1
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Lessard S, Rimmelé P, Ling H, Moran K, Vieira B, Lin YD, Rajani GM, Hong V, Reik A, Boismenu R, Hsu B, Chen M, Cockroft BM, Uchida N, Tisdale J, Alavi A, Krishnamurti L, Abedi M, Galeon I, Reiner D, Wang L, Ramezi A, Rendo P, Walters MC, Levasseur D, Peters R, Harris T, Hicks A. Zinc finger nuclease-mediated gene editing in hematopoietic stem cells results in reactivation of fetal hemoglobin in sickle cell disease. Sci Rep 2024; 14:24298. [PMID: 39414860 PMCID: PMC11484757 DOI: 10.1038/s41598-024-74716-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 09/27/2024] [Indexed: 10/18/2024] Open
Abstract
BIVV003 is a gene-edited autologous cell therapy in clinical development for the potential treatment of sickle cell disease (SCD). Hematopoietic stem cells (HSC) are genetically modified with mRNA encoding zinc finger nucleases (ZFN) that target and disrupt a specific regulatory GATAA motif in the BCL11A erythroid enhancer to reactivate fetal hemoglobin (HbF). We characterized ZFN-edited HSC from healthy donors and donors with SCD. Results of preclinical studies show that ZFN-mediated editing is highly efficient, with enriched biallelic editing and high frequency of on-target indels, producing HSC capable of long-term multilineage engraftment in vivo, and express HbF in erythroid progeny. Interim results from the Phase 1/2 PRECIZN-1 study demonstrated that BIVV003 was well-tolerated in seven participants with SCD, of whom five of the six with more than 3 months of follow-up displayed increased total hemoglobin and HbF, and no severe vaso-occlusive crises. Our data suggest BIVV003 represents a compelling and novel cell therapy for the potential treatment of SCD.
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Affiliation(s)
- Samuel Lessard
- Rare Blood Disorders, Sanofi, Waltham, MA, 02451, USA.
- Precision Medicine and Computational Biology, Sanofi, Cambridge, MA, 02141, USA.
| | | | - Hui Ling
- Rare Blood Disorders, Sanofi, Waltham, MA, 02451, USA
| | - Kevin Moran
- Rare Blood Disorders, Sanofi, Waltham, MA, 02451, USA
| | | | - Yi-Dong Lin
- Rare Blood Disorders, Sanofi, Waltham, MA, 02451, USA
| | | | - Vu Hong
- Rare Blood Disorders, Sanofi, Waltham, MA, 02451, USA
| | | | | | - Ben Hsu
- Sangamo Therapeutics, Richmond, CA, 94804, USA
| | | | | | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institutes/National Institute of Diabetes and Digestive and Kidney Diseases, National Heart, National Institutes of Health (NIH), Bethesda, MD, USA
| | - John Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institutes/National Institute of Diabetes and Digestive and Kidney Diseases, National Heart, National Institutes of Health (NIH), Bethesda, MD, USA
| | - Asif Alavi
- Henry Ford Cancer Institute, Detroit, MI, USA
| | - Lakshmanan Krishnamurti
- Emory University, Aflac Cancer and Blood Disorders Center, Children's Healthcare of Atlanta, Atlanta, GA, USA
| | - Mehrdad Abedi
- University of California-Davis Medical Center, Sacramento, CA, USA
| | | | - David Reiner
- Rare Blood Disorders, Sanofi, Waltham, MA, 02451, USA
| | - Lin Wang
- Rare Blood Disorders, Sanofi, Waltham, MA, 02451, USA
| | - Anne Ramezi
- Rare Blood Disorders, Sanofi, Waltham, MA, 02451, USA
| | - Pablo Rendo
- Rare Blood Disorders, Sanofi, Waltham, MA, 02451, USA
| | - Mark C Walters
- University of California San Francisco Benioff Children's Hospital, Oakland, CA, USA
| | | | - Robert Peters
- Rare Blood Disorders, Sanofi, Waltham, MA, 02451, USA
| | | | - Alexandra Hicks
- Rare Blood Disorders, Sanofi, Waltham, MA, 02451, USA
- Immunology and Inflammation, Sanofi, Cambridge, MA, 02141, USA
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2
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George CA, Sahu SU, de Oñate L, Souza BSDF, Wilson RC. Genome Editing Therapy for the Blood: Ex Vivo Success and In Vivo Prospects. CRISPR J 2024. [PMID: 39324895 DOI: 10.1089/crispr.2024.0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/27/2024] Open
Abstract
Hematopoietic stem cells (HSCs) provide the body with a continuous supply of healthy, functional blood cells. In patients with hematopoietic malignancies, immunodeficiencies, lysosomal storage disorders, and hemoglobinopathies, therapeutic genome editing offers hope for corrective intervention, with even modest editing efficiencies likely to provide clinical benefit. Engineered white blood cells, such as T cells, can be applied therapeutically to address monogenic disorders of the immune system, HIV infection, or cancer. The versatility of CRISPR-based tools allows countless new medical interventions for diseases of the blood, and rapid ex vivo success has been demonstrated in hemoglobinopathies via transplantation of the patient's HSCs following genome editing in a laboratory setting. Here we review recent advances in therapeutic genome editing of HSCs and T cells, focusing on the progress in ex vivo contexts, the promise of improved access via in vivo delivery, as well as the ongoing preclinical efforts that may enable the transition from ex vivo to in vivo administration. We discuss the challenges, limitations, and future prospects of this rapidly developing field, which may one day establish CRISPR as the standard of care for some diseases affecting the blood.
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Affiliation(s)
- Christy A George
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
| | - Srishti U Sahu
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
| | - Lorena de Oñate
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
| | - Bruno Solano de Freitas Souza
- Gonçalo Moniz Institute, Oswaldo Cruz Foundation (FIOCRUZ), Salvador, Brazil
- Pioneer Science Initiative, D'Or Institute for Research and Education (IDOR), Rio de Janeiro, Brazil
| | - Ross C Wilson
- Innovative Genomics Institute, University of California Berkeley, Berkeley, California, USA
- Department of Molecular and Cell Biology, University of California Berkeley, Berkeley, California, USA
- California Institute for Quantitative Biosciences, University of California Berkeley, Berkeley, California, USA
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3
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Lian X, Chatterjee S, Sun Y, Dilliard SA, Moore S, Xiao Y, Bian X, Yamada K, Sung YC, Levine RM, Mayberry K, John S, Liu X, Smith C, Johnson LT, Wang X, Zhang CC, Liu DR, Newby GA, Weiss MJ, Yen JS, Siegwart DJ. Bone-marrow-homing lipid nanoparticles for genome editing in diseased and malignant haematopoietic stem cells. NATURE NANOTECHNOLOGY 2024; 19:1409-1417. [PMID: 38783058 DOI: 10.1038/s41565-024-01680-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2023] [Accepted: 04/15/2024] [Indexed: 05/25/2024]
Abstract
Therapeutic genome editing of haematopoietic stem cells (HSCs) would provide long-lasting treatments for multiple diseases. However, the in vivo delivery of genetic medicines to HSCs remains challenging, especially in diseased and malignant settings. Here we report on a series of bone-marrow-homing lipid nanoparticles that deliver mRNA to a broad group of at least 14 unique cell types in the bone marrow, including healthy and diseased HSCs, leukaemic stem cells, B cells, T cells, macrophages and leukaemia cells. CRISPR/Cas and base editing is achieved in a mouse model expressing human sickle cell disease phenotypes for potential foetal haemoglobin reactivation and conversion from sickle to non-sickle alleles. Bone-marrow-homing lipid nanoparticles were also able to achieve Cre-recombinase-mediated genetic deletion in bone-marrow-engrafted leukaemic stem cells and leukaemia cells. We show evidence that diverse cell types in the bone marrow niche can be edited using bone-marrow-homing lipid nanoparticles.
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Affiliation(s)
- Xizhen Lian
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sumanta Chatterjee
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yehui Sun
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Sean A Dilliard
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Stephen Moore
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yufen Xiao
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaoyan Bian
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Kohki Yamada
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Yun-Chieh Sung
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Rachel M Levine
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Kalin Mayberry
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Samuel John
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xiaoye Liu
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Caroline Smith
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Lindsay T Johnson
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Xu Wang
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - Cheng Cheng Zhang
- Department of Physiology, University of Texas Southwestern Medical Center, Dallas, TX, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Gregory A Newby
- Department of Genetic Medicine, Johns Hopkins University, Baltimore, MD, USA
| | - Mitchell J Weiss
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Jonathan S Yen
- Department of Hematology, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Daniel J Siegwart
- Department of Biomedical Engineering, Department of Biochemistry, Simmons Comprehensive Cancer Center, Program in Genetic Drug Engineering, The University of Texas Southwestern Medical Center, Dallas, TX, USA.
