often inadvertently duplicate research. In a research environment that values being first over being robust, this results in one manuscript "scooping" ongoing research from other groups. Opportunities to demonstrate the solidity of a result through coincidental reproduction are thus lost. Here, two group leaders, one the scooper and one the scoopee, discuss their experiences under PLOS Biology's new "complementary research" policy. In this case, submission of the second article followed publication of the first by mere days. Scooper and scoopee discuss how complementary research is good for everyone by expanding the scientific reach of studies that are overlapping but not identical, demonstrating the robustness of related results, increasing readership for both authors, and making "replication" studies cost effective by creatively using resources that have already been spent.
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Affiliation(s)
- Jin-Soo Kim
- Department of Chemistry, Seoul National University, Seoul, Republic of Korea
- Center for Genome Engineering, Institute for Basic Science, Seoul, Republic of Korea
- * E-mail: (JEC); (JSK)
| | - Jacob E. Corn
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, United States of America
- * E-mail: (JEC); (JSK)
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Wienert B, Shin J, Zelin E, Pestal K, Corn JE. In vitro-transcribed guide RNAs trigger an innate immune response via the RIG-I pathway. PLoS Biol 2018; 16:e2005840. [PMID: 30011268 PMCID: PMC6049001 DOI: 10.1371/journal.pbio.2005840] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [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] [Received: 02/27/2018] [Accepted: 06/01/2018] [Indexed: 02/08/2023] Open
Abstract
Clustered, regularly interspaced, short palindromic repeat (CRISPR)-CRISPR-associated 9 (Cas9) genome editing is revolutionizing fundamental research and has great potential for the treatment of many diseases. While editing of immortalized cell lines has become relatively easy, editing of therapeutically relevant primary cells and tissues can remain challenging. One recent advancement is the delivery of a Cas9 protein and an in vitro-transcribed (IVT) guide RNA (gRNA) as a precomplexed ribonucleoprotein (RNP). This approach allows editing of primary cells such as T cells and hematopoietic stem cells, but the consequences beyond genome editing of introducing foreign Cas9 RNPs into mammalian cells are not fully understood. Here, we show that the IVT gRNAs commonly used by many laboratories for RNP editing trigger a potent innate immune response that is similar to canonical immune-stimulating ligands. IVT gRNAs are recognized in the cytosol through the retinoic acid-inducible gene I (RIG-I) pathway but not the melanoma differentiation-associated gene 5 (MDA5) pathway, thereby triggering a type I interferon response. Removal of the 5'-triphosphate from gRNAs ameliorates inflammatory signaling and prevents the loss of viability associated with genome editing in hematopoietic stem cells. The potential for Cas9 RNP editing to induce a potent antiviral response indicates that care must be taken when designing therapeutic strategies to edit primary cells.
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Affiliation(s)
- Beeke Wienert
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Jiyung Shin
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Elena Zelin
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Kathleen Pestal
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
| | - Jacob E. Corn
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, United States of America
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, United States of America
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34
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Simeonov DR, Gowen BG, Boontanrart M, Roth TL, Gagnon JD, Mumbach MR, Satpathy AT, Lee Y, Bray NL, Chan AY, Lituiev DS, Nguyen ML, Gate RE, Subramaniam M, Li Z, Woo JM, Mitros T, Ray GJ, Curie GL, Naddaf N, Chu JS, Ma H, Boyer E, Van Gool F, Huang H, Liu R, Tobin VR, Schumann K, Daly MJ, Farh KK, Ansel KM, Ye CJ, Greenleaf WJ, Anderson MS, Bluestone JA, Chang HY, Corn JE, Marson A. Author Correction: Discovery of stimulation-responsive immune enhancers with CRISPR activation. Nature 2018; 559:E13. [PMID: 29899441 DOI: 10.1038/s41586-018-0227-7] [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: 11/09/2022]
Abstract
In this Letter, analysis of steady-state regulatory T (Treg) cell percentages from Il2ra enhancer deletion (EDEL) and wild-type (WT) mice revealed no differences between them (Extended Data Fig. 9d). This analysis included two mice whose genotypes were incorrectly assigned. Even after correction of the genotypes, no significant differences in Treg cell percentages were seen when data across experimental cohorts were averaged (as was done in Extended Data Fig. 9d). However, if we normalize the corrected data to account for variation among experimental cohorts, a subtle decrease in EDEL Treg cell percentages is revealed and, using the corrected and normalized data, we have redrawn Extended Data Fig. 9d in Supplementary Fig. 1. The Supplementary Information to this Amendment contains the corrected and reanalysed Extended Data Fig. 9d. The sentence "This enhancer deletion (EDEL) strain also had no obvious T cell phenotypes at steady state (Extended Data Fig. 9)." should read: "This enhancer deletion (EDEL) strain had a small decrease in the percentage of Treg cells (Extended Data Fig. 9).". This error does not affect any of the main figures in the Letter or the data from mice with the human autoimmune-associated single nucleotide polymorphism (SNP) knocked in or with a 12-base-pair deletion at the site (12DEL). In addition, we stated in the Methods that we observed consistent immunophenotypes of EDEL mice across three founders, but in fact, we observed consistent phenotypes in mice from two founders. This does not change any of our conclusions and the original Letter has not been corrected.
