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Stevens CS, Carmichael J, Watkinson R, Kowdle S, Reis RA, Hamane K, Jang J, Park A, Pernet O, Khamaikawin W, Hong P, Thibault P, Gowlikar A, An DS, Lee B. A temperature-sensitive and interferon-silent Sendai virus vector for CRISPR-Cas9 delivery and gene editing in primary human cells. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.05.03.592383. [PMID: 38746439 PMCID: PMC11092779 DOI: 10.1101/2024.05.03.592383] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
The transformative potential of gene editing technologies hinges on the development of safe and effective delivery methods. In this study, we developed a temperature-sensitive and interferon-silent Sendai virus (ts SeV) as a novel delivery vector for CRISPR-Cas9 and for efficient gene editing in sensitive human cell types without inducing IFN responses. ts SeV demonstrates unprecedented transduction efficiency in human CD34+ hematopoietic stem and progenitor cells (HSPCs) including transduction of the CD34+/CD38-/CD45RA-/CD90+(Thy1+)/CD49fhigh stem cell enriched subpopulation. The frequency of CCR5 editing exceeded 90% and bi-allelic CCR5 editing exceeded 70% resulting in significant inhibition of HIV-1 infection in primary human CD14+ monocytes. These results demonstrate the potential of the ts SeV platform as a safe, efficient, and flexible addition to the current gene-editing tool delivery methods, which may help to further expand the possibilities in personalized medicine and the treatment of genetic disorders.
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Affiliation(s)
- Christian S Stevens
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Jillian Carmichael
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Ruth Watkinson
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Shreyas Kowdle
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Rebecca A Reis
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Kory Hamane
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Jason Jang
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Arnold Park
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Olivier Pernet
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Wannisa Khamaikawin
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Patrick Hong
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Patricia Thibault
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Aditya Gowlikar
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
| | - Dong Sung An
- UCLA School of Nursing, Los Angeles, California, 90095
- UCLA AIDS Institute, Los Angeles, California, 90095
| | - Benhur Lee
- Department of Microbiology, Icahn School of Medicine at Mount Sinai, New York, NY 10029
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Zeng S, Lei S, Qu C, Wang Y, Teng S, Huang P. CRISPR/Cas-based gene editing in therapeutic strategies for beta-thalassemia. Hum Genet 2023; 142:1677-1703. [PMID: 37878144 DOI: 10.1007/s00439-023-02610-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 10/10/2023] [Indexed: 10/26/2023]
Abstract
Beta-thalassemia (β-thalassemia) is an autosomal recessive disorder caused by point mutations, insertions, and deletions in the HBB gene cluster, resulting in the underproduction of β-globin chains. The most severe type may demonstrate complications including massive hepatosplenomegaly, bone deformities, and severe growth retardation in children. Treatments for β-thalassemia include blood transfusion, splenectomy, and allogeneic hematopoietic stem cell transplantation (HSCT). However, long-term blood transfusions require regular iron removal therapy. For allogeneic HSCT, human lymphocyte antigen (HLA)-matched donors are rarely available, and acute graft-versus-host disease (GVHD) may occur after the transplantation. Thus, these conventional treatments are facing significant challenges. In recent years, with the advent and advancement of CRISPR (clustered regularly interspaced short palindromic repeats)/Cas9 (CRISPR-associated protein 9) gene editing technology, precise genome editing has achieved encouraging successes in basic and clinical studies for treating various genetic disorders, including β-thalassemia. Target gene-edited autogeneic HSCT helps patients avoid graft rejection and GVHD, making it a promising curative therapy for transfusion-dependent β-thalassemia (TDT). In this review, we introduce the development and mechanisms of CRISPR/Cas9. Recent advances on feasible strategies of CRISPR/Cas9 targeting three globin genes (HBB, HBG, and HBA) and targeting cell selections for β-thalassemia therapy are highlighted. Current CRISPR-based clinical trials in the treatment of β-thalassemia are summarized, which are focused on γ-globin reactivation and fetal hemoglobin reproduction in hematopoietic stem cells. Lastly, the applications of other promising CRISPR-based technologies, such as base editing and prime editing, in treating β-thalassemia and the limitations of the CRISPR/Cas system in therapeutic applications are discussed.
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Affiliation(s)
- Shujun Zeng
- The Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, People's Republic of China
| | - Shuangyin Lei
- The Second Norman Bethune Clinical College of Jilin University, Changchun, Jilin, People's Republic of China
| | - Chao Qu
- The First Norman Bethune Clinical College of Jilin University, Changchun, Jilin, People's Republic of China
| | - Yue Wang
- The Second Norman Bethune Clinical College of Jilin University, Changchun, Jilin, People's Republic of China
| | - Shuzhi Teng
- The Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, People's Republic of China.
| | - Ping Huang
- The Key Laboratory of Pathobiology, Ministry of Education, Norman Bethune College of Medicine, Jilin University, Changchun, Jilin, People's Republic of China.
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3
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Ebrahimi S, Khosravi MA, Raz A, Karimipoor M, Parvizi P. CRISPR-Cas Technology as a Revolutionary Genome Editing tool: Mechanisms and Biomedical Applications. IRANIAN BIOMEDICAL JOURNAL 2023; 27:219-46. [PMID: 37873636 PMCID: PMC10707817 DOI: 10.61186/ibj.27.5.219] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 06/14/2023] [Indexed: 12/17/2023]
Abstract
Programmable nucleases are powerful genomic tools for precise genome editing. These tools precisely recognize, remove, or change DNA at a defined site, thereby, stimulating cellular DNA repair pathways that can cause mutations or accurate replacement or deletion/insertion of a sequence. CRISPR-Cas9 system is the most potent and useful genome editing technique adapted from the defense immune system of certain bacteria and archaea against viruses and phages. In the past decade, this technology made notable progress, and at present, it has largely been used in genome manipulation to make precise gene editing in plants, animals, and human cells. In this review, we aim to explain the basic principle, mechanisms of action, and applications of this system in different areas of medicine, with emphasizing on the detection and treatment of parasitic diseases.
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Affiliation(s)
- Sahar Ebrahimi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Mohammad Ali Khosravi
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Abbasali Raz
- Malaria and Vector Research Group (MVRG), Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Morteza Karimipoor
- Molecular Medicine Department, Biotechnology Research Center (BRC), Pasteur Institute of Iran, Tehran, Iran
| | - Parviz Parvizi
- Molecular Systematics Laboratory, Parasitology Department, Pasteur Institute of Iran, Tehran, Iran
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4
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Finotti A, Gambari R. Combined approaches for increasing fetal hemoglobin (HbF) and de novo production of adult hemoglobin (HbA) in erythroid cells from β-thalassemia patients: treatment with HbF inducers and CRISPR-Cas9 based genome editing. Front Genome Ed 2023; 5:1204536. [PMID: 37529398 PMCID: PMC10387548 DOI: 10.3389/fgeed.2023.1204536] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2023] [Accepted: 06/30/2023] [Indexed: 08/03/2023] Open
Abstract
Genome editing (GE) is one of the most efficient and useful molecular approaches to correct the effects of gene mutations in hereditary monogenetic diseases, including β-thalassemia. CRISPR-Cas9 gene editing has been proposed for effective correction of the β-thalassemia mutation, obtaining high-level "de novo" production of adult hemoglobin (HbA). In addition to the correction of the primary gene mutations causing β-thalassemia, several reports demonstrate that gene editing can be employed to increase fetal hemoglobin (HbF), obtaining important clinical benefits in treated β-thalassemia patients. This important objective can be achieved through CRISPR-Cas9 disruption of genes encoding transcriptional repressors of γ-globin gene expression (such as BCL11A, SOX6, KLF-1) or their binding sites in the HBG promoter, mimicking non-deletional and deletional HPFH mutations. These two approaches (β-globin gene correction and genome editing of the genes encoding repressors of γ-globin gene transcription) can be, at least in theory, combined. However, since multiplex CRISPR-Cas9 gene editing is associated with documented evidence concerning possible genotoxicity, this review is focused on the possibility to combine pharmacologically-mediated HbF induction protocols with the "de novo" production of HbA using CRISPR-Cas9 gene editing.