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4
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Santos GPD, Rabi LT, Bezerra AA, da Cunha MR, Iatecola A, Fernandes VAR. Transcriptional regulators of fetal hemoglobin. Hematol Transfus Cell Ther 2024:S2531-1379(24)00296-7. [PMID: 39237431 DOI: 10.1016/j.htct.2024.06.001] [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: 12/12/2023] [Revised: 06/25/2024] [Accepted: 06/25/2024] [Indexed: 09/07/2024] Open
Abstract
Sickle cell anemia is a hereditary disease caused by sickle-shaped red blood cells that can lead to vaso-occlusive crises. Treatment options are currently limited, highlighting the need to develop new clinical approaches. Studies demonstrated that elevated levels of fetal hemoglobin (Hb F) are associated with a reduction of mortality and morbidity in sickle cell anemia patients. In light of this, researchers have been trying to elucidate the transcriptional regulation of Hb F to develop new therapeutic interventions. The present study aimed to present the main transcription factors of Hb F and discuss the clinical feasibility of these molecular targets. Two search strategies were used in the PubMed, SciELO, and LILACS databases between July and August 2023 to conduct this review. Manual searches were also conducted by checking references of potentially eligible studies. Eligibility criteria consisted of clinical trials and cohort studies from the last five years that investigated transcription factors associated with Hb F. The transcription factors investigated in at least four eligible studies were included in this review. As a result, 56 eligible studies provided data on the BCL11A, LRF, NF-Y, GATA1, KLF1, HRI, ATF4, and MYB factors. The studies demonstrated that Hb F is cooperatively regulated by transcription factors with the BCL11A factor appearing to be the most specific target gene for γ-globin induction. Although these data are promising, there are still significant gaps and intervention limitations due to the adverse functions of the target genes. New studies that clarify the aspects and functionalities of Hb F regulators may enable new clinical approaches for sickle cell anemia patients.
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Affiliation(s)
| | - Larissa Teodoro Rabi
- Nossa Senhora do Patrocínio University Center, Itú, SP, Brazil; Laboratory of Cancer Molecular Genetics, School of Medical Sciences (FCM), University of Campinas (UNICAMP), Campinas, SP, Brazil; Institute of Health Sciences, Paulista University (UNIP), Campinas, SP, Brazil
| | - André Alves Bezerra
- Nossa Senhora do Patrocínio University Center, Itú, SP, Brazil; College of Medicine of Jundiaí, Jundiaí, SP, Brazil
| | - Marcelo Rodrigues da Cunha
- Nossa Senhora do Patrocínio University Center, Itú, SP, Brazil; College of Medicine of Jundiaí, Jundiaí, SP, Brazil
| | - Amilton Iatecola
- Nossa Senhora do Patrocínio University Center, Itú, SP, Brazil; College of Medicine of Jundiaí, Jundiaí, SP, Brazil
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5
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Feng Q, Li Q, Zhou H, Wang Z, Lin C, Jiang Z, Liu T, Wang D. CRISPR technology in human diseases. MedComm (Beijing) 2024; 5:e672. [PMID: 39081515 PMCID: PMC11286548 DOI: 10.1002/mco2.672] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2023] [Revised: 07/01/2024] [Accepted: 07/01/2024] [Indexed: 08/02/2024] Open
Abstract
Gene editing is a growing gene engineering technique that allows accurate editing of a broad spectrum of gene-regulated diseases to achieve curative treatment and also has the potential to be used as an adjunct to the conventional treatment of diseases. Gene editing technology, mainly based on clustered regularly interspaced palindromic repeats (CRISPR)-CRISPR-associated protein systems, which is capable of generating genetic modifications in somatic cells, provides a promising new strategy for gene therapy for a wide range of human diseases. Currently, gene editing technology shows great application prospects in a variety of human diseases, not only in therapeutic potential but also in the construction of animal models of human diseases. This paper describes the application of gene editing technology in hematological diseases, solid tumors, immune disorders, ophthalmological diseases, and metabolic diseases; focuses on the therapeutic strategies of gene editing technology in sickle cell disease; provides an overview of the role of gene editing technology in the construction of animal models of human diseases; and discusses the limitations of gene editing technology in the treatment of diseases, which is intended to provide an important reference for the applications of gene editing technology in the human disease.
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Affiliation(s)
- Qiang Feng
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
- Research and Development CentreBaicheng Medical CollegeBaichengChina
| | - Qirong Li
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Hengzong Zhou
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Zhan Wang
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
| | - Chao Lin
- School of Grain Science and TechnologyJilin Business and Technology CollegeChangchunChina
| | - Ziping Jiang
- Department of Hand and Foot SurgeryThe First Hospital of Jilin UniversityChangchunChina
| | - Tianjia Liu
- Research and Development CentreBaicheng Medical CollegeBaichengChina
| | - Dongxu Wang
- Laboratory Animal CenterCollege of Animal ScienceJilin UniversityChangchunChina
- Department of Hand and Foot SurgeryThe First Hospital of Jilin UniversityChangchunChina
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6
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Zhang C, Xu J, Wu Y, Xu C, Xu P. Base Editors-Mediated Gene Therapy in Hematopoietic Stem Cells for Hematologic Diseases. Stem Cell Rev Rep 2024; 20:1387-1405. [PMID: 38644403 PMCID: PMC11319617 DOI: 10.1007/s12015-024-10715-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/25/2024] [Indexed: 04/23/2024]
Abstract
Base editors, developed from the CRISPR/Cas system, consist of components such as deaminase and Cas variants. Since their emergence in 2016, the precision, efficiency, and safety of base editors have been gradually optimized. The feasibility of using base editors in gene therapy has been demonstrated in several disease models. Compared with the CRISPR/Cas system, base editors have shown great potential in hematopoietic stem cells (HSCs) and HSC-based gene therapy, because they do not generate double-stranded breaks (DSBs) while achieving the precise realization of single-base substitutions. This precise editing mechanism allows for the permanent correction of genetic defects directly at their source within HSCs, thus promising a lasting therapeutic effect. Recent advances in base editors are expected to significantly increase the number of clinical trials for HSC-based gene therapies. In this review, we summarize the development and recent progress of DNA base editors, discuss their applications in HSC gene therapy, and highlight the prospects and challenges of future clinical stem cell therapies.
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Affiliation(s)
- Chengpeng Zhang
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Jinchao Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Yikang Wu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Can Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China
| | - Peng Xu
- Cyrus Tang Medical Institute, National Clinical Research Center for Hematologic Diseases, State Key Laboratory of Radiation Medicine and Protection, Collaborative Innovation Center of Hematology, Soochow Medical College, Soochow University, Suzhou, 215123, Jiangsu Province, China.
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7
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Acharya S, Ansari AH, Kumar Das P, Hirano S, Aich M, Rauthan R, Mahato S, Maddileti S, Sarkar S, Kumar M, Phutela R, Gulati S, Rahman A, Goel A, Afzal C, Paul D, Agrawal T, Pulimamidi VK, Jalali S, Nishimasu H, Mariappan I, Nureki O, Maiti S, Chakraborty D. PAM-flexible Engineered FnCas9 variants for robust and ultra-precise genome editing and diagnostics. Nat Commun 2024; 15:5471. [PMID: 38942756 PMCID: PMC11213958 DOI: 10.1038/s41467-024-49233-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2024] [Accepted: 05/29/2024] [Indexed: 06/30/2024] Open
Abstract
The clinical success of CRISPR therapies hinges on the safety and efficacy of Cas proteins. The Cas9 from Francisella novicida (FnCas9) is highly precise, with a negligible affinity for mismatched substrates, but its low cellular targeting efficiency limits therapeutic use. Here, we rationally engineer the protein to develop enhanced FnCas9 (enFnCas9) variants and broaden their accessibility across human genomic sites by ~3.5-fold. The enFnCas9 proteins with single mismatch specificity expanded the target range of FnCas9-based CRISPR diagnostics to detect the pathogenic DNA signatures. They outperform Streptococcus pyogenes Cas9 (SpCas9) and its engineered derivatives in on-target editing efficiency, knock-in rates, and off-target specificity. enFnCas9 can be combined with extended gRNAs for robust base editing at sites which are inaccessible to PAM-constrained canonical base editors. Finally, we demonstrate an RPE65 mutation correction in a Leber congenital amaurosis 2 (LCA2) patient-specific iPSC line using enFnCas9 adenine base editor, highlighting its therapeutic utility.