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Affiliation(s)
- Dimitre R Simeonov
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Benjamin G Gowen
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Mandy Boontanrart
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Theodore L Roth
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - John D Gagnon
- Biomedical Sciences Graduate Program, University of California, San Francisco, California, 94143, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Sandler Asthma Basic Research Center, University of California, San Francisco, California, 94143, USA
| | - Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Youjin Lee
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Nicolas L Bray
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Alice Y Chan
- Diabetes Center, University of California, San Francisco, California, 94143, USA.,Department of Pediatrics, University of California, San Francisco, California, 94143, USA
| | - Dmytro S Lituiev
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA
| | - Michelle L Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Rachel E Gate
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA.,Biological and Medical Informatics Graduate Program, University of California, San Francisco, California, 94158, USA
| | - Meena Subramaniam
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA.,Biological and Medical Informatics Graduate Program, University of California, San Francisco, California, 94158, USA
| | - Zhongmei Li
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Jonathan M Woo
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Therese Mitros
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Graham J Ray
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Gemma L Curie
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Nicki Naddaf
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Julia S Chu
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Hong Ma
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA
| | - Eric Boyer
- Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Frederic Van Gool
- Diabetes Center, University of California, San Francisco, California, 94143, USA
| | - Hailiang Huang
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Ruize Liu
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Victoria R Tobin
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Kathrin Schumann
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Diabetes Center, University of California, San Francisco, California, 94143, USA.,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA
| | - Mark J Daly
- Broad Institute of MIT and Harvard, Cambridge, Massachusetts, 02142, USA.,Analytic and Translational Genetics Unit, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts, 02114, USA
| | - Kyle K Farh
- Illumina Inc., 5200 Illumina Way, San Diego, California, 92122, USA
| | - K Mark Ansel
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA.,Sandler Asthma Basic Research Center, University of California, San Francisco, California, 94143, USA
| | - Chun J Ye
- Department of Epidemiology and Biostatistics, Department of Bioengineering and Therapeutic Sciences, Institute for Human Genetics (IHG), University of California, San Francisco, California, 94143, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, 94305, USA.,Department of Applied Physics, Stanford University, Stanford, California, 94025, USA.,Chan Zuckerberg Biohub, San Francisco, California, 94158, USA
| | - Mark S Anderson
- Diabetes Center, University of California, San Francisco, California, 94143, USA.,Department of Medicine, University of California, San Francisco, California, 94143, USA
| | - Jeffrey A Bluestone
- Diabetes Center, University of California, San Francisco, California, 94143, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, 94305, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, 94305, USA
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA. .,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, 94720, USA.
| | - Alexander Marson
- Department of Microbiology and Immunology, University of California, San Francisco, California, 94143, USA. .,Diabetes Center, University of California, San Francisco, California, 94143, USA. .,Innovative Genomics Institute, University of California, Berkeley, California, 94720, USA. .,Chan Zuckerberg Biohub, San Francisco, California, 94158, USA. .,Department of Medicine, University of California, San Francisco, California, 94143, USA. .,UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, California, 94158, USA.
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35
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Farboud B, Jarvis E, Roth TL, Shin J, Corn JE, Marson A, Meyer BJ, Patel NH, Hochstrasser ML. Enhanced Genome Editing with Cas9 Ribonucleoprotein in Diverse Cells and Organisms. J Vis Exp 2018:57350. [PMID: 29889198 PMCID: PMC6101420 DOI: 10.3791/57350] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Site-specific eukaryotic genome editing with CRISPR (clustered regularly interspaced short palindromic repeats)-Cas (CRISPR-associated) systems has quickly become a commonplace amongst researchers pursuing a wide variety of biological questions. Users most often employ the Cas9 protein derived from Streptococcus pyogenes in a complex with an easily reprogrammed guide RNA (gRNA). These components are introduced into cells, and through a base pairing with a complementary region of the double-stranded DNA (dsDNA) genome, the enzyme cleaves both strands to generate a double-strand break (DSB). Subsequent repair leads to either random insertion or deletion events (indels) or the incorporation of experimenter-provided DNA at the site of the break. The use of a purified single-guide RNA and Cas9 protein, preassembled to form an RNP and delivered directly to cells, is a potent approach for achieving highly efficient gene editing. RNP editing particularly enhances the rate of gene insertion, an outcome that is often challenging to achieve. Compared to the delivery via a plasmid, the shorter persistence of the Cas9 RNP within the cell leads to fewer off-target events. Despite its advantages, many casual users of CRISPR gene editing are less familiar with this technique. To lower the barrier to entry, we outline detailed protocols for implementing the RNP strategy in a range of contexts, highlighting its distinct benefits and diverse applications. We cover editing in two types of primary human cells, T cells and hematopoietic stem/progenitor cells (HSPCs). We also show how Cas9 RNP editing enables the facile genetic manipulation of entire organisms, including the classic model roundworm Caenorhabditis elegans and the more recently introduced model crustacean, Parhyale hawaiensis.