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Affiliation(s)
- Alessia Finotti
- Center “Chiara Gemmo and Elio Zago” for the Research on Thalassemia, University of Ferrara, Ferrara, Italy
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
| | - Roberto Gambari
- Center “Chiara Gemmo and Elio Zago” for the Research on Thalassemia, University of Ferrara, Ferrara, Italy
- Department of Life Sciences and Biotechnology, University of Ferrara, Ferrara, Italy
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Papaioannou NY, Patsali P, Naiisseh B, Papasavva PL, Koniali L, Kurita R, Nakamura Y, Christou S, Sitarou M, Mussolino C, Cathomen T, Kleanthous M, Lederer CW. High-efficiency editing in hematopoietic stem cells and the HUDEP-2 cell line based on in vitro mRNA synthesis. Front Genome Ed 2023; 5:1141618. [PMID: 36969374 PMCID: PMC10030607 DOI: 10.3389/fgeed.2023.1141618] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2023] [Accepted: 02/17/2023] [Indexed: 03/11/2023] Open
Abstract
Introduction: Genome editing tools, such as CRISPR/Cas, TALE nucleases and, more recently, double-strand-break-independent editors, have been successfully used for gene therapy and reverse genetics. Among various challenges in the field, tolerable and efficient delivery of editors to target cells and sites, as well as independence from commercially available tools for flexibility and fast adoption of new editing technology are the most pressing. For many hematopoietic research applications, primary CD34+ cells and the human umbilical cord-derived progenitor erythroid 2 (HUDEP-2) cell line are highly informative substrates and readily accessible for in vitro manipulation. Moreover, ex vivo editing of CD34+ cells has immediate therapeutic relevance. Both cell types are sensitive to standard transfection procedures and reagents, such as lipofection with plasmid DNA, calling for more suitable methodology in order to achieve high efficiency and tolerability of editing with editors of choice. These challenges can be addressed by RNA delivery, either as a mixture of guide RNA and mRNA for CRISRP/Cas-based systems or as a mixture of mRNAs for TALENs. Compared to ribonucleoproteins or proteins, RNA as vector creates flexibility by removing dependence on commercial availability or laborious in-house preparations of novel editor proteins. Compared to DNA, RNA is less toxic and by obviating nuclear transcription and export of mRNA offers faster kinetics and higher editing efficiencies. Methods: Here, we detail an in vitro transcription protocol based on plasmid DNA templates with the addition of Anti-Reverse Cap Analog (ARCA) using T7 RNA polymerase, and poly (A) tailing using poly (A) polymerase, combined with nucleofection of HUDEP-2 and patient-derived CD34+ cells. Our protocol for RNA-based delivery employs widely available reagents and equipment and can easily be adopted for universal in vitro delivery of genome editing tools. Results and Discussion: Drawing on a common use case, we employ the protocol to target a β-globin mutation and to reactivate γ-globin expression as two potential therapies for β-hemoglobinopathies, followed by erythroid differentiation and functional analyses. Our protocol allows high editing efficiencies and unimpaired cell viability and differentiation, with scalability, suitability for functional assessment of editing outcomes and high flexibility in the application to different editors.
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Affiliation(s)
- Nikoletta Y. Papaioannou
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Petros Patsali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Basma Naiisseh
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Panayiota L. Papasavva
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Lola Koniali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Ryo Kurita
- Research and Development Department, Central Blood Institute, Blood Service Headquarters Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN BioResource Research Center, Tsukuba, Japan
| | - Soteroula Christou
- Thalassaemia Centre, State Health Services Organisation of Cyprus, Nicosia, Cyprus
| | - Maria Sitarou
- Thalassaemia Centre, State Health Services Organisation of Cyprus, Larnaca, Cyprus
| | - Claudio Mussolino
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center—University of Freiburg, Freiburg, Germany
- Center for Chronic Immunodeficiency (CCI), Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia, Cyprus
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Abstract
Sickle cell disease (SCD) results from a single base pair change in the sixth codon of the β-globin chain of hemoglobin, which promotes aggregation of deoxyhemoglobin, increasing rigidity of red blood cells and causing vaso-occlusive and hemolytic complications. Allogeneic transplant of hematopoietic stem cells (HSCs) can eliminate SCD manifestations but is limited by absence of well-matched donors and immune complications. Gene therapy with transplantation of autologous HSCs that are gene-modified may provide similar benefits without the immune complications. Much progress has been made, and patients are realizing significant clinical improvements in multiple trials using different approaches with lentiviral vector-mediated gene addition to inhibit hemoglobin aggregation. Gene editing approaches are under development to provide additional therapeutic opportunities. Gene therapy for SCD has advanced from an attractive concept to clinical reality.
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Affiliation(s)
- Shanna L White
- Department of Pediatrics, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, USA;
| | - Kevyn Hart
- Department of Human Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
| | - Donald B Kohn
- Department of Pediatrics, Division of Hematology/Oncology, David Geffen School of Medicine, University of California, Los Angeles, USA;
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, USA
- The Eli & Edythe Broad Center of Regenerative Medicine and Stem Cell Research at UCLA, David Geffen School of Medicine, University of California, Los Angeles, USA
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Li H, Lin R, Li H, Ou R, Wang K, Lin J, Li C. MicroRNA-92a-3p-mediated inhibition of BCL11A upregulates γ-globin expression and inhibits oxidative stress and apoptosis in erythroid precursor cells. HEMATOLOGY (AMSTERDAM, NETHERLANDS) 2022; 27:1152-1162. [PMID: 36178486 DOI: 10.1080/16078454.2022.2128258] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
OBJECTIVE This study attempted to investigate miR-92a-3p expression in peripheral blood of patients with severe β-thalassemia, and the effect and action mechanism of miR-92a-3p on γ-globin expression and oxidative stress in erythroid precursor cells. METHODS CD34+ hematopoietic progenitor cells (HPCs) were isolated from peripheral blood of healthy volunteers and patients with severe β-thalassemia. The levels of miR-92a-3p, BCL11A, and γ-globin were measured in erythroid precursor cells. High-performance liquid chromatography (HPLC) was used to analyze hemoglobin F (HbF) content. HPCs were induced with erythroid differentiation and erythroid precursor cells were then obtained. The relevance between miR-92a-3p and BCL11A was studied using dual luciferase reporter gene assay, and the correlation between miR-92a-3p and HbF was assayed by Pearson correlation analysis. Reactive oxygen species (ROS), glutathione (GSH), malondialdehyde (MDA), and superoxide dismutase (SOD) in erythroid precursor cells were tested to evaluate oxidative stress. Cell apoptosis was examined by flow cytometry. RESULTS Remarkably higher expression of miR-92a-3p was observed in erythroid precursor cells. Increased expression of miR-92a-3p resulted in elevated levels of γ-globin, GSH, and SOD, reduced expression of ROS and MDA, and decreased cell apoptosis. BCL11A was identified as a target of miR-92a-3p and to be downregulated by miR-92a-3p. Moreover, BCL11A knockdown alone increased the expression of γ-globin, SOD and GSH, and repressed the levels of ROS and MDA and cell apoptosis, and the following inhibition of miR-92a-3p changed these patterns. CONCLUSIONS Our data indicated that miR-92a-3p might increase γ-globin level and reduce oxidative stress and apoptosis in erythroid precursor cells by downregulating BCL11A.
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Affiliation(s)
- Huili Li
- Department of Pediatrics, The First School of Clinical Medicine, Southern Medical University, Guangzhou, People's Republic of China
| | - Ruoping Lin
- Department of Pediatrics, Huizhou First Maternal and Child Health Care Hospital, Huizhou, People's Republic of China
| | - Huan Li
- Department of Laboratory, Nanfang-Chunfu Children's Institute of Hematology & Oncology, Dongguan, People's Republic of China
| | - Rilan Ou
- Department of Laboratory, Nanfang-Chunfu Children's Institute of Hematology & Oncology, Dongguan, People's Republic of China
| | - Kaiping Wang
- Department of Pediatrics, Huizhou First Maternal and Child Health Care Hospital, Huizhou, People's Republic of China
| | - Junrong Lin
- Department of Pediatrics, Huizhou First Maternal and Child Health Care Hospital, Huizhou, People's Republic of China
| | - Chunfu Li
- Department of Pediatrics, The First School of Clinical Medicine, Southern Medical University, Guangzhou, People's Republic of China
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8
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Porteus MH, Pavel-Dinu M, Pai SY. A Curative DNA Code for Hematopoietic Defects: Novel Cell Therapies for Monogenic Diseases of the Blood and Immune System. Hematol Oncol Clin North Am 2022; 36:647-665. [PMID: 35773054 PMCID: PMC9365196 DOI: 10.1016/j.hoc.2022.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew H Porteus
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford Medical School, Lokey Stem Cell Research Building, G3040B, MC 5462, 265 Campus Drive, Stanford, CA 94305, USA.
| | - Mara Pavel-Dinu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford Medical School, Lokey Stem Cell Research Building, G3045, MC 5175, 265 Campus Drive, Stanford, CA 94305, USA.
| | - Sung-Yun Pai
- Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, 10 Center Drive, MSC 1102, Bethesda, MD 20892, USA
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Qin S, Tang X, Chen Y, Chen K, Fan N, Xiao W, Zheng Q, Li G, Teng Y, Wu M, Song X. mRNA-based therapeutics: powerful and versatile tools to combat diseases. Signal Transduct Target Ther 2022; 7:166. [PMID: 35597779 PMCID: PMC9123296 DOI: 10.1038/s41392-022-01007-w] [Citation(s) in RCA: 201] [Impact Index Per Article: 100.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Revised: 04/04/2022] [Accepted: 04/19/2022] [Indexed: 02/06/2023] Open
Abstract
The therapeutic use of messenger RNA (mRNA) has fueled great hope to combat a wide range of incurable diseases. Recent rapid advances in biotechnology and molecular medicine have enabled the production of almost any functional protein/peptide in the human body by introducing mRNA as a vaccine or therapeutic agent. This represents a rising precision medicine field with great promise for preventing and treating many intractable or genetic diseases. In addition, in vitro transcribed mRNA has achieved programmed production, which is more effective, faster in design and production, as well as more flexible and cost-effective than conventional approaches that may offer. Based on these extraordinary advantages, mRNA vaccines have the characteristics of the swiftest response to large-scale outbreaks of infectious diseases, such as the currently devastating pandemic COVID-19. It has always been the scientists’ desire to improve the stability, immunogenicity, translation efficiency, and delivery system to achieve efficient and safe delivery of mRNA. Excitingly, these scientific dreams have gradually been realized with the rapid, amazing achievements of molecular biology, RNA technology, vaccinology, and nanotechnology. In this review, we comprehensively describe mRNA-based therapeutics, including their principles, manufacture, application, effects, and shortcomings. We also highlight the importance of mRNA optimization and delivery systems in successful mRNA therapeutics and discuss the key challenges and opportunities in developing these tools into powerful and versatile tools to combat many genetic, infectious, cancer, and other refractory diseases.