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Affiliation(s)
- Sundaram Acharya
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
| | - Asgar Hussain Ansari
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prosad Kumar Das
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Seiichi Hirano
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Meghali Aich
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Riya Rauthan
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sudipta Mahato
- Center for Ocular Regeneration, Prof. Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, LV Prasad Eye Institute, Hyderabad, 500034, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Savitri Maddileti
- Center for Ocular Regeneration, Prof. Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, LV Prasad Eye Institute, Hyderabad, 500034, Telangana, India
| | - Sajal Sarkar
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Manoj Kumar
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Rhythm Phutela
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Sneha Gulati
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Abdul Rahman
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Arushi Goel
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - C Afzal
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Deepanjan Paul
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
| | - Trupti Agrawal
- Center for Ocular Regeneration, Prof. Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, LV Prasad Eye Institute, Hyderabad, 500034, Telangana, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Vinay Kumar Pulimamidi
- Center for Ocular Regeneration, Prof. Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, LV Prasad Eye Institute, Hyderabad, 500034, Telangana, India
- Schepens Eye Research Institute, Massachusetts Eye and Ear, Harvard Medical School, Boston, MA, 02114, USA
| | - Subhadra Jalali
- Srimati Kannuri Santhamma Centre for vitreoretinal diseases, Anant Bajaj Retina Institute, Kallam Anji Reddy Campus, L V Prasad Eye Institute, Hyderabad, Telangana, India
| | - Hiroshi Nishimasu
- Department of Chemistry and Biotechnology, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-8656, Japan
- Research Center for Advanced Science and Technology, The University of Tokyo, 4-6-1 Komaba, Meguro-ku, Tokyo, 153-8904, Japan
- Inamori Research Institute for Science, 620 Suiginya-cho, Shimogyo-ku, Kyoto, 600-8411, Japan
| | - Indumathi Mariappan
- Center for Ocular Regeneration, Prof. Brien Holden Eye Research Centre, Hyderabad Eye Research Foundation, LV Prasad Eye Institute, Hyderabad, 500034, Telangana, India
| | - Osamu Nureki
- Department of Biological Sciences, Graduate School of Science, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo, 113-0033, Japan
| | - Souvik Maiti
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Debojyoti Chakraborty
- CSIR-Institute of Genomics & Integrative Biology, Mathura Road, New Delhi, 110025, India.
- Academy of Scientific & Innovative Research (AcSIR), Ghaziabad, 201002, India.
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8
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Kul E, Okoroafor U, Dougherty A, Palkovic L, Li H, Valiño-Ramos P, Aberman L, Young SM. Development of adenoviral vectors that transduce Purkinje cells and other cerebellar cell-types in the cerebellum of a humanized mouse model. Mol Ther Methods Clin Dev 2024; 32:101243. [PMID: 38605812 PMCID: PMC11007541 DOI: 10.1016/j.omtm.2024.101243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Accepted: 03/22/2024] [Indexed: 04/13/2024]
Abstract
Viral vector gene therapy has immense promise for treating central nervous system (CNS) disorders. Although adeno-associated virus vectors (AAVs) have had success, their small packaging capacity limits their utility to treat the root cause of many CNS disorders. Adenoviral vectors (Ad) have tremendous potential for CNS gene therapy approaches. Currently, the most common vectors utilize the Group C Ad5 serotype capsid proteins, which rely on the Coxsackievirus-Adenovirus receptor (CAR) to infect cells. However, these Ad5 vectors are unable to transduce many neuronal cell types that are dysfunctional in many CNS disorders. The human CD46 (hCD46) receptor is widely expressed throughout the human CNS and is the primary attachment receptor for many Ad serotypes. Therefore, to overcome the current limitations of Ad vectors to treat CNS disorders, we created chimeric first generation Ad vectors that utilize the hCD46 receptor. Using a "humanized" hCD46 mouse model, we demonstrate these Ad vectors transduce cerebellar cell types, including Purkinje cells, that are refractory to Ad5 transduction. Since Ad vector transduction properties are dependent on their capsid proteins, these chimeric first generation Ad vectors open new avenues for high-capacity helper-dependent adenovirus (HdAd) gene therapy approaches for cerebellar disorders and multiple neurological disorders.
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Affiliation(s)
- Emre Kul
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Uchechi Okoroafor
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
- Cell Developmental Biology Graduate Program, University of Iowa, Iowa City, IA 52242, USA
| | - Amanda Dougherty
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Lauren Palkovic
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Hao Li
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Paula Valiño-Ramos
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Leah Aberman
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
| | - Samuel M. Young
- Department of Anatomy and Cell Biology, University of Iowa, Iowa City, IA 52242, USA
- Cell Developmental Biology Graduate Program, University of Iowa, Iowa City, IA 52242, USA
- Department of Otolaryngology, University of Iowa, Iowa City, IA 52242, USA
- Iowa Neuroscience Institute, University of Iowa, Iowa City, IA 52242, USA
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9
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Cheng YHH, Bohaczuk SC, Stergachis AB. Functional categorization of gene regulatory variants that cause Mendelian conditions. Hum Genet 2024; 143:559-605. [PMID: 38436667 PMCID: PMC11078748 DOI: 10.1007/s00439-023-02639-w] [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: 06/21/2023] [Accepted: 12/30/2023] [Indexed: 03/05/2024]
Abstract
Much of our current understanding of rare human diseases is driven by coding genetic variants. However, non-coding genetic variants play a pivotal role in numerous rare human diseases, resulting in diverse functional impacts ranging from altered gene regulation, splicing, and/or transcript stability. With the increasing use of genome sequencing in clinical practice, it is paramount to have a clear framework for understanding how non-coding genetic variants cause disease. To this end, we have synthesized the literature on hundreds of non-coding genetic variants that cause rare Mendelian conditions via the disruption of gene regulatory patterns and propose a functional classification system. Specifically, we have adapted the functional classification framework used for coding variants (i.e., loss-of-function, gain-of-function, and dominant-negative) to account for features unique to non-coding gene regulatory variants. We identify that non-coding gene regulatory variants can be split into three distinct categories by functional impact: (1) non-modular loss-of-expression (LOE) variants; (2) modular loss-of-expression (mLOE) variants; and (3) gain-of-ectopic-expression (GOE) variants. Whereas LOE variants have a direct corollary with coding loss-of-function variants, mLOE and GOE variants represent disease mechanisms that are largely unique to non-coding variants. These functional classifications aim to provide a unified terminology for categorizing the functional impact of non-coding variants that disrupt gene regulatory patterns in Mendelian conditions.
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Affiliation(s)
- Y H Hank Cheng
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Stephanie C Bohaczuk
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA
| | - Andrew B Stergachis
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA, USA.
- Department of Genome Sciences, University of Washington, Seattle, WA, USA.
- Brotman Baty Institute for Precision Medicine, Seattle, WA, USA.
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10
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Xu F, Zheng C, Xu W, Zhang S, Liu S, Chen X, Yao K. Breaking genetic shackles: The advance of base editing in genetic disorder treatment. Front Pharmacol 2024; 15:1364135. [PMID: 38510648 PMCID: PMC10953296 DOI: 10.3389/fphar.2024.1364135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The rapid evolution of gene editing technology has markedly improved the outlook for treating genetic diseases. Base editing, recognized as an exceptionally precise genetic modification tool, is emerging as a focus in the realm of genetic disease therapy. We provide a comprehensive overview of the fundamental principles and delivery methods of cytosine base editors (CBE), adenine base editors (ABE), and RNA base editors, with a particular focus on their applications and recent research advances in the treatment of genetic diseases. We have also explored the potential challenges faced by base editing technology in treatment, including aspects such as targeting specificity, safety, and efficacy, and have enumerated a series of possible solutions to propel the clinical translation of base editing technology. In conclusion, this article not only underscores the present state of base editing technology but also envisions its tremendous potential in the future, providing a novel perspective on the treatment of genetic diseases. It underscores the vast potential of base editing technology in the realm of genetic medicine, providing support for the progression of gene medicine and the development of innovative approaches to genetic disease therapy.