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Affiliation(s)
- Behnom Farboud
- Department of Molecular Cell Biology, University of California, Berkeley; Howard Hughes Medical Institute, University of California, Berkeley
| | - Erin Jarvis
- Department of Molecular Cell Biology, University of California, Berkeley
| | - Theodore L Roth
- Innovative Genomics Institute, University of California, Berkeley; Biomedical Sciences Graduate Program, University of California, San Francisco; Department of Microbiology and Immunology, University of California, San Francisco; Diabetes Center, University of California, San Francisco
| | - Jiyung Shin
- Department of Molecular Cell Biology, University of California, Berkeley; Innovative Genomics Institute, University of California, Berkeley
| | - Jacob E Corn
- Department of Molecular Cell Biology, University of California, Berkeley; Innovative Genomics Institute, University of California, Berkeley
| | - Alexander Marson
- Innovative Genomics Institute, University of California, Berkeley; Department of Microbiology and Immunology, University of California, San Francisco; Diabetes Center, University of California, San Francisco; Chan Zuckerberg Biohub; Department of Medicine, University of California, San Francisco; UCSF Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco
| | - Barbara J Meyer
- Department of Molecular Cell Biology, University of California, Berkeley; Howard Hughes Medical Institute, University of California, Berkeley
| | - Nipam H Patel
- Department of Molecular Cell Biology, University of California, Berkeley; Department of Integrative Biology, University of California, Berkeley
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36
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Abstract
CRISPR-Cas systems have been harnessed as modular genome editing reagents for functional genomics and show promise to cure genetic diseases. Directed by a guide RNA, a Cas effector introduces a double stranded break in DNA and host cell DNA repair leads to the introduction of errors (e.g., to knockout a gene) or a programmed change. Introduction of a Cas effector and guide RNA as a purified Cas ribonucleoprotein complex (CasRNP) has recently emerged as a powerful approach to alter cell types and organisms. Not only does CasRNP editing exhibit increased efficacy and specificity, it avoids optimization and iteration of species-specific factors such as codon usage, promoters, and terminators. CasRNP editing has been rapidly adopted for research use in many contexts and is quickly becoming a popular method to edit primary cells for therapeutic application. This article describes how to make a Cas9 RNP and outlines its use for gene editing in human cells. © 2017 by John Wiley & Sons, Inc.
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Affiliation(s)
- Emily Lingeman
- Department of Molecular and Cell Biology, University of California, Berkeley, California
- Innovative Genomics Institute, University of California, Berkeley, California
| | - Chris Jeans
- QB3 MacroLab, University of California, Berkeley, California
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, California
- Innovative Genomics Institute, University of California, Berkeley, California
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37
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Mumbach MR, Satpathy AT, Boyle EA, Dai C, Gowen BG, Cho SW, Nguyen ML, Rubin AJ, Granja JM, Kazane KR, Wei Y, Nguyen T, Greenside PG, Corces MR, Tycko J, Simeonov DR, Suliman N, Li R, Xu J, Flynn RA, Kundaje A, Khavari PA, Marson A, Corn JE, Quertermous T, Greenleaf WJ, Chang HY. Enhancer connectome in primary human cells identifies target genes of disease-associated DNA elements. Nat Genet 2017; 49:1602-1612. [PMID: 28945252 DOI: 10.1038/ng.3963] [Citation(s) in RCA: 305] [Impact Index Per Article: 43.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 09/01/2017] [Indexed: 12/14/2022]
Abstract
The challenge of linking intergenic mutations to target genes has limited molecular understanding of human diseases. Here we show that H3K27ac HiChIP generates high-resolution contact maps of active enhancers and target genes in rare primary human T cell subtypes and coronary artery smooth muscle cells. Differentiation of naive T cells into T helper 17 cells or regulatory T cells creates subtype-specific enhancer-promoter interactions, specifically at regions of shared DNA accessibility. These data provide a principled means of assigning molecular functions to autoimmune and cardiovascular disease risk variants, linking hundreds of noncoding variants to putative gene targets. Target genes identified with HiChIP are further supported by CRISPR interference and activation at linked enhancers, by the presence of expression quantitative trait loci, and by allele-specific enhancer loops in patient-derived primary cells. The majority of disease-associated enhancers contact genes beyond the nearest gene in the linear genome, leading to a fourfold increase in the number of potential target genes for autoimmune and cardiovascular diseases.