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Affiliation(s)
- Shugang Qin
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Xiaoshan Tang
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuting Chen
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Kepan Chen
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Na Fan
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Wen Xiao
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Qian Zheng
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Guohong Li
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Yuqing Teng
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China
| | - Min Wu
- Department of Biomedical Sciences, School of Medicine and Health Sciences, University of North Dakota, Grand Forks, ND, 58203, USA
| | - Xiangrong Song
- Department of Critical Care Medicine, Frontiers Science Center for Disease-related Molecular Network, State Key Laboratory of Biotherapy and Cancer Center, West China Hospital, Sichuan University, Chengdu, China.
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10
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Chauhan W, Shoaib S, Fatma R, Zaka‐ur‐Rab Z, Afzal M. β‐thalassemia, and the advent of new Interventions beyond Transfusion and Iron chelation. Br J Clin Pharmacol 2022; 88:3610-3626. [DOI: 10.1111/bcp.15343] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2021] [Revised: 03/10/2022] [Accepted: 03/29/2022] [Indexed: 01/19/2023] Open
Affiliation(s)
- Waseem Chauhan
- Human Genetics and Toxicology Laboratory, Department of Zoology Aligarh Muslim University Aligarh India
| | - Shoaib Shoaib
- Department of Biochemistry, JNMC Aligarh Muslim University Aligarh India
| | - Rafat Fatma
- Human Genetics and Toxicology Laboratory, Department of Zoology Aligarh Muslim University Aligarh India
| | - Zeeba Zaka‐ur‐Rab
- Department of Pediatrics, JNMC Aligarh Muslim University Aligarh India
| | - Mohammad Afzal
- Human Genetics and Toxicology Laboratory, Department of Zoology Aligarh Muslim University Aligarh India
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11
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Gray DH, Santos J, Keir AG, Villegas I, Maddock S, Trope EC, Long JD, Kuo CY. A comparison of DNA repair pathways to achieve a site-specific gene modification of the Bruton's tyrosine kinase gene. MOLECULAR THERAPY. NUCLEIC ACIDS 2022; 27:505-516. [PMID: 35036061 PMCID: PMC8728535 DOI: 10.1016/j.omtn.2021.12.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 12/09/2021] [Indexed: 01/08/2023]
Abstract
Gene editing utilizing homology-directed repair has advanced significantly for many monogenic diseases of the hematopoietic system in recent years but has also been hindered by decreases between in vitro and in vivo gene integration rates. Homology-directed repair occurs primarily in the S/G2 phases of the cell cycle, whereas long-term engrafting hematopoietic stem cells are typically quiescent. Alternative methods for a targeted integration have been proposed including homology-independent targeted integration and precise integration into target chromosome, which utilize non-homologous end joining and microhomology-mediated end joining, respectively. Non-homologous end joining occurs throughout the cell cycle, while microhomology-mediated end joining occurs predominantly in the S phase. We compared these pathways for the integration of a corrective DNA cassette at the Bruton's tyrosine kinase gene for the treatment of X-linked agammaglobulinemia. Homology-directed repair generated the most integration in K562 cells; however, synchronizing cells into G1 resulted in the highest integration rates with homology-independent targeted integration. Only homology-directed repair produced seamless junctions, making it optimal for targets where insertions and deletions are impermissible. Bulk CD34+ cells were best edited by homology-directed repair and precise integration into the target chromosome, while sorted hematopoietic stem cells contained similar integration rates using all corrective donors.
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Affiliation(s)
- David H. Gray
- Molecular Biology Interdepartmental Graduate Program, University of California, Los Angeles, CA 90095, USA
| | - Jasmine Santos
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Alexandra Grace Keir
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Isaac Villegas
- Division of Allergy and Immunology, Department of Pediatrics, David Geffen School of Medicine at the University of California, 10833 Le Conte MDCC 12-430, Los Angeles, CA 90095, USA
| | - Simon Maddock
- Department of Microbiology, Immunology & Molecular Genetics, University of California, Los Angeles, CA 90095, USA
| | - Edward C. Trope
- Division of Allergy and Immunology, Department of Pediatrics, David Geffen School of Medicine at the University of California, 10833 Le Conte MDCC 12-430, Los Angeles, CA 90095, USA
| | - Joseph D. Long
- Division of Allergy and Immunology, Department of Pediatrics, David Geffen School of Medicine at the University of California, 10833 Le Conte MDCC 12-430, Los Angeles, CA 90095, USA
| | - Caroline Y. Kuo
- Division of Allergy and Immunology, Department of Pediatrics, David Geffen School of Medicine at the University of California, 10833 Le Conte MDCC 12-430, Los Angeles, CA 90095, USA
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12
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Li G, Li X, Zhuang S, Wang L, Zhu Y, Chen Y, Sun W, Wu Z, Zhou Z, Chen J, Huang X, Wang J, Li D, Li W, Wang H, Wei W. Gene editing and its applications in biomedicine. SCIENCE CHINA. LIFE SCIENCES 2022; 65:660-700. [PMID: 35235150 PMCID: PMC8889061 DOI: 10.1007/s11427-021-2057-0] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/06/2021] [Indexed: 02/06/2023]
Abstract
The steady progress in genome editing, especially genome editing based on the use of clustered regularly interspaced short palindromic repeats (CRISPR) and programmable nucleases to make precise modifications to genetic material, has provided enormous opportunities to advance biomedical research and promote human health. The application of these technologies in basic biomedical research has yielded significant advances in identifying and studying key molecular targets relevant to human diseases and their treatment. The clinical translation of genome editing techniques offers unprecedented biomedical engineering capabilities in the diagnosis, prevention, and treatment of disease or disability. Here, we provide a general summary of emerging biomedical applications of genome editing, including open challenges. We also summarize the tools of genome editing and the insights derived from their applications, hoping to accelerate new discoveries and therapies in biomedicine.
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Affiliation(s)
- Guanglei Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Xiangyang Li
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China
| | - Songkuan Zhuang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China
| | - Liren Wang
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yifan Zhu
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China
| | - Yangcan Chen
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wen Sun
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China
| | - Zeguang Wu
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Zhuo Zhou
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Jia Chen
- Gene Editing Center, School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Xingxu Huang
- School of Life Science and Technology, ShanghaiTech University, Shanghai, 201210, China.
| | - Jin Wang
- Department of Clinical Laboratory, Shenzhen Institute of Translational Medicine, The First Affiliated Hospital of Shenzhen University, Shenzhen Second People's Hospital, Shenzhen, 518035, China.
| | - Dali Li
- Shanghai Frontiers Science Research Base of Genome Editing and Cell Therapy, Shanghai Key Laboratory of Regulatory Biology, School of Life Sciences, East China Normal University, Shanghai, 200241, China.
| | - Wei Li
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
- Bejing Institute for Stem Cell and Regenerative Medicine, Beijing, 100101, China.
- HIT Center for Life Sciences, Harbin Institute of Technology, Harbin, 150001, China.
| | - Haoyi Wang
- State Key Laboratory of Stem Cell and Reproductive Biology, Institute of Zoology, Chinese Academy of Sciences, Beijing, 100101, China.
- University of Chinese Academy of Sciences, Beijing, 100049, China.
- Institute for Stem Cell and Regenerative Medicine, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Wensheng Wei
- Biomedical Pioneering Innovation Center, Beijing Advanced Innovation Center for Genomics, Peking-Tsinghua Center for Life Sciences, Peking University Genome Editing Research Center, State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China.
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13
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Musallam KM, Bou‐Fakhredin R, Cappellini MD, Taher AT. 2021 update on clinical trials in β-thalassemia. Am J Hematol 2021; 96:1518-1531. [PMID: 34347889 DOI: 10.1002/ajh.26316] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2021] [Revised: 07/29/2021] [Accepted: 08/02/2021] [Indexed: 01/19/2023]
Abstract
The treatment landscape for patients with β-thalassemia is witnessing a swift evolution, yet several unmet needs continue to persist. Patients with transfusion-dependent β-thalassemia (TDT) primarily rely on regular transfusion and iron chelation therapy, which can be associated with considerable treatment burden and cost. Patients with non-transfusion-dependent β-thalassemia (NTDT) are also at risk of significant morbidity due to the underlying anemia and iron overload, but treatment options in this patient subgroup are limited. In this review, we provide updates on clinical trials of novel therapies targeting the underlying pathology in β-thalassemia, including the α/non-α-globin chain imbalance, ineffective erythropoiesis, and iron dysregulation.