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Affiliation(s)
- Fang Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Caiyan Zheng
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Weihui Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shiyao Zhang
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shanshan Liu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Xiaopeng Chen
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Kai Yao
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
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11
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Ghanim HY, Porteus MH. Gene regulation in inborn errors of immunity: Implications for gene therapy design and efficacy. Immunol Rev 2024; 322:157-177. [PMID: 38233996 DOI: 10.1111/imr.13305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 12/28/2023] [Accepted: 01/02/2024] [Indexed: 01/19/2024]
Abstract
Inborn errors of immunity (IEI) present a unique paradigm in the realm of gene therapy, emphasizing the need for precision in therapeutic design. As gene therapy transitions from broad-spectrum gene addition to careful modification of specific genes, the enduring safety and effectiveness of these therapies in clinical settings have become crucial. This review discusses the significance of IEIs as foundational models for pioneering and refining precision medicine. We explore the capabilities of gene addition and gene correction platforms in modifying the DNA sequence of primary cells tailored for IEIs. The review uses four specific IEIs to highlight key issues in gene therapy strategies: X-linked agammaglobulinemia (XLA), X-linked chronic granulomatous disease (X-CGD), X-linked hyper IgM syndrome (XHIGM), and immune dysregulation, polyendocrinopathy, enteropathy, X-linked (IPEX). We detail the regulatory intricacies and therapeutic innovations for each disorder, incorporating insights from relevant clinical trials. For most IEIs, regulated expression is a vital aspect of the underlying biology, and we discuss the importance of endogenous regulation in developing gene therapy strategies.
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Affiliation(s)
- Hana Y Ghanim
- Division of Pediatrics, Division of Oncology, Hematology, Stem Cell Transplantation, Stanford University, Stanford, California, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
| | - Matthew H Porteus
- Division of Pediatrics, Division of Oncology, Hematology, Stem Cell Transplantation, Stanford University, Stanford, California, USA
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, California, USA
- Center for Definitive and Curative Medicine, Stanford University School of Medicine, Stanford, California, USA
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12
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Zhang Y, Wu ZY. Gene therapy for monogenic disorders: challenges, strategies, and perspectives. J Genet Genomics 2024; 51:133-143. [PMID: 37586590 DOI: 10.1016/j.jgg.2023.08.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2023] [Revised: 08/02/2023] [Accepted: 08/05/2023] [Indexed: 08/18/2023]
Abstract
Monogenic disorders refer to a group of human diseases caused by mutations in single genes. While disease-modifying therapies have offered some relief from symptoms and delayed progression for some monogenic diseases, most of these diseases still lack effective treatments. In recent decades, gene therapy has emerged as a promising therapeutic strategy for genetic disorders. Researchers have developed various gene manipulation tools and gene delivery systems to treat monogenic diseases. Despite this progress, concerns about inefficient delivery, persistent expression, immunogenicity, toxicity, capacity limitation, genomic integration, and limited tissue specificity still need to be addressed. This review gives an overview of commonly used gene therapy and delivery tools, along with the challenges they face and potential strategies to counter them.
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Affiliation(s)
- Yi Zhang
- Department of Medical Genetics and Center for Rare Diseases, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Key Laboratory of Medical Neurobiology of Zhejiang Province, Hangzhou, Zhejiang 310009, China
| | - Zhi-Ying Wu
- Department of Medical Genetics and Center for Rare Diseases, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Department of Neurology, Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou, Zhejiang 310009, China; Key Laboratory of Medical Neurobiology of Zhejiang Province, Hangzhou, Zhejiang 310009, China.
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13
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Leclerc D, Siroky MD, Miller SM. Next-generation biological vector platforms for in vivo delivery of genome editing agents. Curr Opin Biotechnol 2024; 85:103040. [PMID: 38103518 DOI: 10.1016/j.copbio.2023.103040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2023] [Revised: 10/04/2023] [Accepted: 11/22/2023] [Indexed: 12/19/2023]
Abstract
CRISPR-based genome editing holds promise for addressing genetic disease, infectious disease, and cancer and has rapidly advanced from primary research to clinical trials in recent years. However, the lack of safe and potent in vivo delivery methods for CRISPR components has limited most ongoing clinical trials to ex vivo gene therapy. Effective CRISPR in vivo genome editing necessitates an effective vehicle ensuring target cell transduction while minimizing off-target effects, toxicity, and immune reactions. In this review, we examine promising biological-derived platforms to deliver DNA editing agents in vivo and the engineering thereof, encompassing potent viral-based vehicles, flexible protein nanocages, and mammalian-derived particles.
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Affiliation(s)
- Delphine Leclerc
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Michael D Siroky
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - Shannon M Miller
- Department of Chemistry, The Scripps Research Institute, La Jolla, CA 92037, USA.
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14
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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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15
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Madigan V, Zhang F, Dahlman JE. Drug delivery systems for CRISPR-based genome editors. Nat Rev Drug Discov 2023; 22:875-894. [PMID: 37723222 DOI: 10.1038/s41573-023-00762-x] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/06/2023] [Indexed: 09/20/2023]
Abstract
CRISPR-based drugs can theoretically manipulate any genetic target. In practice, however, these drugs must enter the desired cell without eliciting an unwanted immune response, so a delivery system is often required. Here, we review drug delivery systems for CRISPR-based genome editors, focusing on adeno-associated viruses and lipid nanoparticles. After describing how these systems are engineered and their subsequent characterization in preclinical animal models, we highlight data from recent clinical trials. Preclinical targeting mediated by polymers, proteins, including virus-like particles, and other vehicles that may deliver CRISPR systems in the future is also discussed.
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Affiliation(s)
- Victoria Madigan
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - Feng Zhang
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- McGovern Institute for Brain Research at MIT, Cambridge, MA, USA
- Department of Brain and Cognitive Science, Massachusetts Institute of Technology, Cambridge, MA, USA
- Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA
- Howard Hughes Medical Institute, Cambridge, MA, USA
| | - James E Dahlman
- Wallace H. Coulter Department of Biomedical Engineering, Georgia Institute of Technology and Emory University School of Medicine, Atlanta, GA, USA.
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16
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Murugesan R, Karuppusamy KV, Marepally S, Thangavel S. Current approaches and potential challenges in the delivery of gene editing cargos into hematopoietic stem and progenitor cells. Front Genome Ed 2023; 5:1148693. [PMID: 37780116 PMCID: PMC10540692 DOI: 10.3389/fgeed.2023.1148693] [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: 01/20/2023] [Accepted: 08/17/2023] [Indexed: 10/03/2023] Open
Abstract
Advancements in gene delivery and editing have expanded the applications of autologous hematopoietic stem and progenitor cells (HSPCs) for the treatment of monogenic and acquired diseases. The gene editing toolbox is growing, and the ability to achieve gene editing with mRNA or protein delivered intracellularly by vehicles, such as electroporation and nanoparticles, has highlighted the potential of gene editing in HSPCs. Ongoing phase I/II clinical trials with gene-edited HSPCs for β-hemoglobinopathies provide hope for treating monogenic diseases. The development of safe and efficient gene editing reagents and their delivery into hard-to-transfect HSPCs have been critical drivers in the rapid translation of HSPC gene editing into clinical studies. This review article summarizes the available payloads and delivery vehicles for gene editing HSPCs and their potential impact on therapeutic applications.
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Affiliation(s)
- Ramya Murugesan
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Karthik V. Karuppusamy
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu, India
- Manipal Academy of Higher Education, Manipal, Karnataka, India
| | - Srujan Marepally
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu, India
| | - Saravanabhavan Thangavel
- Centre for Stem Cell Research (CSCR), A Unit of InStem Bengaluru, Christian Medical College Campus, Vellore, Tamil Nadu, India
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17
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Canarutto D, Omer Javed A, Pedrazzani G, Ferrari S, Naldini L. Mobilization-based engraftment of haematopoietic stem cells: a new perspective for chemotherapy-free gene therapy and transplantation. Br Med Bull 2023; 147:108-120. [PMID: 37460391 PMCID: PMC10502445 DOI: 10.1093/bmb/ldad017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 06/30/2023] [Indexed: 09/16/2023]
Abstract
INTRODUCTION In haematopoietic stem cell transplantation (HSCT), haematopoietic stem cells (HSCs) from a healthy donor replace the patient's ones. Ex vivo HSC gene therapy (HSC-GT) is a form of HSCT in which HSCs, usually from an autologous source, are genetically modified before infusion, to generate a progeny of gene-modified cells. In HSCT and HSC-GT, chemotherapy is administered before infusion to free space in the bone marrow (BM) niche, which is required for the engraftment of infused cells. Here, we review alternative chemotherapy-free approaches to niche voidance that could replace conventional regimens and alleviate the morbidity of the procedure. SOURCES OF DATA Literature was reviewed from PubMed-listed peer-reviewed articles. No new data are presented in this article. AREAS OF AGREEMENT Chemotherapy exerts short and long-term toxicity to haematopoietic and non-haematopoietic organs. Whenever chemotherapy is solely used to allow engraftment of donor HSCs, rather than eliminating malignant cells, as in the case of HSC-GT for inborn genetic diseases, non-genotoxic approaches sparing off-target tissues are highly desirable. AREAS OF CONTROVERSY In principle, HSCs can be temporarily moved from the BM niches using mobilizing drugs or selectively cleared with targeted antibodies or immunotoxins to make space for the infused cells. However, translation of these principles into clinically relevant settings is only at the beginning, and whether therapeutically meaningful levels of chimerism can be safely established with these approaches remains to be determined. GROWING POINTS In pre-clinical models, mobilization of HSCs from the niche can be tailored to accommodate the exchange and engraftment of infused cells. Infused cells can be further endowed with a transient engraftment advantage. AREAS TIMELY FOR DEVELOPING RESEARCH Inter-individual efficiency and kinetics of HSC mobilization need to be carefully assessed. Investigations in large animal models of emerging non-genotoxic approaches will further strengthen the rationale and encourage application to the treatment of selected diseases.