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Affiliation(s)
- Maxwell R Mumbach
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Ansuman T Satpathy
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Pathology, Stanford University School of Medicine, Stanford, California, USA
| | - Evan A Boyle
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Chao Dai
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Benjamin G Gowen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Seung Woo Cho
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Michelle L Nguyen
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA
| | - Adam J Rubin
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Jeffrey M Granja
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Katelynn R Kazane
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Yuning Wei
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Trieu Nguyen
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Peyton G Greenside
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - M Ryan Corces
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Josh Tycko
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Dimitre R Simeonov
- Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Biomedical Sciences Graduate Program, University of California, San Francisco, San Francisco, California, USA
| | - Nabeela Suliman
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Rui Li
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Jin Xu
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA
| | - Anshul Kundaje
- Department of Genetics, Stanford University School of Medicine, Stanford, California, USA
| | - Paul A Khavari
- Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
| | - Alexander Marson
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA.,Department of Microbiology and Immunology, University of California, San Francisco, San Francisco, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA.,Innovative Genomics Institute, University of California, Berkeley, Berkeley, California, USA
| | - Thomas Quertermous
- Department of Medicine, Division of Cardiovascular Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - William J Greenleaf
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, California, USA.,Chan Zuckerberg Biohub, San Francisco, California, USA.,Department of Applied Physics, Stanford University, Stanford, California, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, California, USA.,Program in Epithelial Biology, Stanford University School of Medicine, Stanford, California, USA
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Tesar D, Luoma J, Wyatt EA, Shi C, Shatz W, Hass PE, Mathieu M, Yi L, Corn JE, Maass KF, Wang K, Dion MZ, Andersen N, Loyet KM, van Lookeren Campagne M, Rajagopal K, Dickmann L, Scheer JM, Kelley RF. Protein engineering to increase the potential of a therapeutic antibody Fab for long-acting delivery to the eye. MAbs 2017; 9:1297-1305. [PMID: 28854082 PMCID: PMC5680807 DOI: 10.1080/19420862.2017.1372078] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [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] [Indexed: 11/30/2022] Open
Abstract
To date, ocular antibody therapies for the treatment of retinal diseases rely on injection of the drug into the vitreous chamber of the eye. Given the burden for patients undergoing this procedure, less frequent dosing through the use of long-acting delivery (LAD) technologies is highly desirable. These technologies usually require a highly concentrated formulation and the antibody must be stable against extended exposure to physiological conditions. Here we have increased the potential of a therapeutic antibody antigen-binding fragment (Fab) for LAD by using protein engineering to enhance the chemical and physical stability of the molecule. Structure-guided amino acid substitutions in a negatively charged complementarity determining region (CDR-L1) of an anti-factor D (AFD) Fab resulted in increased chemical stability and solubility. A variant of AFD (AFD.v8), which combines light chain substitutions (VL-D28S:D30E:D31S) with a substitution (VH-D61E) to stabilize a heavy chain isomerization site, retained complement factor D binding and inhibition potency and has properties suitable for LAD. This variant was amenable to high protein concentration (>250 mg/mL), low ionic strength formulation suitable for intravitreal injection. AFD.v8 had acceptable pharmacokinetic (PK) properties upon intravitreal injection in rabbits, and improved stability under both formulation and physiological conditions. Simulations of expected human PK behavior indicated greater exposure with a 25-mg dose enabled by the increased solubility of AFD.v8.
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Affiliation(s)
- Devin Tesar
- a Departments of Drug Delivery , South San Francisco , CA
| | - Jacob Luoma
- a Departments of Drug Delivery , South San Francisco , CA
| | - Emily A Wyatt
- a Departments of Drug Delivery , South San Francisco , CA
| | - Catherine Shi
- a Departments of Drug Delivery , South San Francisco , CA
| | - Whitney Shatz
- b Departments of Protein Chemistry , South San Francisco , CA
| | - Philip E Hass
- b Departments of Protein Chemistry , South San Francisco , CA
| | - Mary Mathieu
- c Departments of Antibody Engineering , South San Francisco , CA
| | - Li Yi
- d Departments of Pharmaceutical Development , South San Francisco , CA
| | - Jacob E Corn
- e Departments of Early Discovery Biochemistry , South San Francisco , CA
| | - Katie F Maass
- f Departments of Clinical Pharmacology , South San Francisco , CA
| | - Kathryn Wang
- a Departments of Drug Delivery , South San Francisco , CA
| | | | - Nisana Andersen
- g Departments of Protein Analytical Chemistry , South San Francisco , CA
| | - Kelly M Loyet
- h Departments of Biochemical and Cellular Pharmacology , South San Francisco , CA
| | | | | | - Leslie Dickmann
- f Departments of Clinical Pharmacology , South San Francisco , CA
| | - Justin M Scheer
- b Departments of Protein Chemistry , South San Francisco , CA
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39
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Shin J, Jiang F, Liu JJ, Bray NL, Rauch BJ, Baik SH, Nogales E, Bondy-Denomy J, Corn JE, Doudna JA. Disabling Cas9 by an anti-CRISPR DNA mimic. Sci Adv 2017; 3:e1701620. [PMID: 28706995 PMCID: PMC5507636 DOI: 10.1126/sciadv.1701620] [Citation(s) in RCA: 233] [Impact Index Per Article: 33.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/15/2017] [Accepted: 06/14/2017] [Indexed: 05/24/2023]
Abstract
CRISPR (clustered regularly interspaced short palindromic repeats)-Cas9 gene editing technology is derived from a microbial adaptive immune system, where bacteriophages are often the intended target. Natural inhibitors of CRISPR-Cas9 enable phages to evade immunity and show promise in controlling Cas9-mediated gene editing in human cells. However, the mechanism of CRISPR-Cas9 inhibition is not known, and the potential applications for Cas9 inhibitor proteins in mammalian cells have not been fully established. We show that the anti-CRISPR protein AcrIIA4 binds only to assembled Cas9-single-guide RNA (sgRNA) complexes and not to Cas9 protein alone. A 3.9 Å resolution cryo-electron microscopy structure of the Cas9-sgRNA-AcrIIA4 complex revealed that the surface of AcrIIA4 is highly acidic and binds with a 1:1 stoichiometry to a region of Cas9 that normally engages the DNA protospacer adjacent motif. Consistent with this binding mode, order-of-addition experiments showed that AcrIIA4 interferes with DNA recognition but has no effect on preformed Cas9-sgRNA-DNA complexes. Timed delivery of AcrIIA4 into human cells as either protein or expression plasmid allows on-target Cas9-mediated gene editing while reducing off-target edits. These results provide a mechanistic understanding of AcrIIA4 function and demonstrate that inhibitors can modulate the extent and outcomes of Cas9-mediated gene editing.