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Affiliation(s)
- Khaled M. Musallam
- Thalassemia Center, Burjeel Medical City Abu Dhabi United Arab Emirates
- International Network of Hematology London UK
| | - Rayan Bou‐Fakhredin
- Department of Internal Medicine American University of Beirut Medical Center Beirut Lebanon
| | - Maria Domenica Cappellini
- Department of Clinical Sciences and Community University of Milan, Ca’ Granda Foundation IRCCS Maggiore Policlinico Hospital Milan Italy
| | - Ali T. Taher
- Department of Internal Medicine American University of Beirut Medical Center Beirut Lebanon
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14
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Benitez EK, Lomova Kaufman A, Cervantes L, Clark DN, Ayoub PG, Senadheera S, Osborne K, Sanchez JM, Crisostomo RV, Wang X, Reuven N, Shaul Y, Hollis RP, Romero Z, Kohn DB. Global and Local Manipulation of DNA Repair Mechanisms to Alter Site-Specific Gene Editing Outcomes in Hematopoietic Stem Cells. Front Genome Ed 2021; 2:601541. [PMID: 34713224 PMCID: PMC8525354 DOI: 10.3389/fgeed.2020.601541] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 11/16/2020] [Indexed: 12/26/2022] Open
Abstract
Monogenic disorders of the blood system have the potential to be treated by autologous stem cell transplantation of ex vivo genetically modified hematopoietic stem and progenitor cells (HSPCs). The sgRNA/Cas9 system allows for precise modification of the genome at single nucleotide resolution. However, the system is reliant on endogenous cellular DNA repair mechanisms to mend a Cas9-induced double stranded break (DSB), either by the non-homologous end joining (NHEJ) pathway or by the cell-cycle regulated homology-directed repair (HDR) pathway. Here, we describe a panel of ectopically expressed DNA repair factors and Cas9 variants assessed for their ability to promote gene correction by HDR or inhibit gene disruption by NHEJ at the HBB locus. Although transient global overexpression of DNA repair factors did not improve the frequency of gene correction in primary HSPCs, localization of factors to the DSB by fusion to the Cas9 protein did alter repair outcomes toward microhomology-mediated end joining (MMEJ) repair, an HDR event. This strategy may be useful when predictable gene editing outcomes are imperative for therapeutic success.
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Affiliation(s)
- Elizabeth K Benitez
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Anastasia Lomova Kaufman
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Lilibeth Cervantes
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Danielle N Clark
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Paul G Ayoub
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Shantha Senadheera
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Kyle Osborne
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Julie M Sanchez
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Ralph Valentine Crisostomo
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Xiaoyan Wang
- Department of General Internal Medicine and Health Services Research, University of California, Los Angeles, Los Angeles, CA, United States
| | - Nina Reuven
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Yosef Shaul
- Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel
| | - Roger P Hollis
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Zulema Romero
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
| | - Donald B Kohn
- Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, United States
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15
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Sun J, Wang J, Zheng D, Hu X. Advances in therapeutic application of CRISPR-Cas9. Brief Funct Genomics 2021; 19:164-174. [PMID: 31769791 DOI: 10.1093/bfgp/elz031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2019] [Revised: 09/04/2019] [Accepted: 10/03/2019] [Indexed: 02/06/2023] Open
Abstract
Clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (Cas9) is one of the most versatile and efficient gene editing technologies, which is derived from adaptive immune strategies for bacteria and archaea. With the remarkable development of programmable nuclease-based genome engineering these years, CRISPR-Cas9 system has developed quickly in recent 5 years and has been widely applied in countless areas, including genome editing, gene function investigation and gene therapy both in vitro and in vivo. In this paper, we briefly introduce the mechanisms of CRISPR-Cas9 tool in genome editing. More importantly, we review the recent therapeutic application of CRISPR-Cas9 in various diseases, including hematologic diseases, infectious diseases and malignant tumor. Finally, we discuss the current challenges and consider thoughtfully what advances are required in order to further develop the therapeutic application of CRISPR-Cas9 in the future.
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Affiliation(s)
- Jinyu Sun
- Sparkfire Scientific Research Group, Nanjing Medical University, China
| | - Jianchu Wang
- Department of Hepatobiliary Surgery, Affiliated Hospital of Youjiang Medical University for Nationalities, No. 18 Zhongshan Road, Baise 533000, Guangxi Zhuang Autonomous Region, China
| | - Donghui Zheng
- Department of Nephrology, Huai'an Second People's Hospital and The Affiliated Huai'an Hospital of Xuzhou Medical University, Huai'an, China
| | - Xiaorong Hu
- Department of Cardiology, Zhongnan Hospital of Wuhan University, Wuhan, Hubei 430071, P.R. China
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16
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Shahryari A, Burtscher I, Nazari Z, Lickert H. Engineering Gene Therapy: Advances and Barriers. ADVANCED THERAPEUTICS 2021. [DOI: 10.1002/adtp.202100040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alireza Shahryari
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- School of Medicine Department of Human Genetics Technical University of Munich Klinikum Rechts der Isar 81675 München Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
- Stem Cell Research Center Golestan University of Medical Sciences Gorgan 49341‐74515 Iran
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
| | - Zahra Nazari
- Department of Biology School of Basic Sciences Golestan University Gorgan 49361‐79142 Iran
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- School of Medicine Department of Human Genetics Technical University of Munich Klinikum Rechts der Isar 81675 München Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
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17
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Koniali L, Lederer CW, Kleanthous M. Therapy Development by Genome Editing of Hematopoietic Stem Cells. Cells 2021; 10:1492. [PMID: 34198536 PMCID: PMC8231983 DOI: 10.3390/cells10061492] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2021] [Revised: 06/09/2021] [Accepted: 06/10/2021] [Indexed: 12/12/2022] Open
Abstract
Accessibility of hematopoietic stem cells (HSCs) for the manipulation and repopulation of the blood and immune systems has placed them at the forefront of cell and gene therapy development. Recent advances in genome-editing tools, in particular for clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein (Cas) and CRISPR/Cas-derived editing systems, have transformed the gene therapy landscape. Their versatility and the ability to edit genomic sequences and facilitate gene disruption, correction or insertion, have broadened the spectrum of potential gene therapy targets and accelerated the development of potential curative therapies for many rare diseases treatable by transplantation or modification of HSCs. Ongoing developments seek to address efficiency and precision of HSC modification, tolerability of treatment and the distribution and affordability of corresponding therapies. Here, we give an overview of recent progress in the field of HSC genome editing as treatment for inherited disorders and summarize the most significant findings from corresponding preclinical and clinical studies. With emphasis on HSC-based therapies, we also discuss technical hurdles that need to be overcome en route to clinical translation of genome editing and indicate advances that may facilitate routine application beyond the most common disorders.
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Affiliation(s)
- Lola Koniali
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (L.K.); (M.K.)
| | - Carsten W. Lederer
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (L.K.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
| | - Marina Kleanthous
- Department of Molecular Genetics Thalassemia, The Cyprus Institute of Neurology and Genetics, Nicosia 2371, Cyprus; (L.K.); (M.K.)
- Cyprus School of Molecular Medicine, Nicosia 2371, Cyprus
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18
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Wessels MW, Cnossen MH, van Dijk TB, Gillemans N, Schmidt KLJ, van Lom K, Vinjamur DS, Coyne S, Kurita R, Nakamura Y, de Man SA, Pfundt R, Azmani Z, Brouwer RWW, Bauer DE, van den Hout MCGN, van IJcken WFJ, Philipsen S. Molecular analysis of the erythroid phenotype of a patient with BCL11A haploinsufficiency. Blood Adv 2021; 5:2339-2349. [PMID: 33938942 PMCID: PMC8114548 DOI: 10.1182/bloodadvances.2020003753] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2020] [Accepted: 03/12/2021] [Indexed: 12/29/2022] Open
Abstract
The BCL11A gene encodes a transcriptional repressor with essential functions in multiple tissues during human development. Haploinsufficiency for BCL11A causes Dias-Logan syndrome (OMIM 617101), an intellectual developmental disorder with hereditary persistence of fetal hemoglobin (HPFH). Due to the severe phenotype, disease-causing variants in BCL11A occur de novo. We describe a patient with a de novo heterozygous variant, c.1453G>T, in the BCL11A gene, resulting in truncation of the BCL11A-XL protein (p.Glu485X). The truncated protein lacks the 3 C-terminal DNA-binding zinc fingers and the nuclear localization signal, rendering it inactive. The patient displayed high fetal hemoglobin (HbF) levels (12.1-18.7% of total hemoglobin), in contrast to the parents who had HbF levels of 0.3%. We used cultures of patient-derived erythroid progenitors to determine changes in gene expression and chromatin accessibility. In addition, we investigated DNA methylation of the promoters of the γ-globin genes HBG1 and HBG2. HUDEP1 and HUDEP2 cells were used as models for fetal and adult human erythropoiesis, respectively. Similar to HUDEP1 cells, the patient's cells displayed Assay for Transposase-Accessible Chromatin (ATAC) peaks at the HBG1/2 promoters and significant expression of HBG1/2 genes. In contrast, HBG1/2 promoter methylation and genome-wide gene expression profiling were consistent with normal adult erythropoiesis. We conclude that HPFH is the major erythroid phenotype of constitutive BCL11A haploinsufficiency. Given the essential functions of BCL11A in other hematopoietic lineages and the neuronal system, erythroid-specific targeting of the BCL11A gene has been proposed for reactivation of γ-globin expression in β-hemoglobinopathy patients. Our data strongly support this approach.