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Affiliation(s)
- Daniele Canarutto
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, 20132 Milano, MI, Italy
- Vita-Salute San Raffaele University, Via Olgettina, 60, 20132 Milano, MI, Italy
- Pediatric Immunohematology Unit and BMT Program, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, 20132 Milano, MI, Italy
| | - Attya Omer Javed
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, 20132 Milano, MI, Italy
| | - Gabriele Pedrazzani
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, 20132 Milano, MI, Italy
- Vita-Salute San Raffaele University, Via Olgettina, 60, 20132 Milano, MI, Italy
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, 20132 Milano, MI, Italy
- Vita-Salute San Raffaele University, Via Olgettina, 60, 20132 Milano, MI, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Via Olgettina, 60, 20132 Milano, MI, Italy
- Vita-Salute San Raffaele University, Via Olgettina, 60, 20132 Milano, MI, Italy
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18
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Piel FB, Rees DC, DeBaun MR, Nnodu O, Ranque B, Thompson AA, Ware RE, Abboud MR, Abraham A, Ambrose EE, Andemariam B, Colah R, Colombatti R, Conran N, Costa FF, Cronin RM, de Montalembert M, Elion J, Esrick E, Greenway AL, Idris IM, Issom DZ, Jain D, Jordan LC, Kaplan ZS, King AA, Lloyd-Puryear M, Oppong SA, Sharma A, Sung L, Tshilolo L, Wilkie DJ, Ohene-Frempong K. Defining global strategies to improve outcomes in sickle cell disease: a Lancet Haematology Commission. Lancet Haematol 2023; 10:e633-e686. [PMID: 37451304 PMCID: PMC11459696 DOI: 10.1016/s2352-3026(23)00096-0] [Citation(s) in RCA: 29] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2023] [Revised: 03/31/2023] [Accepted: 04/12/2023] [Indexed: 07/18/2023]
Abstract
All over the world, people with sickle cell disease (an inherited condition) have premature deaths and preventable severe chronic complications, which considerably affect their quality of life, career progression, and financial status. In addition, these people are often affected by stigmatisation or structural racism, which can contribute to stress and poor mental health. Inequalities affecting people with sickle cell disease are also reflected in the distribution of the disease—mainly in sub-Saharan Africa, India, and the Caribbean—whereas interventions, clinical trials, and funding are mostly available in North America, Europe, and the Middle East. Although some of these characteristics also affect people with other genetic diseases, the fate of people with sickle cell disease seems to be particularly unfair. Simple, effective interventions to reduce the mortality and morbidity associated with sickle cell disease are available. The main obstacle preventing better outcomes in this condition, which is a neglected disease, is associated with inequalities impacting the patient populations. The aim of this Commission is to highlight the problems associated with sickle cell disease and to identify achievable goals to improve outcomes both in the short and long term. The ambition for the management of people with sickle cell disease is that curative treatments become available to every person with the condition. Although this would have seemed unrealistic a decade ago, developments in gene therapy make this potentially achievable, albeit in the distant future. Until these curative technologies are fully developed and become widely available, health-care professionals (with the support of policy makers, funders, etc) should make sure that a minimum standard of care (including screening, prophylaxis against infection, acute medical care, safe blood transfusion, and hydroxyurea) is available to all patients. In considering what needs to be achieved to reduce the global burden of sickle cell disease and improve the quality of life of patients, this Commission focuses on five key areas: the epidemiology of sickle cell disease (Section 1 ); screening and prevention (Section 2 ); established and emerging treatments for the management of the disease (Section 3 ); cellular therapies with curative potential (Section 4 ); and training and education needs (Section 5 ). As clinicians, researchers, and patients, our objective to reduce the global burden of sickle cell disease aligns with wider public health aims to reduce inequalities, improve health for all, and develop personalised treatment options. We have observed in the past few years some long-awaited momentum following the development of innovative point-of-care testing devices, new approved drugs, and emerging curative options. Reducing the burden of sickle cell disease will require substantial financial and political commitment, but it will impact the lives of millions of patients and families worldwide and the lessons learned in achieving this goal would unarguably benefit society as a whole.
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Affiliation(s)
- Frédéric B Piel
- Department of Epidemiology and Biostatistics, School of Public Health, Imperial College London, London, UK.
| | - David C Rees
- Department of Paediatric Haematology, King's College London, King's College Hospital, London, UK
| | - Michael R DeBaun
- Department of Pediatrics, Vanderbilt-Meharry Center of Excellence for Sickle Cell Disease, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Obiageli Nnodu
- Department of Haematology and Blood Transfusion, College of Health Sciences and Centre of Excellence for Sickle Cell Disease Research and Training, University of Abuja, Abuja, Nigeria
| | - Brigitte Ranque
- Department of Internal Medicine, Georges Pompidou European Hospital, Assistance Publique-Hopitaux de Paris Centre, University of Paris Cité, Paris, France
| | - Alexis A Thompson
- Division of Hematology, Children's Hospital of Philadelphia, Philadelphia, PA, USA
| | - Russell E Ware
- Division of Hematology and Global Health Center, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Miguel R Abboud
- Department of Pediatrics and Adolescent Medicine, and Sickle Cell Program, American University of Beirut, Beirut, Lebanon
| | - Allistair Abraham
- Division of Blood and Marrow Transplantation, Children's National Hospital, Washington, DC, USA
| | - Emmanuela E Ambrose
- Department of Paediatrics and Child Health, Bugando Medical Centre, Mwanza, Tanzania
| | - Biree Andemariam
- New England Sickle Cell Institute, University of Connecticut Health, Connecticut, USA
| | - Roshan Colah
- Department of Haematogenetics, Indian Council of Medical Research National Institute of Immunohaematology, Mumbai, India
| | - Raffaella Colombatti
- Pediatric Oncology Hematology Unit, Department of Women's and Children's Health, University of Padua, Padua, Italy
| | - Nicola Conran
- Department of Clinical Medicine, School of Medical Sciences, Center of Hematology and Hemotherapy (Hemocentro), University of Campinas-UNICAMP, Campinas, Brazil
| | - Fernando F Costa
- Department of Clinical Medicine, School of Medical Sciences, Center of Hematology and Hemotherapy (Hemocentro), University of Campinas-UNICAMP, Campinas, Brazil
| | - Robert M Cronin
- Department of Internal Medicine, The Ohio State University, Columbus, OH, USA
| | - Mariane de Montalembert
- Department of Pediatrics, Necker-Enfants Malades Hospital, Assistance Publique-Hopitaux de Paris Centre, Paris, France
| | - Jacques Elion
- Paris Cité University and University of the Antilles, Inserm, BIGR, Paris, France
| | - Erica Esrick
- Dana-Farber/Boston Children's Cancer and Blood Disorders Center, Harvard Medical School, Boston, MA, USA
| | - Anthea L Greenway
- Department Clinical Haematology, Royal Children's Hospital, Parkville and Department Haematology, Monash Health, Clayton, VIC, Australia
| | - Ibrahim M Idris
- Department of Hematology, Aminu Kano Teaching Hospital/Bayero University Kano, Kano, Nigeria
| | - David-Zacharie Issom
- Department of Business Information Systems, School of Management, HES-SO University of Applied Sciences and Arts of Western Switzerland, Geneva, Switzerland
| | - Dipty Jain
- Department of Paediatrics, Government Medical College, Nagpur, India
| | - Lori C Jordan
- Department of Pediatrics, Division of Pediatric Neurology, Vanderbilt University Medical Center, Nashville, TN, USA
| | - Zane S Kaplan
- Department of Clinical Haematology, Monash Health and Monash University, Melbourne, VIC, Australia
| | - Allison A King
- Departments of Pediatrics and Internal Medicine, Divisions of Pediatric Hematology and Oncology and Hematology, Washington University School of Medicine, St Louis, MO, USA
| | - Michele Lloyd-Puryear
- Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Samuel A Oppong
- Department of Obstetrics and Gynecology, University of Ghana Medical School, Accra, Ghana
| | - Akshay Sharma
- Department of Bone Marrow Transplantation and Cellular Therapy, St Jude Children's Research Hospital, Memphis, TN, USA
| | - Lillian Sung
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - Leon Tshilolo
- Institute of Biomedical Research/CEFA Monkole Hospital Centre and Official University of Mbuji-Mayi, Mbuji-Mayi, Democratic Republic of the Congo
| | - Diana J Wilkie
- Department of Biobehavioral Nursing Science, College of Nursing, University of Florida, Gainesville, FL, USA
| | - Kwaku Ohene-Frempong
- Division of Hematology, Children's Hospital of Philadelphia, Pennsylvania, USA; Sickle Cell Foundation of Ghana, Kumasi, Ghana
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19
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Mayuranathan T, Newby GA, Feng R, Yao Y, Mayberry KD, Lazzarotto CR, Li Y, Levine RM, Nimmagadda N, Dempsey E, Kang G, Porter SN, Doerfler PA, Zhang J, Jang Y, Chen J, Bell HW, Crossley M, Bhoopalan SV, Sharma A, Tisdale JF, Pruett-Miller SM, Cheng Y, Tsai SQ, Liu DR, Weiss MJ, Yen JS. Potent and uniform fetal hemoglobin induction via base editing. Nat Genet 2023; 55:1210-1220. [PMID: 37400614 PMCID: PMC10722557 DOI: 10.1038/s41588-023-01434-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Accepted: 05/23/2023] [Indexed: 07/05/2023]
Abstract
Inducing fetal hemoglobin (HbF) in red blood cells can alleviate β-thalassemia and sickle cell disease. We compared five strategies in CD34+ hematopoietic stem and progenitor cells, using either Cas9 nuclease or adenine base editors. The most potent modification was adenine base editor generation of γ-globin -175A>G. Homozygous -175A>G edited erythroid colonies expressed 81 ± 7% HbF versus 17 ± 11% in unedited controls, whereas HbF levels were lower and more variable for two Cas9 strategies targeting a BCL11A binding motif in the γ-globin promoter or a BCL11A erythroid enhancer. The -175A>G base edit also induced HbF more potently than a Cas9 approach in red blood cells generated after transplantation of CD34+ hematopoietic stem and progenitor cells into mice. Our data suggest a strategy for potent, uniform induction of HbF and provide insights into γ-globin gene regulation. More generally, we demonstrate that diverse indels generated by Cas9 can cause unexpected phenotypic variation that can be circumvented by base editing.