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Affiliation(s)
- Jiyung Shin
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Fuguo Jiang
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
| | - Jun-Jie Liu
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Nicolas L. Bray
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Benjamin J. Rauch
- Department of Microbiology and Immunology and Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Seung Hyun Baik
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Eva Nogales
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Joseph Bondy-Denomy
- Department of Microbiology and Immunology and Quantitative Biosciences Institute, University of California, San Francisco, San Francisco, CA 94158, USA
| | - Jacob E. Corn
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer A. Doudna
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- California Institute for Quantitative Biosciences, University of California, Berkeley, CA 94720, USA
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
- Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
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40
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Abstract
The CRISPR-Cas genome editing system is very powerful. The format of the CRISPR reagents and the means of delivery are often important factors in targeting efficiency. Delivery of recombinant Cas9 protein and guide RNA (gRNA) as a preformed ribonucleoprotein (RNP) complex has recently emerged as a powerful and general approach to genome editing. Here we outline methods to produce and deliver Cas9 RNPs. A donor DNA carrying desired sequence changes can also be included to program precise sequence introduction or replacement. RNP delivery limits exposure to genome editing reagents, reduces off-target events, drives high rates of homology-dependent repair, and can be applied to embryos to rapidly generate animal models. RNP delivery thus minimizes some of the pitfalls of alternative editing modalities and is rapidly being adopted by the genome editing community.
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Affiliation(s)
- Mark A DeWitt
- Innovative Genomics Institute, University of California, Berkeley, CA, United States
| | - Jacob E Corn
- Innovative Genomics Institute, University of California, Berkeley, CA, United States; Department of Molecular and Cell Biology, University of California, Berkeley, CA, United States
| | - Dana Carroll
- Innovative Genomics Institute, University of California, Berkeley, CA, United States; Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT, United States
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41
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Lee K, Mackley VA, Rao A, Chong AT, Dewitt MA, Corn JE, Murthy N. Synthetically modified guide RNA and donor DNA are a versatile platform for CRISPR-Cas9 engineering. eLife 2017; 6:e25312. [PMID: 28462777 PMCID: PMC5413346 DOI: 10.7554/elife.25312] [Citation(s) in RCA: 94] [Impact Index Per Article: 13.4] [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: 01/20/2017] [Accepted: 03/31/2017] [Indexed: 11/18/2022] Open
Abstract
Chemical modification of the gRNA and donor DNA has great potential for improving the gene editing efficiency of Cas9 and Cpf1, but has not been investigated extensively. In this report, we demonstrate that the gRNAs of Cas9 and Cpf1, and donor DNA can be chemically modified at their terminal positions without losing activity. Moreover, we show that 5' fluorescently labeled donor DNA can be used as a marker to enrich HDR edited cells by a factor of two through cell sorting. In addition, we demonstrate that the gRNA and donor DNA can be directly conjugated together into one molecule, and show that this gRNA-donor DNA conjugate is three times better at transfecting cells and inducing HDR, with cationic polymers, than unconjugated gRNA and donor DNA. The tolerance of the gRNA and donor DNA to chemical modifications has the potential to enable new strategies for genome engineering.
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Affiliation(s)
| | | | - Anirudh Rao
- Department of Bioengineering, University of California, Berkeley, Berkeley, United States
| | - Anthony T Chong
- Department of Bioengineering, University of California, Berkeley, Berkeley, United States
| | - Mark A Dewitt
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Jacob E Corn
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
- Innovative Genomics Institute, University of California, Berkeley, Berkeley, United States
| | - Niren Murthy
- Department of Bioengineering, University of California, Berkeley, Berkeley, United States
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42
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Dillon M, Yin Y, Zhou J, McCarty L, Ellerman D, Slaga D, Junttila TT, Han G, Sandoval W, Ovacik MA, Lin K, Hu Z, Shen A, Corn JE, Spiess C, Carter PJ. Efficient production of bispecific IgG of different isotypes and species of origin in single mammalian cells. MAbs 2016; 9:213-230. [PMID: 27929752 PMCID: PMC5297516 DOI: 10.1080/19420862.2016.1267089] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [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] [Indexed: 01/07/2023] Open
Abstract
Bispecific IgG production in single host cells has been a much sought-after goal to support the clinical development of these complex molecules. Current routes to single cell production of bispecific IgG include engineering heavy chains for heterodimerization and redesign of Fab arms for selective pairing of cognate heavy and light chains. Here, we describe novel designs to facilitate selective Fab arm assembly in conjunction with previously described knobs-into-holes mutations for preferential heavy chain heterodimerization. The top Fab designs for selective pairing, namely variants v10 and v11, support near quantitative assembly of bispecific IgG in single cells for multiple different antibody pairs as judged by high-resolution mass spectrometry. Single-cell and in vitro-assembled bispecific IgG have comparable physical, in vitro biological and in vivo pharmacokinetics properties. Efficient single-cell production of bispecific IgG was demonstrated for human IgG1, IgG2 and IgG4 thereby allowing the heavy chain isotype to be tailored for specific therapeutic applications. Additionally, a reverse chimeric bispecific IgG2a with humanized variable domains and mouse constant domains was generated for preclinical proof-of-concept studies in mice. Efficient production of a bispecific IgG in stably transfected mammalian (CHO) cells was shown. Individual clones with stable titer and bispecific IgG composition for >120 days were readily identified. Such long-term cell line stability is needed for commercial manufacture of bispecific IgG. The single-cell bispecific IgG designs developed here may be broadly applicable to biotechnology research, including screening bispecific IgG panels, and to support clinical development.