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Affiliation(s)
| | - Marjon H Cnossen
- Department of Pediatric Hematology
- Academic Center for Hemoglobinopathies and Rare Anemias
| | - Thamar B van Dijk
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - Nynke Gillemans
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - K L Juliëtte Schmidt
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
| | - Kirsten van Lom
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Hematology, Erasmus MC, Rotterdam, The Netherlands
| | - Divya S Vinjamur
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Steven Coyne
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | - Ryo Kurita
- Department of Research and Development, Central Blood Institute, Blood Service Headquarters, Japanese Red Cross Society, Tokyo, Japan
| | - Yukio Nakamura
- Cell Engineering Division, RIKEN, BioResource Center, Tsukuba, Japan
| | - Stella A de Man
- Department of Pediatrics, Amphia Hospital, Breda, The Netherlands
| | - Rolph Pfundt
- Department of Human Genetics, Radboud University Medical Center, Nijmegen, The Netherlands; and
| | - Zakia Azmani
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Rutger W W Brouwer
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Daniel E Bauer
- Division of Hematology/Oncology, Department of Pediatric Oncology, Boston Children's Hospital, Boston, MA
- Dana-Farber Cancer Institute, Boston, MA
- Harvard Stem Cell Institute, Boston, MA
- Broad Institute, Boston, MA
- Department of Pediatrics, Harvard Medical School, Boston, MA
| | | | - Wilfred F J van IJcken
- Department of Cell Biology, and
- Center for Biomics, Erasmus MC, Rotterdam, The Netherlands
| | - Sjaak Philipsen
- Academic Center for Hemoglobinopathies and Rare Anemias
- Department of Cell Biology, and
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19
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Miah M, Goh I, Haniffa M. Prenatal Development and Function of Human Mononuclear Phagocytes. Front Cell Dev Biol 2021; 9:649937. [PMID: 33898444 PMCID: PMC8060508 DOI: 10.3389/fcell.2021.649937] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 03/01/2021] [Indexed: 12/14/2022] Open
Abstract
The human mononuclear phagocyte (MP) system, which includes dendritic cells, monocytes, and macrophages, is a critical regulator of innate and adaptive immune responses. During embryonic development, MPs derive sequentially in yolk sac progenitors, fetal liver, and bone marrow haematopoietic stem cells. MPs maintain tissue homeostasis and confer protective immunity in post-natal life. Recent evidence - primarily in animal models - highlight their critical role in coordinating the remodeling, maturation, and repair of target organs during embryonic and fetal development. However, the molecular regulation governing chemotaxis, homeostasis, and functional diversification of resident MP cells in their respective organ systems during development remains elusive. In this review, we summarize the current understanding of the development and functional contribution of tissue MPs during human organ development and morphogenesis and its relevance to regenerative medicine. We outline how single-cell multi-omic approaches and next-generation ex-vivo organ-on-chip models provide new experimental platforms to study the role of human MPs during development and disease.
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Affiliation(s)
- Mohi Miah
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Issac Goh
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom
| | - Muzlifah Haniffa
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, United Kingdom.,Department of Dermatology and NIHR Newcastle Biomedical Research Centre, Newcastle Hospitals NHS Foundation Trust, Newcastle upon Tyne, United Kingdom.,Wellcome Sanger Institute, Hinxton, United Kingdom
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20
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Maldonado R, Jalil S, Wartiovaara K. Curative gene therapies for rare diseases. J Community Genet 2021; 12:267-276. [PMID: 32803721 PMCID: PMC8141081 DOI: 10.1007/s12687-020-00480-6] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Accepted: 07/29/2020] [Indexed: 02/06/2023] Open
Abstract
Diseases caused by alterations in the DNA can be overcome by providing the cells or tissues with a functional copy of the mutated gene. The most common form of gene therapy implies adding an extra genetic unit into the cell. However, new genome engineering techniques also allow the modification or correction of the existing allele, providing new possibilities, especially for dominant diseases. Gene therapies have been tested for 30 years in thousands of clinical trials, but presently, we have only three authorised gene therapy products for the treatment of inherited diseases in European Union. Here, we describe the gene therapy alternatives already on the market in the European Union and expand the scope to some clinical trials. Additionally, we discuss the ethical and regulatory issues raised by the development of these new kinds of therapies.
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Affiliation(s)
- Rocio Maldonado
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Sami Jalil
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland
| | - Kirmo Wartiovaara
- Stem Cells and Metabolism Research Program, University of Helsinki, Helsinki, Finland.
- Clinical Genetics, Helsinki University Hospital, Helsinki, Finland.
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21
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Dasgupta I, Flotte TR, Keeler AM. CRISPR/Cas-Dependent and Nuclease-Free In Vivo Therapeutic Gene Editing. Hum Gene Ther 2021; 32:275-293. [PMID: 33750221 PMCID: PMC7987363 DOI: 10.1089/hum.2021.013] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 02/27/2021] [Indexed: 12/19/2022] Open
Abstract
Precise gene manipulation by gene editing approaches facilitates the potential to cure several debilitating genetic disorders. Gene modification stimulated by engineered nucleases induces a double-stranded break (DSB) in the target genomic locus, thereby activating DNA repair mechanisms. DSBs triggered by nucleases are repaired either by the nonhomologous end-joining or the homology-directed repair pathway, enabling efficient gene editing. While there are several ongoing ex vivo genome editing clinical trials, current research underscores the therapeutic potential of CRISPR/Cas-based (clustered regularly interspaced short palindrome repeats-associated Cas nuclease) in vivo gene editing. In this review, we provide an overview of the CRISPR/Cas-mediated in vivo genome therapy applications and explore their prospective clinical translatability to treat human monogenic disorders. In addition, we discuss the various challenges associated with in vivo genome editing technologies and strategies used to circumvent them. Despite the robust and precise nuclease-mediated gene editing, a promoterless, nuclease-independent gene targeting strategy has been utilized to evade the drawbacks of the nuclease-dependent system, such as off-target effects, immunogenicity, and cytotoxicity. Thus, the rapidly evolving paradigm of gene editing technologies will continue to foster the progress of gene therapy applications.
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Affiliation(s)
- Ishani Dasgupta
- Department of Pediatrics, Horae Gene Therapy Center, University of Massachusetts, Worcester, Massachusetts, USA
| | - Terence R. Flotte
- Department of Pediatrics, Horae Gene Therapy Center, University of Massachusetts, Worcester, Massachusetts, USA
| | - Allison M. Keeler
- Department of Pediatrics, Horae Gene Therapy Center, University of Massachusetts, Worcester, Massachusetts, USA
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22
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Konishi CT, Long C. Progress and challenges in CRISPR-mediated therapeutic genome editing for monogenic diseases. J Biomed Res 2020; 35:148-162. [PMID: 33402545 PMCID: PMC8038532 DOI: 10.7555/jbr.34.20200105] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
There are an estimated 10 000 monogenic diseases affecting tens of millions of individuals worldwide. The application of CRISPR/Cas genome editing tools to treat monogenic diseases is an emerging strategy with the potential to generate personalized treatment approaches for these patients. CRISPR/Cas-based systems are programmable and sequence-specific genome editing tools with the capacity to generate base pair resolution manipulations to DNA or RNA. The complexity of genomic insults resulting in heritable disease requires patient-specific genome editing strategies with consideration of DNA repair pathways, and CRISPR/Cas systems of different types, species, and those with additional enzymatic capacity and/or delivery methods. In this review we aim to discuss broad and multifaceted therapeutic applications of CRISPR/Cas gene editing systems including in harnessing of homology directed repair, non-homologous end joining, microhomology-mediated end joining, and base editing to permanently correct diverse monogenic diseases.
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Affiliation(s)
- Colin T Konishi
- Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York, NY 10016, USA
| | - Chengzu Long
- Leon H. Charney Division of Cardiology, New York University Grossman School of Medicine, New York, NY 10016, USA.,Helen and Martin Kimmel Center for Stem Cell Biology, New York University Grossman School of Medicine, New York, NY 10016, USA.,Department of Neurology, New York University Grossman School of Medicine, New York, NY 10016, USA.,Department of Neuroscience and Physiology, New York University Grossman School of Medicine, New York, NY 10016, USA
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23
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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] [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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24
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Hirakawa M, Krishnakumar R, Timlin J, Carney J, Butler K. Gene editing and CRISPR in the clinic: current and future perspectives. Biosci Rep 2020; 40:BSR20200127. [PMID: 32207531 PMCID: PMC7146048 DOI: 10.1042/bsr20200127] [Citation(s) in RCA: 102] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 03/23/2020] [Accepted: 03/23/2020] [Indexed: 12/26/2022] Open
Abstract
Genome editing technologies, particularly those based on zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and CRISPR (clustered regularly interspaced short palindromic repeat DNA sequences)/Cas9 are rapidly progressing into clinical trials. Most clinical use of CRISPR to date has focused on ex vivo gene editing of cells followed by their re-introduction back into the patient. The ex vivo editing approach is highly effective for many disease states, including cancers and sickle cell disease, but ideally genome editing would also be applied to diseases which require cell modification in vivo. However, in vivo use of CRISPR technologies can be confounded by problems such as off-target editing, inefficient or off-target delivery, and stimulation of counterproductive immune responses. Current research addressing these issues may provide new opportunities for use of CRISPR in the clinical space. In this review, we examine the current status and scientific basis of clinical trials featuring ZFNs, TALENs, and CRISPR-based genome editing, the known limitations of CRISPR use in humans, and the rapidly developing CRISPR engineering space that should lay the groundwork for further translation to clinical application.