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Affiliation(s)
| | - Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Ruopeng Feng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yu Yao
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Kalin D Mayberry
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Cicera R Lazzarotto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yichao Li
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Rachel M Levine
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Nikitha Nimmagadda
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Erin Dempsey
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Guolian Kang
- Department of Biostatistics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shaina N Porter
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Phillip A Doerfler
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingjing Zhang
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yoonjeong Jang
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Jingjing Chen
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Henry W Bell
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | - Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, New South Wales, Australia
| | | | - Akshay Sharma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute and National Institute of Diabetes and Digestive and Kidney Diseases, Bethesda, MD, USA
| | - Shondra M Pruett-Miller
- Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yong Cheng
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Shengdar Q Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA, USA.
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA.
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
| | - Jonathan S Yen
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, USA.
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20
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Paschoudi K, Yannaki E, Psatha N. Precision Editing as a Therapeutic Approach for β-Hemoglobinopathies. Int J Mol Sci 2023; 24:9527. [PMID: 37298481 PMCID: PMC10253463 DOI: 10.3390/ijms24119527] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/19/2023] [Accepted: 05/26/2023] [Indexed: 06/12/2023] Open
Abstract
Beta-hemoglobinopathies are the most common genetic disorders worldwide, caused by a wide spectrum of mutations in the β-globin locus, and associated with morbidity and early mortality in case of patient non-adherence to supportive treatment. Allogeneic transplantation of hematopoietic stem cells (allo-HSCT) used to be the only curative option, although the indispensable need for an HLA-matched donor markedly restricted its universal application. The evolution of gene therapy approaches made possible the ex vivo delivery of a therapeutic β- or γ- globin gene into patient-derived hematopoietic stem cells followed by the transplantation of corrected cells into myeloablated patients, having led to high rates of transfusion independence (thalassemia) or complete resolution of painful crises (sickle cell disease-SCD). Hereditary persistence of fetal hemoglobin (HPFH), a syndrome characterized by increased γ-globin levels, when co-inherited with β-thalassemia or SCD, converts hemoglobinopathies to a benign condition with mild clinical phenotype. The rapid development of precise genome editing tools (ZFN, TALENs, CRISPR/Cas9) over the last decade has allowed the targeted introduction of mutations, resulting in disease-modifying outcomes. In this context, genome editing tools have successfully been used for the introduction of HPFH-like mutations both in HBG1/HBG2 promoters or/and in the erythroid enhancer of BCL11A to increase HbF expression as an alternative curative approach for β-hemoglobinopathies. The current investigation of new HbF modulators, such as ZBTB7A, KLF-1, SOX6, and ZNF410, further expands the range of possible genome editing targets. Importantly, genome editing approaches have recently reached clinical translation in trials investigating HbF reactivation in both SCD and thalassemic patients. Showing promising outcomes, these approaches are yet to be confirmed in long-term follow-up studies.
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Affiliation(s)
- Kiriaki Paschoudi
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
- Gene and Cell Therapy Center, Hematology Clinic, George Papanikolaou Hospital, Exokhi, 57010 Thessaloniki, Greece;
| | - Evangelia Yannaki
- Gene and Cell Therapy Center, Hematology Clinic, George Papanikolaou Hospital, Exokhi, 57010 Thessaloniki, Greece;
- Department of Hematology, School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Nikoletta Psatha
- Department of Genetics, Development and Molecular Biology, School of Biology, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece;
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21
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Ferrari S, Valeri E, Conti A, Scala S, Aprile A, Di Micco R, Kajaste-Rudnitski A, Montini E, Ferrari G, Aiuti A, Naldini L. Genetic engineering meets hematopoietic stem cell biology for next-generation gene therapy. Cell Stem Cell 2023; 30:549-570. [PMID: 37146580 DOI: 10.1016/j.stem.2023.04.014] [Citation(s) in RCA: 18] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 03/31/2023] [Accepted: 04/12/2023] [Indexed: 05/07/2023]
Abstract
The growing clinical success of hematopoietic stem/progenitor cell (HSPC) gene therapy (GT) relies on the development of viral vectors as portable "Trojan horses" for safe and efficient gene transfer. The recent advent of novel technologies enabling site-specific gene editing is broadening the scope and means of GT, paving the way to more precise genetic engineering and expanding the spectrum of diseases amenable to HSPC-GT. Here, we provide an overview of state-of-the-art and prospective developments of the HSPC-GT field, highlighting how advances in biological characterization and manipulation of HSPCs will enable the design of the next generation of these transforming therapeutics.
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Affiliation(s)
- Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Erika Valeri
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Anastasia Conti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Serena Scala
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Annamaria Aprile
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Raffaella Di Micco
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Anna Kajaste-Rudnitski
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy
| | - Giuliana Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan 20132, Italy; Vita-Salute San Raffaele University, Milan 20132, Italy.
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22
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Li C, Georgakopoulou A, Newby GA, Chen PJ, Everette KA, Paschoudi K, Vlachaki E, Gil S, Anderson AK, Koob T, Huang L, Wang H, Kiem HP, Liu DR, Yannaki E, Lieber A. In vivo HSC prime editing rescues sickle cell disease in a mouse model. Blood 2023; 141:2085-2099. [PMID: 36800642 PMCID: PMC10163316 DOI: 10.1182/blood.2022018252] [Citation(s) in RCA: 14] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 01/20/2023] [Accepted: 01/24/2023] [Indexed: 02/19/2023] Open
Abstract
Sickle cell disease (SCD) is a monogenic disease caused by a nucleotide mutation in the β-globin gene. Current gene therapy studies are mainly focused on lentiviral vector-mediated gene addition or CRISPR/Cas9-mediated fetal globin reactivation, leaving the root cause unfixed. We developed a vectorized prime editing system that can directly repair the SCD mutation in hematopoietic stem cells (HSCs) in vivo in a SCD mouse model (CD46/Townes mice). Our approach involved a single intravenous injection of a nonintegrating, prime editor-expressing viral vector into mobilized CD46/Townes mice and low-dose drug selection in vivo. This procedure resulted in the correction of ∼40% of βS alleles in HSCs. On average, 43% of sickle hemoglobin was replaced by adult hemoglobin, thereby greatly mitigating the SCD phenotypes. Transplantation in secondary recipients demonstrated that long-term repopulating HSCs were edited. Highly efficient target site editing was achieved with minimal generation of insertions and deletions and no detectable off-target editing. Because of its simplicity and portability, our in vivo prime editing approach has the potential for application in resource-poor countries where SCD is prevalent.