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Affiliation(s)
- Michael Dillon
- a Department of Antibody Engineering , Genentech, Inc. , South San Francisco , CA , USA
| | - Yiyuan Yin
- a Department of Antibody Engineering , Genentech, Inc. , South San Francisco , CA , USA
| | - Jianhui Zhou
- a Department of Antibody Engineering , Genentech, Inc. , South San Francisco , CA , USA
| | - Luke McCarty
- b Department of Protein Chemistry , Genentech, Inc. , South San Francisco , CA , USA
| | - Diego Ellerman
- b Department of Protein Chemistry , Genentech, Inc. , South San Francisco , CA , USA
| | - Dionysos Slaga
- c Department of Translational Oncology , Genentech, Inc. , South San Francisco , CA , USA
| | - Teemu T Junttila
- c Department of Translational Oncology , Genentech, Inc. , South San Francisco , CA , USA
| | - Guanghui Han
- d Department of Microchemistry, Proteomics and Lipidomics , Genentech, Inc. , South San Francisco , CA , USA
| | - Wendy Sandoval
- d Department of Microchemistry, Proteomics and Lipidomics , Genentech, Inc. , South San Francisco , CA , USA
| | - Meric A Ovacik
- e Department of Preclinical and Translational Pharmacokinetics , Genentech, Inc. , South San Francisco , CA , USA
| | - Kedan Lin
- e Department of Preclinical and Translational Pharmacokinetics , Genentech, Inc. , South San Francisco , CA , USA
| | - Zhilan Hu
- f Department of Early Stage Cell Culture , Genentech, Inc. , South San Francisco , CA , USA
| | - Amy Shen
- f Department of Early Stage Cell Culture , Genentech, Inc. , South San Francisco , CA , USA
| | - Jacob E Corn
- g Department of Early Discovery Biochemistry, Genentech, Inc. , South San Francisco , CA , USA
| | - Christoph Spiess
- a Department of Antibody Engineering , Genentech, Inc. , South San Francisco , CA , USA
| | - Paul J Carter
- a Department of Antibody Engineering , Genentech, Inc. , South San Francisco , CA , USA
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43
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DeWitt MA, Magis W, Bray NL, Wang T, Berman JR, Urbinati F, Heo SJ, Mitros T, Muñoz DP, Boffelli D, Kohn DB, Walters MC, Carroll D, Martin DIK, Corn JE. Selection-free genome editing of the sickle mutation in human adult hematopoietic stem/progenitor cells. Sci Transl Med 2016; 8:360ra134. [PMID: 27733558 PMCID: PMC5500303 DOI: 10.1126/scitranslmed.aaf9336] [Citation(s) in RCA: 317] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Accepted: 09/22/2016] [Indexed: 12/19/2022]
Abstract
Genetic diseases of blood cells are prime candidates for treatment through ex vivo gene editing of CD34+ hematopoietic stem/progenitor cells (HSPCs), and a variety of technologies have been proposed to treat these disorders. Sickle cell disease (SCD) is a recessive genetic disorder caused by a single-nucleotide polymorphism in the β-globin gene (HBB). Sickle hemoglobin damages erythrocytes, causing vasoocclusion, severe pain, progressive organ damage, and premature death. We optimize design and delivery parameters of a ribonucleoprotein (RNP) complex comprising Cas9 protein and unmodified single guide RNA, together with a single-stranded DNA oligonucleotide donor (ssODN), to enable efficient replacement of the SCD mutation in human HSPCs. Corrected HSPCs from SCD patients produced less sickle hemoglobin RNA and protein and correspondingly increased wild-type hemoglobin when differentiated into erythroblasts. When engrafted into immunocompromised mice, ex vivo treated human HSPCs maintain SCD gene edits throughout 16 weeks at a level likely to have clinical benefit. These results demonstrate that an accessible approach combining Cas9 RNP with an ssODN can mediate efficient HSPC genome editing, enables investigator-led exploration of gene editing reagents in primary hematopoietic stem cells, and suggests a path toward the development of new gene editing treatments for SCD and other hematopoietic diseases.
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Affiliation(s)
- Mark A DeWitt
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA. Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Wendy Magis
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Nicolas L Bray
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA. Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Tianjiao Wang
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA. Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Jennifer R Berman
- Digital Biology Center, Bio-Rad Laboratories, Pleasanton, CA 94588, USA
| | - Fabrizia Urbinati
- Departments of Microbiology, Immunology, and Molecular Genetics; Pediatrics; and Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Seok-Jin Heo
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Therese Mitros
- Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Denise P Muñoz
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Dario Boffelli
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Donald B Kohn
- Departments of Microbiology, Immunology, and Molecular Genetics; Pediatrics; and Molecular and Medical Pharmacology, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Mark C Walters
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA. Blood and Marrow Transplant Program, Division of Hematology, UCSF Benioff Children's Hospital, Oakland, CA 94609, USA
| | - Dana Carroll
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA. Department of Biochemistry, University of Utah School of Medicine, Salt Lake City, UT 84112, USA.
| | - David I K Martin
- Children's Hospital Oakland Research Institute, University of California San Francisco (UCSF) Benioff Children's Hospital, Oakland, CA 94609, USA.