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Affiliation(s)
| | - Raga Krishnakumar
- Systems Biology, Sandia National Laboratories, Livermore, CA 94551, U.S.A
| | - Jerilyn A. Timlin
- Molecular and Microbiology, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
| | - James P. Carney
- Advanced Materials Laboratory, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
| | - Kimberly S. Butler
- Molecular and Microbiology, Sandia National Laboratories, Albuquerque, NM 87185, U.S.A
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25
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Bou-Fakhredin R, Tabbikha R, Daadaa H, Taher AT. Emerging therapies in β-thalassemia: toward a new era in management. Expert Opin Emerg Drugs 2020; 25:113-122. [DOI: 10.1080/14728214.2020.1752180] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Rayan Bou-Fakhredin
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Rami Tabbikha
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Hisham Daadaa
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
| | - Ali T. Taher
- Division of Hematology and Oncology, Department of Internal Medicine, American University of Beirut Medical Center, Beirut, Lebanon
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26
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Benabdellah K, Sánchez-Hernández S, Aguilar-González A, Maldonado-Pérez N, Gutierrez-Guerrero A, Cortijo-Gutierrez M, Ramos-Hernández I, Tristán-Manzano M, Galindo-Moreno P, Herrera C, Martin F. Genome-edited adult stem cells: Next-generation advanced therapy medicinal products. Stem Cells Transl Med 2020; 9:674-685. [PMID: 32141715 PMCID: PMC7214650 DOI: 10.1002/sctm.19-0338] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Accepted: 01/10/2020] [Indexed: 12/14/2022] Open
Abstract
Over recent decades, gene therapy, which has enabled the treatment of several incurable diseases, has undergone a veritable revolution. Cell therapy has also seen major advances in the treatment of various diseases, particularly through the use of adult stem cells (ASCs). The combination of gene and cell therapy (GCT) has opened up new opportunities to improve advanced therapy medicinal products for the treatment of several diseases. Despite the considerable potential of GCT, the use of retroviral vectors has major limitations with regard to oncogene transactivation and the lack of physiological expression. Recently, gene therapists have focused on genome editing (GE) technologies as an alternative strategy. In this review, we discuss the potential benefits of using GE technologies to improve GCT approaches based on ASCs. We will begin with a brief summary of different GE platforms and techniques and will then focus on key therapeutic approaches that have been successfully used to treat diseases in animal models. Finally, we discuss whether ASC GE could become a real alternative to retroviral vectors in a GCT setting.
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Affiliation(s)
- Karim Benabdellah
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Sabina Sánchez-Hernández
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Araceli Aguilar-González
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain.,Department of Medicinal and Organic Chemistry, Faculty of Pharmacy, University of Granada, Granada, Spain
| | - Noelia Maldonado-Pérez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Alejandra Gutierrez-Guerrero
- Gastroenterology and Hepatology Division, Joan and Sanford I. Weill Department of Medicine, Weill Cornell Medicine, Cornell University, Jill Roberts, Inflammatory Bowel Disease Research Institute, New York, New York, USA
| | - Marina Cortijo-Gutierrez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Iris Ramos-Hernández
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - María Tristán-Manzano
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
| | - Pablo Galindo-Moreno
- Oral Surgery and Implant Dentistry Department, School of Dentistry, University of Granada, Granada, Spain
| | - Concha Herrera
- Department of Hematology, Reina Sofía University Hospital, Córdoba, Spain.,Maimonides Biomedical Research Institute of Cordoba (IMIBIC), University of Córdoba, Córdoba, Spain
| | - Francisco Martin
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada (Andalusian Regional Government), Health Sciences Technology Park, Granada, Spain
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27
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Zhang ZY, Thrasher AJ, Zhang F. Gene therapy and genome editing for primary immunodeficiency diseases. Genes Dis 2020; 7:38-51. [PMID: 32181274 PMCID: PMC7063425 DOI: 10.1016/j.gendis.2019.07.007] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 07/20/2019] [Accepted: 07/22/2019] [Indexed: 12/12/2022] Open
Abstract
In past two decades the gene therapy using genetic modified autologous hematopoietic stem cells (HSCs) transduced with the viral vector has become a promising alternative option for treating primary immunodeficiency diseases (PIDs). Despite of some pitfalls at early stage clinical trials, the field of gene therapy has advanced significantly in the last decade with improvements in viral vector safety, preparatory regime for manufacturing high quality virus, automated CD34 cell purification. Hence, the overall outcome from the clinical trials for the different PIDs has been very encouraging. In addition to the viral vector based gene therapy, the recent fast moving forward developments in genome editing using engineered nucleases in HSCs has provided a new promising platform for the treatment of PIDs. This review provides an overall outcome and progress in gene therapy clinical trials for SCID-X, ADA-SCID, WAS, X- CGD, and the recent developments in genome editing technology applied in HSCs for developing potential therapy, particular in the key studies for PIDs.
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Affiliation(s)
- Zhi-Yong Zhang
- Department of Immunology and Rheumatology, Children's Hospital of Chongqing Medical University, China
| | - Adrian J. Thrasher
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University Colleage London, UK
| | - Fang Zhang
- Molecular and Cellular Immunology, Great Ormond Street Institute of Child Health, University Colleage London, UK
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28
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29
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Ghiaccio V, Chappell M, Rivella S, Breda L. Gene Therapy for Beta-Hemoglobinopathies: Milestones, New Therapies and Challenges. Mol Diagn Ther 2019; 23:173-186. [PMID: 30701409 DOI: 10.1007/s40291-019-00383-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Inherited monogenic disorders such as beta-hemoglobinopathies (BH) are fitting candidates for treatment via gene therapy by gene transfer or gene editing. The reported safety and efficacy of lentiviral vectors in preclinical studies have led to the development of several clinical trials for the addition of a functional beta-globin gene. Across trials, dozens of transfusion-dependent patients with sickle cell disease (SCD) and transfusion-dependent beta-thalassemia (TDT) have been treated via gene therapy and have achieved reduced transfusion requirements. While overall results are encouraging, the outcomes appear to be strongly influenced by the level of lentiviral integration in transduced cells after engraftment, as well as the underlying genotype resulting in thalassemia. In addition, the method of procurement of hematopoietic stem cells can affect their quality and thus the outcome of gene therapy both in SCD and TDT. This suggests that new studies aimed at maximizing the number of corrected cells with long-term self-renewal potential are crucial to ensure successful treatment for every patient. Recent advancements in gene transfer and bone marrow transplantation have improved the success of this approach, and the results obtained by using these strategies demonstrated significant improvement of gene transfer outcome in patients. The advent of new gene-editing technologies has suggested additional therapeutic options. These are primarily focused on correcting the defective beta-globin gene or editing the expression of genes or genomic segments that regulate fetal hemoglobin synthesis. In this review, we aim to establish the potential benefits of gene therapy for BH, to summarize the status of the ongoing trials, and to discuss the possible improvement or direction for future treatments.
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Affiliation(s)
- Valentina Ghiaccio
- Hematology Division, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Maxwell Chappell
- Hematology Division, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Stefano Rivella
- Hematology Division, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA
| | - Laura Breda
- Hematology Division, Children's Hospital of Philadelphia, Philadelphia, PA, 19104, USA.
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30
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Porter SN, Levine RM, Pruett-Miller SM. A Practical Guide to Genome Editing Using Targeted Nuclease Technologies. Compr Physiol 2019; 9:665-714. [PMID: 30873595 DOI: 10.1002/cphy.c180022] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Genome engineering using programmable nucleases is a rapidly evolving technique that enables precise genetic manipulations within complex genomes. Although this technology first surfaced with the creation of meganucleases, zinc finger nucleases, and transcription activator-like effector nucleases, CRISPR-Cas9 has been the most widely adopted platform because of its ease of use. This comprehensive review presents a basic overview of genome engineering and discusses the major technological advances in the field. In addition to nucleases, we discuss CRISPR-derived base editors and epigenetic modifiers. We also delve into practical applications of these tools, including creating custom-edited cell and animal models as well as performing genetic screens. Finally, we discuss the potential for therapeutic applications and ethical considerations related to employing this technology in humans. © 2019 American Physiological Society. Compr Physiol 9:665-714, 2019.
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Affiliation(s)
- Shaina N Porter
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rachel M Levine
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Shondra M Pruett-Miller
- Department of Cell & Molecular Biology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
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31
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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] [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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32
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Bak RO, Gomez-Ospina N, Porteus MH. Gene Editing on Center Stage. Trends Genet 2018; 34:600-611. [PMID: 29908711 DOI: 10.1016/j.tig.2018.05.004] [Citation(s) in RCA: 91] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2017] [Accepted: 05/16/2018] [Indexed: 12/15/2022]
Abstract
Smithies et al. (1985) and Jasin and colleagues (1994) provided proof of concept that homologous recombination (HR) could be applied to the treatment of human disease and that its efficiency could be improved by the induction of double-strand breaks (DSBs). A key advance was the discovery of engineered nucleases, such as zinc-finger nucleases (ZFNs) and transcription activator-like (TAL) effector nucleases (TALENs), that can generate site-specific DSBs. The democratization and widespread use of genome editing was enabled by the discovery of the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 nuclease system. While genome editing using ZFNs and TALENs has already reached clinical trials, the pace at which genome editing enters human trials is bound to accelerate in the next several years with multiple promising preclinical studies heralding cures for monogenic diseases that are currently difficult to manage or even incurable. Here we review recent advances and current limitations and discuss the path forward using genome editing to understand, treat, and cure genetic diseases.