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Affiliation(s)
- Chang Li
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Aphrodite Georgakopoulou
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
| | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA
| | - Peter J. Chen
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA
| | - Kelcee A. Everette
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA
| | - Kiriaki Paschoudi
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Efthymia Vlachaki
- Hematological Laboratory, Second Department of Internal Medicine, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, Hippokration General Hospital, Thessaloniki, Greece
| | - Sucheol Gil
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Anna K. Anderson
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Theodore Koob
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Lishan Huang
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Hongjie Wang
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Hans-Peter Kiem
- Stem and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA
- Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA
- Howard Hughes Medical Institute, Harvard University, Cambridge, MA
| | - Evangelia Yannaki
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
| | - André Lieber
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
- Department of Pathology, University of Washington, Seattle, WA
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23
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Shi D, Toyonaga S, Anderson DG. In Vivo RNA Delivery to Hematopoietic Stem and Progenitor Cells via Targeted Lipid Nanoparticles. NANO LETTERS 2023; 23:2938-2944. [PMID: 36988645 PMCID: PMC10103292 DOI: 10.1021/acs.nanolett.3c00304] [Citation(s) in RCA: 45] [Impact Index Per Article: 45.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 03/23/2023] [Indexed: 05/22/2023]
Abstract
Ex vivo autologous hematopoietic stem cell (HSC) gene therapy has provided new therapies for the treatment of hematological disorders. However, these therapies have several limitations owing to the manufacturing complexities and toxicity resulting from required conditioning regimens. Here, we developed a c-kit (CD117) antibody-targeted lipid nanoparticle (LNP) that, following a single intravenous injection, can deliver RNA (both siRNA and mRNA) to HSCs in vivo in rodents. This targeted delivery system does not require stem cell harvest, culture, or mobilization of HSCs to facilitate delivery. We also show that delivery of Cre recombinase mRNA at a dose of 1 mg kg-1 can facilitate gene editing to almost all (∼90%) hematopoietic stem and progenitor cells (HSPCs) in vivo, and edited cells retain their stemness and functionality to generate high levels of edited mature immune cells.
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Affiliation(s)
- Dennis Shi
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Sho Toyonaga
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- FUJIFILM
Pharmaceuticals U.S.A., Inc., Cambridge, Massachusetts 02142, United States
| | - Daniel G. Anderson
- Department
of Chemical Engineering, Massachusetts Institute
of Technology, Cambridge, Massachusetts 02139, United States
- David
H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Harvard-Massachusetts
Institute of Technology, Division of Health Science and Technology, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
- Institute
for Medical Engineering and Science, Massachusetts
Institute of Technology, Cambridge, Massachusetts 02139, United States
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24
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Christakopoulos GE, Telange R, Yen J, Weiss MJ. Gene Therapy and Gene Editing for β-Thalassemia. Hematol Oncol Clin North Am 2023; 37:433-447. [PMID: 36907613 PMCID: PMC10355137 DOI: 10.1016/j.hoc.2022.12.012] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023]
Abstract
After many years of intensive research, emerging data from clinical trials indicate that gene therapy for transfusion-dependent β-thalassemia is now possible. Strategies for therapeutic manipulation of patient hematopoietic stem cells include lentiviral transduction of a functional erythroid-expressed β-globin gene and genome editing to activate fetal hemoglobin production in patient red blood cells. Gene therapy for β-thalassemia and other blood disorders will invariably improve as experience accumulates over time. The best overall approaches are not known and perhaps not yet established. Gene therapy comes at a high cost, and collaboration between multiple stakeholders is required to ensure that these new medicines are administered equitably.
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Affiliation(s)
- Georgios E Christakopoulos
- Department of Oncology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS #355, Memphis, TN 38105, USA
| | - Raul Telange
- Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS #355, Memphis, TN 38105, USA
| | - Jonathan Yen
- Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS #355, Memphis, TN 38105, USA
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, 262 Danny Thomas Place, MS #355, Memphis, TN 38105, USA.
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25
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Wolff JH, Mikkelsen JG. Prime editing in hematopoietic stem cells—From ex vivo to in vivo CRISPR-based treatment of blood disorders. Front Genome Ed 2023; 5:1148650. [PMID: 36969373 PMCID: PMC10036844 DOI: 10.3389/fgeed.2023.1148650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2023] [Accepted: 02/28/2023] [Indexed: 03/12/2023] Open
Abstract
Prime editing of human hematopoietic stem cells has the potential to become a safe and efficient way of treating diseases of the blood directly in patients. By allowing site-targeted gene intervention without homology-directed repair donor templates and DNA double-stranded breaks, the invention of prime editing fuels the exploration of alternatives to conventional recombination-based ex vivo genome editing of hematopoietic stem cells. Prime editing is as close as we get today to a true genome editing drug that does not require a separate DNA donor. However, to adapt the technology to perform in vivo gene correction, key challenges remain to be solved, such as identifying effective prime editing guide RNAs for clinical targets as well as developing efficient vehicles to deliver prime editors to stem cells in vivo. In this review, we summarize the current progress in delivery of prime editors both in vitro and in vivo and discuss future challenges that need to be adressed to allow in vivo prime editing as a cure for blood disorders.
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26
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Bhoopalan SV, Yen JS, Levine RM, Sharma A. Editing human hematopoietic stem cells: advances and challenges. Cytotherapy 2023; 25:261-269. [PMID: 36123234 DOI: 10.1016/j.jcyt.2022.08.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 07/29/2022] [Accepted: 08/08/2022] [Indexed: 02/07/2023]
Abstract
Genome editing of hematopoietic stem and progenitor cells is being developed for the treatment of several inherited disorders of the hematopoietic system. The adaptation of CRISPR-Cas9-based technologies to make precise changes to the genome, and developments in altering the specificity and efficiency, and improving the delivery of nucleases to target cells have led to several breakthroughs. Many clinical trials are ongoing, and several pre-clinical models have been reported that would allow these genetic therapies to one day offer a potential cure to patients with diseases where limited options currently exist. However, there remain several challenges with respect to establishing safety, expanding accessibility and improving the manufacturing processes of these therapeutic products. This review focuses on some of the recent advances in the field of genome editing of hematopoietic stem and progenitor cells and illustrates the ongoing challenges.
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Affiliation(s)
- Senthil Velan Bhoopalan
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA; Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jonathan S Yen
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Rachel M Levine
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Akshay Sharma
- Department of Bone Marrow Transplantation and Cellular Therapy, St. Jude Children's Research Hospital, Memphis, Tennessee, USA.
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27
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Lahr WS, Sipe CJ, Skeate JG, Webber BR, Moriarity BS. CRISPR-Cas9 base editors and their current role in human therapeutics. Cytotherapy 2023; 25:270-276. [PMID: 36635153 PMCID: PMC10887149 DOI: 10.1016/j.jcyt.2022.11.013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 11/16/2022] [Accepted: 11/30/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Consistent progress has been made to create more efficient and useful CRISPR-Cas9-based molecular toolsfor genomic modification. METHODS This review focuses on recent articles that have employed base editors (BEs) for both clinical and research purposes. RESULTS CRISPR-Cas9 BEs are a useful system because of their highefficiency and broad applicability to gene correction and disruption. In addition, base editing has beensuggested as a safer approach than other CRISPR-Cas9-based systems, as it limits double-strand breaksduring multiplex gene knockout and does not require a toxic DNA donor molecule for genetic correction. CONCLUSION As such, numerous industry and academic groups are currently developing base editing strategies withclinical applications in cancer immunotherapy and gene therapy, which this review will discuss, with a focuson current and future applications of in vivo BE delivery.