| | - Jacob E Corn
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, CA 94720, USA. Department of Molecular and Cellular Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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44
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Horlbeck MA, Gilbert LA, Villalta JE, Adamson B, Pak RA, Chen Y, Fields AP, Park CY, Corn JE, Kampmann M, Weissman JS. Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation. eLife 2016; 5:e19760. [PMID: 27661255 PMCID: PMC5094855 DOI: 10.7554/elife.19760] [Citation(s) in RCA: 455] [Impact Index Per Article: 56.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 09/22/2016] [Indexed: 12/16/2022] Open
Abstract
We recently found that nucleosomes directly block access of CRISPR/Cas9 to DNA (Horlbeck et al., 2016). Here, we build on this observation with a comprehensive algorithm that incorporates chromatin, position, and sequence features to accurately predict highly effective single guide RNAs (sgRNAs) for targeting nuclease-dead Cas9-mediated transcriptional repression (CRISPRi) and activation (CRISPRa). We use this algorithm to design next-generation genome-scale CRISPRi and CRISPRa libraries targeting human and mouse genomes. A CRISPRi screen for essential genes in K562 cells demonstrates that the large majority of sgRNAs are highly active. We also find CRISPRi does not exhibit any detectable non-specific toxicity recently observed with CRISPR nuclease approaches. Precision-recall analysis shows that we detect over 90% of essential genes with minimal false positives using a compact 5 sgRNA/gene library. Our results establish CRISPRi and CRISPRa as premier tools for loss- or gain-of-function studies and provide a general strategy for identifying Cas9 target sites.
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Affiliation(s)
- Max A Horlbeck
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Luke A Gilbert
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Jacqueline E Villalta
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Britt Adamson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Ryan A Pak
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, United States
| | - Yuwen Chen
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Alexander P Fields
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
| | - Chong Yon Park
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, United States
| | - Jacob E Corn
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, United States
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, United States
| | - Martin Kampmann
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
- Institute for Neurodegenerative Diseases, University of California, San Francisco, San Francisco, United states
| | - Jonathan S Weissman
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, San Francisco, United States
- Howard Hughes Medical Institute, University of California, San Francisco, San Francisco, United States
- California Institute for Quantitative Biomedical Research, University of California, San Francisco, San Francisco, United States
- Center for RNA Systems Biology, University of California, San Francisco, San Francisco, United States
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45
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Richardson CD, Ray GJ, DeWitt MA, Curie GL, Corn JE. Enhancing homology-directed genome editing by catalytically active and inactive CRISPR-Cas9 using asymmetric donor DNA. Nat Biotechnol 2016; 34:339-44. [PMID: 26789497 DOI: 10.1038/nbt.3481] [Citation(s) in RCA: 719] [Impact Index Per Article: 89.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2015] [Accepted: 01/13/2016] [Indexed: 12/31/2022]
Abstract
Targeted genomic manipulation by Cas9 can efficiently generate knockout cells and organisms via error-prone nonhomologous end joining (NHEJ), but the efficiency of precise sequence replacement by homology-directed repair (HDR) is substantially lower. Here we investigate the interaction of Cas9 with target DNA and use our findings to improve HDR efficiency. We show that dissociation of Cas9 from double-stranded DNA (dsDNA) substrates is slow (lifetime ∼6 h) but that, before complete dissociation, Cas9 asymmetrically releases the 3' end of the cleaved DNA strand that is not complementary to the sgRNA (nontarget strand). By rationally designing single-stranded DNA (ssDNA) donors of the optimal length complementary to the strand that is released first, we increase the rate of HDR in human cells when using Cas9 or nickase variants to up to 60%. We also demonstrate HDR rates of up to 0.7% using a catalytically inactive Cas9 mutant (dCas9), which binds DNA without cleaving it.
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Affiliation(s)
- Christopher D Richardson
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Graham J Ray
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Mark A DeWitt
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Gemma L Curie
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
| | - Jacob E Corn
- Innovative Genomics Initiative, University of California, Berkeley, Berkeley, California, USA.,Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, California, USA
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46
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Abstract
Eukaryotes use a tiny protein called ubiquitin to send a variety of signals, most often by post-translationally attaching ubiquitins to substrate proteins and to each other, thereby forming polyubiquitin chains. A combination of biophysical, biochemical, and biological studies has shown that complex macromolecular dynamics are central to many aspects of ubiquitin signaling. This review focuses on how equilibrium fluctuations and coordinated motions of ubiquitin itself, the ubiquitin conjugation machinery, and deubiquitinating enzymes enable activity and regulation on many levels, with implications for how such a tiny protein can send so many signals.