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Affiliation(s)
- Rasmus O Bak
- Aarhus Institute of Advanced Studies (AIAS), Aarhus University, DK-8000 Aarhus C., Denmark; Department of Biomedicine, Aarhus University, DK-8000 Aarhus C., Denmark
| | | | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
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33
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Li C, Psatha N, Gil S, Wang H, Papayannopoulou T, Lieber A. HDAd5/35 ++ Adenovirus Vector Expressing Anti-CRISPR Peptides Decreases CRISPR/Cas9 Toxicity in Human Hematopoietic Stem Cells. Mol Ther Methods Clin Dev 2018; 9:390-401. [PMID: 30038942 PMCID: PMC6054697 DOI: 10.1016/j.omtm.2018.04.008] [Citation(s) in RCA: 54] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 04/26/2018] [Indexed: 01/12/2023]
Abstract
We generated helper-dependent HDAd5/35++ adenovirus vectors expressing CRISPR/Cas9 for potential hematopoietic stem cells (HSCs) gene therapy of β-thalassemia and sickle cell disease through re-activation of fetal γ-globin expression (HDAd-globin-CRISPR). The process of CRISPR/Cas9 gene transfer using these vectors was not associated with death of human CD34+ cells and did not affect their in vitro expansion and erythroid differentiation. However, functional assays for primitive HSCs, e.g., multi-lineage progenitor colony formation and engraftment in irradiated NOD/Shi-scid/interleukin-2 receptor γ (IL-2Rγ) null (NSG) mice, revealed toxicity of HDAd-globin-CRISPR vectors related to the prolonged expression and activity of CRISPR/Cas9. To control the duration of CRISPR/Cas9 activity, we generated an HDAd5/35++ vector that expressed two anti-CRISPR (Acr) peptides (AcrII4 and AcrII2) capable of binding to the CRISPR/Cas9 complex (HDAd-Acr). CD34+ cells that were sequentially infected with HDAd-CRISPR and HDAd-Acr engrafted at a significantly higher rate. Target site disruption frequencies in engrafted human cells were similar to those in pre-transplantation CD34+ cells, indicating that genome-edited primitive HSCs survived. In vitro differentiated HSCs isolated from transplanted mice demonstrated increased γ-globin expression as a result of genome editing. Our data indicate that the HDAd-Acr vector can be used as a tool to reduce HSC cytotoxicity of the CRISPR/Cas9 complex.
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Affiliation(s)
- Chang Li
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 357720, Seattle, WA 98195, USA
| | - Nikoletta Psatha
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 357720, Seattle, WA 98195, USA
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Sucheol Gil
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 357720, Seattle, WA 98195, USA
| | - Hongjie Wang
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 357720, Seattle, WA 98195, USA
| | - Thalia Papayannopoulou
- Division of Hematology, Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - André Lieber
- Division of Medical Genetics, Department of Medicine, University of Washington, Box 357720, Seattle, WA 98195, USA
- Department of Pathology, University of Washington, Seattle, WA 98195, USA
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34
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Antony JS, Haque AA, Lamsfus-Calle A, Daniel-Moreno A, Mezger M, Kormann MS. CRISPR/Cas9 system: A promising technology for the treatment of inherited and neoplastic hematological diseases. ACTA ACUST UNITED AC 2018. [DOI: 10.1002/acg2.10] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Justin S. Antony
- Department of Pediatrics I; Pediatric Infectiology and Immunology; Translational Genomics and Gene Therapy in Pediatrics; University of Tübingen; Tübingen Germany
- University Children's Hospital; Department of Paediatrics I, Hematology and Oncology; University of Tübingen; Tübingen Germany
- Department of Hematology, Oncology; Clinical Immunology; University of Tübingen; Tübingen Germany
| | - A.K.M. Ashiqul Haque
- Department of Pediatrics I; Pediatric Infectiology and Immunology; Translational Genomics and Gene Therapy in Pediatrics; University of Tübingen; Tübingen Germany
| | - Andrés Lamsfus-Calle
- University Children's Hospital; Department of Paediatrics I, Hematology and Oncology; University of Tübingen; Tübingen Germany
| | - Alberto Daniel-Moreno
- University Children's Hospital; Department of Paediatrics I, Hematology and Oncology; University of Tübingen; Tübingen Germany
| | - Markus Mezger
- University Children's Hospital; Department of Paediatrics I, Hematology and Oncology; University of Tübingen; Tübingen Germany
| | - Michael S.D. Kormann
- Department of Pediatrics I; Pediatric Infectiology and Immunology; Translational Genomics and Gene Therapy in Pediatrics; University of Tübingen; Tübingen Germany
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35
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Reactivation of γ-globin in adult β-YAC mice after ex vivo and in vivo hematopoietic stem cell genome editing. Blood 2018; 131:2915-2928. [PMID: 29789357 DOI: 10.1182/blood-2018-03-838540] [Citation(s) in RCA: 58] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2018] [Accepted: 05/14/2018] [Indexed: 12/12/2022] Open
Abstract
Disorders involving β-globin gene mutations, primarily β-thalassemia and sickle cell disease, represent a major target for hematopoietic stem/progenitor cell (HSPC) gene therapy. This includes CRISPR/Cas9-mediated genome editing approaches in adult CD34+ cells aimed toward the reactivation of fetal γ-globin expression in red blood cells. Because models involving erythroid differentiation of CD34+ cells have limitations in assessing γ-globin reactivation, we focused on human β-globin locus-transgenic (β-YAC) mice. We used a helper-dependent human CD46-targeting adenovirus vector expressing CRISPR/Cas9 (HDAd-HBG-CRISPR) to disrupt a repressor binding region within the γ-globin promoter. We transduced HSPCs from β-YAC/human CD46-transgenic mice ex vivo and subsequently transplanted them into irradiated recipients. Furthermore, we used an in vivo HSPC transduction approach that involves HSPC mobilization and the intravenous injection of HDAd-HBG-CRISPR into β-YAC/CD46-transgenic mice. In both models, we demonstrated efficient target site disruption, resulting in a pronounced switch from human β- to γ-globin expression in red blood cells of adult mice that was maintained after secondary transplantation of HSPCs. In long-term follow-up studies, we did not detect hematological abnormalities, indicating that HBG promoter editing does not negatively affect hematopoiesis. This is the first study that shows successful in vivo HSPC genome editing by CRISPR/Cas9.
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Abstract
At present, the only definitive cure for β-thalassemia is a bone marrow transplant (BMT); however, HLA-blood-matched donors are scarcely available. Current therapies undergoing clinical investigation with most potential for therapeutic benefit are the β-globin gene transfer of patient-specific hematopoietic stem cells followed by autologous BMT. Other emerging therapies deliver exogenous regulators of several key modulators of erythropoiesis or iron homeostasis. This review focuses on current approaches for the treatment of hemoglobinopathies caused by disruptions of β-globin.
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Affiliation(s)
- Amaliris Guerra
- Department of Pediatrics, Division of Hematology, Children's Hospital of Philadelphia (CHOP), Philadelphia, PA, USA
| | - Khaled M Musallam
- International Network of Hematology, 31-33 High Holborn, London WC1V 6AX, UK
| | - Ali T Taher
- Department of Internal Medicine, American University of Beirut Medical Center, PO Box: 11-0236, Cairo Street, Hamra, Raid E Solh, Beirut 1107 2020, Lebanon
| | - Stefano Rivella
- Department of Pediatrics, Division of Hematology, Children's Hospital of Philadelphia (CHOP), Philadelphia, PA, USA; Cell and Molecular Biology Graduate Group (CAMB), University of Pennsylvania, 421 Curie Boulevard/6064 160 Biomedical Research Building (BRB) 2/3, Philadelphia, PA 19104-6064, USA.
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37
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The changing landscape of gene editing in hematopoietic stem cells: a step towards Cas9 clinical translation. Curr Opin Hematol 2018; 24:481-488. [PMID: 28806273 DOI: 10.1097/moh.0000000000000385] [Citation(s) in RCA: 46] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
PURPOSE OF REVIEW Since the discovery two decades ago that programmable endonucleases can be engineered to modify human cells at single nucleotide resolution, the concept of genome editing was born. Now these technologies are being applied to therapeutically relevant cell types, including hematopoietic stem cells (HSC), which possess the power to repopulate an entire blood and immune system. The purpose of this review is to discuss the changing landscape of genome editing in hematopoietic stem cells (GE-HSC) from the discovery stage to the preclinical stage, with the imminent goal of clinical translation for the treatment of serious genetic diseases of the blood and immune system. RECENT FINDINGS With the discovery that the RNA-programmable (sgRNA) clustered regularly interspace short palindromic repeats (CRISPR)-Cas9 nuclease (Cas9/sgRNA) systems can be easily used to precisely modify the human genome in 2012, a genome-editing revolution of hematopoietic stem cells (HSC) has bloomed. We have observed that over the last 2 years, academic institutions and small biotech companies are developing HSC-based Cas9/sgRNA genome-editing curative strategies to treat monogenic disorders, including β-hemoglobinopathies and primary immunodeficiencies. We will focus on recent publications (within the past 2 years) that employ different genome-editing strategies to 'hijack' the cell's endogenous double-strand repair pathways to confer a disease-specific therapeutic advantage. SUMMARY The number of genome-editing strategies in HSCs that could offer therapeutic potential for diseases of the blood and immune system have dramatically risen over the past 2 years. The HSC-based genome-editing field is primed to enter clinical trials in the subsequent years. We will summarize the major advancements for the development of novel autologous GE-HSC cell and gene therapy strategies for hematopoietic diseases that are candidates for curative allogeneic bone marrow transplantation.