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Affiliation(s)
- Aaron H Phillips
- From the Innovative Genomics Initiative, University of California, Berkeley, California 94702
| | - Jacob E Corn
- From the Innovative Genomics Initiative, University of California, Berkeley, California 94702
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47
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Baltimore D, Berg P, Botchan M, Carroll D, Charo RA, Church G, Corn JE, Daley GQ, Doudna JA, Fenner M, Greely HT, Jinek M, Martin GS, Penhoet E, Puck J, Sternberg SH, Weissman JS, Yamamoto KR. Biotechnology. A prudent path forward for genomic engineering and germline gene modification. Science 2015; 348:36-8. [PMID: 25791083 DOI: 10.1126/science.aab1028] [Citation(s) in RCA: 305] [Impact Index Per Article: 33.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- David Baltimore
- California Institute of Technology, Mail Code 147-75, Pasadena, CA 91125, USA
| | - Paul Berg
- Stanford University School of Medicine, 291 Campus Drive, Stanford, CA 94305, USA
| | - Michael Botchan
- University of California, Berkeley, 450 Li Ka Shing no. 3370, Berkeley, CA 94720-3370, USA. Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA
| | - Dana Carroll
- Department of Biochemistry, University of Utah School of Medicine, 15 North Medical Drive East, Room 4100, Salt Lake City, UT 84112-5650, USA
| | - R Alta Charo
- Department of Medical History and Bioethics, School of Medicine and Public Health, University of Wisconsin Law School, 975 Bascom Mall, Madison, WI 53706, USA
| | - George Church
- Department of Genetics, Harvard Medical School, 77 Avenue Louis Pasteur, Boston, MA 02115, USA
| | - Jacob E Corn
- Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA
| | - George Q Daley
- Boston Children's Hospital, 300 Longwood Avenue, Karp Family Building, 7th Floor, Boston, MA 02115, USA. Howard Hughes Medical Institute, 4000 Jones Bridge Road, Chevy Chase, MD 20815, USA
| | - Jennifer A Doudna
- Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA. Departments of Molecular and Cell Biology and Chemistry, Howard Hughes Medical Institute, 731 Stanley Hall, MS 3220, University of California, Berkeley, Berkeley, CA 94720-3220, USA.
| | - Marsha Fenner
- Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA
| | - Henry T Greely
- Center for Law and the Biosciences, Crown Quadrangle 559 Nathan Abbott Way Stanford, CA 94305-8610, USA
| | - Martin Jinek
- Department of Biochemistry, University of Zurich, Winterthurerstrasse 190, CH-8057 Zurich, Switzerland
| | - G Steven Martin
- Department of Molecular and Cell Biology, College of Letters and Science, University of California, Berkeley, 210K Durant Hall, Berkeley, CA 94720-2920, USA
| | - Edward Penhoet
- Alta Partners, One Embarcadero Center, 37th Floor, San Francisco, CA 94111, USA
| | - Jennifer Puck
- Department of Pediatrics UCSF School of Medicine, 513 Parnassus Avenue, San Francisco, CA 94143, USA
| | - Samuel H Sternberg
- Department of Chemistry, 731 Stanley Hall, MS 3220, University of California, Berkeley, CA 94720-3220, USA
| | - Jonathan S Weissman
- Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA. Department of Cellular and Molecular Pharmacology, Howard Hughes Medical Institute, University of California, San Francisco, Byers Hall, 1700 4th Street, San Francisco, CA 94158-2330, USA
| | - Keith R Yamamoto
- Innovative Genomics Initiative, University of California, Berkeley, 188 Li Ka Shing Center, Berkeley, CA 94720-3370, USA. UCSF School of Medicine, 600 16th Street, San Francisco, CA 94158, USA
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48
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Cunningham CN, Baughman JM, Phu L, Tea JS, Yu C, Coons M, Kirkpatrick DS, Bingol B, Corn JE. USP30 and parkin homeostatically regulate atypical ubiquitin chains on mitochondria. Nat Cell Biol 2015; 17:160-9. [PMID: 25621951 DOI: 10.1038/ncb3097] [Citation(s) in RCA: 223] [Impact Index Per Article: 24.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2014] [Accepted: 12/17/2014] [Indexed: 12/30/2022]
Abstract
Multiple lines of evidence indicate that mitochondrial dysfunction is central to Parkinson's disease. Here we investigate the mechanism by which parkin, an E3 ubiquitin ligase, and USP30, a mitochondrion-localized deubiquitylase, regulate mitophagy. We find that mitochondrial damage stimulates parkin to assemble Lys 6, Lys 11 and Lys 63 chains on mitochondria, and that USP30 is a ubiquitin-specific deubiquitylase with a strong preference for cleaving Lys 6- and Lys 11-linked multimers. Using mass spectrometry, we show that recombinant USP30 preferentially removes these linkage types from intact ubiquitylated mitochondria and counteracts parkin-mediated ubiquitin chain formation in cells. These results, combined with a series of chimaera and localization studies, afford insights into the mechanism by which a balance of ubiquitylation and deubiquitylation regulates mitochondrial homeostasis, and suggest a general mechanism for organelle autophagy.
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Affiliation(s)
- Christian N Cunningham
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Joshua M Baughman
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Lilian Phu
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Joy S Tea
- Department of Neuroscience, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Christine Yu
- Department of Structural Biology, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Mary Coons
- Department of Structural Biology, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Donald S Kirkpatrick
- Department of Protein Chemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Baris Bingol
- Department of Neuroscience, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
| | - Jacob E Corn
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way South San Francisco, California 94080, USA
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49
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Affiliation(s)
- Jacob E Corn
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, USA
| | - Domagoj Vucic
- Department of Early Discovery Biochemistry, Genentech, South San Francisco, California, USA
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50
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Cunningham CN, Corn JE. Decoding a chain letter for degradation. Structure 2014; 21:1068-70. [PMID: 23823323 DOI: 10.1016/j.str.2013.06.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Abstract
Ubiquitin chains can have distinct signaling outcomes, depending on their conjugation point. In this issue of Structure, Castañeda and colleagues describe a new structure of K11 diubiquitin and investigate its recognition by effectors to target substrates to the proteasome.
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Affiliation(s)
- Christian N Cunningham
- Department of Early Discovery Biochemistry, Genentech, Inc., 1 DNA Way, South San Francisco, CA 94080, USA
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