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Lohani N, Bhargava N, Munshi A, Ramalingam S. Pharmacological and molecular approaches for the treatment of β-hemoglobin disorders. J Cell Physiol 2017; 233:4563-4577. [PMID: 29159826 DOI: 10.1002/jcp.26292] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Accepted: 11/07/2017] [Indexed: 12/25/2022]
Abstract
β-hemoglobin disorders, such as β-thalassemia and sickle cell anemia are among the most prevalent inherited genetic disorders worldwide. These disorders are caused by mutations in the gene encoding hemoglobin-β (HBB), a vital protein found in red blood cells (RBCs) that carries oxygen from lungs to all parts of the human body. As a consequence, there has been an enduring interest in this field in formulating therapeutic strategies for the treatment of these diseases. Currently, there is no cure available for hemoglobin disorders, although, some patients have been treated with bone marrow transplantation, whose scope is limited because of the difficulty in finding a histocompatible donor and also due to transplant-associated clinical complications that can arise during the treatment. On account of these constraints, reactivation of fetal hemoglobin (HbF) synthesis holds immense promise and is a viable strategy to alleviate the symptoms of β-hemoglobin disorders. Development of new genomic tools has led to the identification of important natural genetic modifiers of hemoglobin switching which include BCL11A, KLF1, HBSIL-MYB, LRF, LSD1, LDB1, histone deacetylases 1 and 2 (HDAC1 and HDAC2). miRNAs are also promising therapeutic targets for development of more effective strategies for the induction of HbF production. Many new small molecule pharmacological inducers of HbF production are already under pre-clinical and clinical development. Furthermore, recent advancements in gene and cell therapy includes targeted genome editing and iPS cell technologies, both of which utilizes a patient's own cells, are emerging as extremely promising approaches for significantly reducing the burden of β-hemoglobin disorders.
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Affiliation(s)
- Neelam Lohani
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Nupur Bhargava
- CSIR-Institute of Genomics and Integrative Biology, New Delhi, India
| | - Anjana Munshi
- Centre for Human Genetics and Molecular Medicine, Central University of Punjab, Bathinda, India
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Long J, Hoban MD, Cooper AR, Kaufman ML, Kuo CY, Campo-Fernandez B, Lumaquin D, Hollis RP, Wang X, Kohn DB, Romero Z. Characterization of Gene Alterations following Editing of the β-Globin Gene Locus in Hematopoietic Stem/Progenitor Cells. Mol Ther 2017; 26:468-479. [PMID: 29221806 DOI: 10.1016/j.ymthe.2017.11.001] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 10/27/2017] [Accepted: 11/02/2017] [Indexed: 02/09/2023] Open
Abstract
The use of engineered nucleases combined with a homologous DNA donor template can result in targeted gene correction of the sickle cell disease mutation in hematopoietic stem and progenitor cells. However, because of the high homology between the adjacent human β- and δ-globin genes, off-target cleavage is observed at δ-globin when using some endonucleases targeted to the sickle mutation in β-globin. Introduction of multiple double-stranded breaks by endonucleases has the potential to induce intergenic alterations. Using a novel droplet digital PCR assay and high-throughput sequencing, we characterized the frequency of rearrangements between the β- and δ-globin paralogs when delivering these nucleases. Pooled CD34+ cells and colony-forming units from sickle bone marrow were treated with nuclease only or including a donor template and then analyzed for potential gene rearrangements. It was observed that, in pooled CD34+ cells and colony-forming units, the intergenic β-δ-globin deletion was the most frequent rearrangement, followed by inversion of the intergenic fragment, with the inter-chromosomal translocation as the least frequent. No rearrangements were observed when endonuclease activity was restricted to on-target β-globin cleavage. These findings demonstrate the need to develop site-specific endonucleases with high specificity to avoid unwanted gene alterations.
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Affiliation(s)
- Joseph Long
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Biology Department, California State University, Northridge, Northridge, CA 91330, USA
| | - Megan D Hoban
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Aaron R Cooper
- Molecular Biology Interdepartmental Ph.D. Program, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Michael L Kaufman
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Caroline Y Kuo
- Division of Allergy and Immunology, Department of Pediatrics, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Beatriz Campo-Fernandez
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Dianne Lumaquin
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Roger P Hollis
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Xiaoyan Wang
- Department of Internal Medicine and Health Services Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Donald B Kohn
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA; Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, Los Angeles, CA 90095, USA
| | - Zulema Romero
- Department of Microbiology, Immunology and Molecular Genetics, University of California, Los Angeles, Los Angeles, CA 90095, USA.
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Morgan RA, Gray D, Lomova A, Kohn DB. Hematopoietic Stem Cell Gene Therapy: Progress and Lessons Learned. Cell Stem Cell 2017; 21:574-590. [PMID: 29100011 PMCID: PMC6039108 DOI: 10.1016/j.stem.2017.10.010] [Citation(s) in RCA: 155] [Impact Index Per Article: 22.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The use of allogeneic hematopoietic stem cells (HSCs) to treat genetic blood cell diseases has become a clinical standard but is limited by the availability of suitable matched donors and potential immunologic complications. Gene therapy using autologous HSCs should avoid these limitations and thus may be safer. Progressive improvements in techniques for genetic correction of HSCs, by either vector gene addition or gene editing, are facilitating successful treatments for an increasing number of diseases. We highlight the progress, successes, and remaining challenges toward the development of HSC gene therapies and discuss lessons they provide for the development of future clinical stem cell therapies.
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Affiliation(s)
- Richard A Morgan
- Charles R. Drew University of Medicine and Science, Los Angeles, CA, 90059; Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, Los Angeles, CA, 90095
| | - David Gray
- Molecular Biology Institute Interdepartmental Doctoral Program, University of California, Los Angeles, CA, 90095
| | - Anastasia Lomova
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, Los Angeles, CA, 90095
| | - Donald B Kohn
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine at University of California, Los Angeles, CA, 90095; Department of Microbiology, Immunology & Molecular Genetics, David Geffen School of Medicine at University of California, Los Angeles, CA, 90095; Department of Pediatrics, David Geffen School of Medicine at University of California, Los Angeles, CA, 90095; The Eli & Edythe Broad Center of Regenerative Medicine & Stem Cell Research, University of California, Los Angeles, CA, USA.
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41
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Long-Term Engraftment and Fetal Globin Induction upon BCL11A Gene Editing in Bone-Marrow-Derived CD34 + Hematopoietic Stem and Progenitor Cells. MOLECULAR THERAPY-METHODS & CLINICAL DEVELOPMENT 2017; 4:137-148. [PMID: 28344999 PMCID: PMC5363298 DOI: 10.1016/j.omtm.2016.12.009] [Citation(s) in RCA: 117] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/01/2016] [Accepted: 12/28/2016] [Indexed: 12/28/2022]
Abstract
To develop an effective and sustainable cell therapy for sickle cell disease (SCD), we investigated the feasibility of targeted disruption of the BCL11A gene, either within exon 2 or at the GATAA motif in the intronic erythroid-specific enhancer, using zinc finger nucleases in human bone marrow (BM) CD34+ hematopoietic stem and progenitor cells (HSPCs). Both targeting strategies upregulated fetal globin expression in erythroid cells to levels predicted to inhibit hemoglobin S polymerization. However, complete inactivation of BCL11A resulting from bi-allelic frameshift mutations in BCL11A exon 2 adversely affected erythroid enucleation. In contrast, bi-allelic disruption of the GATAA motif in the erythroid enhancer of BCL11A did not negatively impact enucleation. Furthermore, BCL11A exon 2-edited BM-CD34+ cells demonstrated a significantly reduced engraftment potential in immunodeficient mice. Such an adverse effect on HSPC function was not observed upon BCL11A erythroid-enhancer GATAA motif editing, because enhancer-edited CD34+ cells achieved robust long-term engraftment and gave rise to erythroid cells with elevated levels of fetal globin expression when chimeric BM was cultured ex vivo. Altogether, our results support further clinical development of the BCL11A erythroid-specific enhancer editing in BM-CD34+ HSPCs as an autologous stem cell therapy in SCD patients.
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Chandrasegaran S. Recent advances in the use of ZFN-mediated gene editing for human gene therapy. ACTA ACUST UNITED AC 2017; 3:33-41. [PMID: 29270315 DOI: 10.18609/cgti.2017.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Targeted genome editing with programmable nucleases has revolutionized biomedical research. The ability to make site-specific modifications to the human genome, has invoked a paradigm shift in gene therapy. Using gene editing technologies, the sequence in the human genome can now be precisely engineered to achieve a therapeutic effect. Zinc finger nucleases (ZFNs) were the first programmable nucleases designed to target and cleave custom sites. This article summarizes the advances in the use of ZFN-mediated gene editing for human gene therapy and discusses the challenges associated with translating this gene editing technology into clinical use.
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Affiliation(s)
- Srinivasan Chandrasegaran
- Department of Environmental Health and Engineering, Johns Hopkins School of Public Health, Baltimore, Maryland 21205, USA
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