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Affiliation(s)
- Walker S. Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Christopher J. Sipe
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Joseph G. Skeate
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
| | - Beau R. Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
| | - Branden S. Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN, USA
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN, USA
- Department of Genetics, Cell Biology and Development, University of Minnesota, Minneapolis, MN, USA
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28
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Borot F, Humbert O, Newby GA, Fields E, Kohli S, Radtke S, Laszlo GS, Mayuranathan T, Ali AM, Weiss MJ, Yen JS, Walter RB, Liu DR, Mukherjee S, Kiem HP. Multiplex Base Editing to Protect from CD33-Directed Therapy: Implications for Immune and Gene Therapy. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.02.23.529353. [PMID: 36865281 PMCID: PMC9980058 DOI: 10.1101/2023.02.23.529353] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/25/2023]
Abstract
On-target toxicity to normal cells is a major safety concern with targeted immune and gene therapies. Here, we developed a base editing (BE) approach exploiting a naturally occurring CD33 single nucleotide polymorphism leading to removal of full-length CD33 surface expression on edited cells. CD33 editing in human and nonhuman primate (NHP) hematopoietic stem and progenitor cells (HSPCs) protects from CD33-targeted therapeutics without affecting normal hematopoiesis in vivo , thus demonstrating potential for novel immunotherapies with reduced off-leukemia toxicity. For broader applications to gene therapies, we demonstrated highly efficient (>70%) multiplexed adenine base editing of the CD33 and gamma globin genes, resulting in long-term persistence of dual gene-edited cells with HbF reactivation in NHPs. In vitro , dual gene-edited cells could be enriched via treatment with the CD33 antibody-drug conjugate, gemtuzumab ozogamicin (GO). Together, our results highlight the potential of adenine base editors for improved immune and gene therapies. Graphical abstract
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29
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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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30
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Buffa V, Alvarez Vargas JR, Galy A, Spinozzi S, Rocca CJ. Hematopoietic stem and progenitors cells gene editing: Beyond blood disorders. Front Genome Ed 2023; 4:997142. [PMID: 36698790 PMCID: PMC9868335 DOI: 10.3389/fgeed.2022.997142] [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: 07/18/2022] [Accepted: 12/19/2022] [Indexed: 01/10/2023] Open
Abstract
Lessons learned from decades-long practice in the transplantation of hematopoietic stem and progenitor cells (HSPCs) to treat severe inherited disorders or cancer, have set the stage for the current ex vivo gene therapies using autologous gene-modified hematopoietic stem and progenitor cells that have treated so far, hundreds of patients with monogenic disorders. With increased knowledge of hematopoietic stem and progenitor cell biology, improved modalities for patient conditioning and with the emergence of new gene editing technologies, a new era of hematopoietic stem and progenitor cell-based gene therapies is poised to emerge. Gene editing has the potential to restore physiological expression of a mutated gene, or to insert a functional gene in a precise locus with reduced off-target activity and toxicity. Advances in patient conditioning has reduced treatment toxicities and may improve the engraftment of gene-modified cells and specific progeny. Thanks to these improvements, new potential treatments of various blood- or immune disorders as well as other inherited diseases will continue to emerge. In the present review, the most recent advances in hematopoietic stem and progenitor cell gene editing will be reported, with a focus on how this approach could be a promising solution to treat non-blood-related inherited disorders and the mechanisms behind the therapeutic actions discussed.
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Affiliation(s)
- Valentina Buffa
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - José Roberto Alvarez Vargas
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - Anne Galy
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - Simone Spinozzi
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France
| | - Céline J. Rocca
- Genethon, Evry, France,Integrare Research Unit UMR_S951, Université Paris-Saclay, University Evry, Inserm, Genethon, Evry, France,*Correspondence: Céline J. Rocca,
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31
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Mahmoud Ahmed NH, Lai MI. The Novel Role of the B-Cell Lymphoma/Leukemia 11A (BCL11A) Gene in β-Thalassaemia Treatment. Cardiovasc Hematol Disord Drug Targets 2023; 22:226-236. [PMID: 36734897 DOI: 10.2174/1871529x23666230123140926] [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: 09/01/2022] [Revised: 12/21/2022] [Accepted: 12/30/2022] [Indexed: 02/01/2023]
Abstract
β-thalassaemia is a genetic disorder resulting in a reduction or absence of β-globin gene expression. Due to the high prevalence of β-thalassaemia and the lack of available treatment other than blood transfusion and haematopoietic stem cell (HSC) transplantation, the disease represents a considerable burden to clinical and economic systems. Foetal haemoglobin has an appreciated ameliorating effect in β-haemoglobinopathy, as the γ-globin chain substitutes the β-globin chain reduction by pairing with the excess α-globin chain in β-thalassaemia and reduces sickling in sickle cell disease (SCD). BCL11A is a critical regulator and repressor of foetal haemoglobin. Downregulation of BCL11A in adult erythroblasts and cell lines expressing adult haemoglobin led to a significant increase in foetal haemoglobin levels. Disruption of BCL11A erythroid enhancer resulted in disruption of the BCL11A gene solely in the erythroid lineages and increased γ-globin expression in adult erythroid cells. Autologous haematopoietic stem cell gene therapy represents an attractive treatment option to overcome the immune complications and donor availability associated with allogeneic transplantation. Using genome editing technologies, the disruption of BCL11A to induce γ- globin expression in HSCs has emerged as an alternative approach to treat β-thalassaemia. Targeting the +58 BCL11A erythroid enhancer or BCL11A binding motif at the γ-gene promoter with CRISPR-Cas9 or base editors has successfully disrupted the gene and the binding motif with a subsequent increment in HbF levels. This review outlines the critical role of BCL11A in γ-globin gene silencing and discusses the different genome editing approaches to downregulate BCL11A as a means for ameliorating β-thalassaemia.
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Affiliation(s)
- Nahil Hassan Mahmoud Ahmed
- Haematology Unit, Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
| | - Mei I Lai
- Haematology Unit, Department of Pathology, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia.,Genetics and Regenerative Medicine Research Centre, Faculty of Medicine and Health Sciences, Universiti Putra Malaysia (UPM), Serdang, Selangor, Malaysia
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32
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Fañanas-Baquero S, Morín M, Fernández S, Ojeda-Perez I, Dessy-Rodriguez M, Giurgiu M, Bueren JA, Moreno-Pelayo MA, Segovia JC, Quintana-Bustamante O. Specific correction of pyruvate kinase deficiency-causing point mutations by CRISPR/Cas9 and single-stranded oligodeoxynucleotides. Front Genome Ed 2023; 5:1104666. [PMID: 37188156 PMCID: PMC10175809 DOI: 10.3389/fgeed.2023.1104666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Pyruvate kinase deficiency (PKD) is an autosomal recessive disorder caused by mutations in the PKLR gene. PKD-erythroid cells suffer from an energy imbalance caused by a reduction of erythroid pyruvate kinase (RPK) enzyme activity. PKD is associated with reticulocytosis, splenomegaly and iron overload, and may be life-threatening in severely affected patients. More than 300 disease-causing mutations have been identified as causing PKD. Most mutations are missense mutations, commonly present as compound heterozygous. Therefore, specific correction of these point mutations might be a promising therapy for the treatment of PKD patients. We have explored the potential of precise gene editing for the correction of different PKD-causing mutations, using a combination of single-stranded oligodeoxynucleotides (ssODN) with the CRISPR/Cas9 system. We have designed guide RNAs (gRNAs) and single-strand donor templates to target four different PKD-causing mutations in immortalized patient-derived lymphoblastic cell lines, and we have detected the precise correction in three of these mutations. The frequency of the precise gene editing is variable, while the presence of additional insertions/deletions (InDels) has also been detected. Significantly, we have identified high mutation-specificity for two of the PKD-causing mutations. Our results demonstrate the feasibility of a highly personalized gene-editing therapy to treat point mutations in cells derived from PKD patients.
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Affiliation(s)
- Sara Fañanas-Baquero
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Matías Morín
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Sergio Fernández
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Isabel Ojeda-Perez
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Mercedes Dessy-Rodriguez
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Miruna Giurgiu
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Juan A. Bueren
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Miguel Angel Moreno-Pelayo
- Servicio de Genética, Hospital Universitario Ramón y Cajal, IRYCIS and Centro de Investigaciones Biomédicas en Red de Enfermedades Raras (CIBERER), Madrid, Spain
| | - Jose Carlos Segovia
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
- *Correspondence: Jose Carlos Segovia, ; Oscar Quintana-Bustamante,
| | - Oscar Quintana-Bustamante
- Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER), Madrid, Spain
- Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
- *Correspondence: Jose Carlos Segovia, ; Oscar Quintana-Bustamante,
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Crossley M, Christakopoulos GE, Weiss MJ. Effective therapies for sickle cell disease: are we there yet? Trends Genet 2022; 38:1284-1298. [PMID: 35934593 PMCID: PMC9837857 DOI: 10.1016/j.tig.2022.07.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Revised: 06/30/2022] [Accepted: 07/11/2022] [Indexed: 01/24/2023]
Abstract
Sickle cell disease (SCD) is a common genetic blood disorder associated with acute and chronic pain, progressive multiorgan damage, and early mortality. Recent advances in technologies to manipulate the human genome, a century of research and the development of techniques enabling the isolation, efficient genetic modification, and reimplantation of autologous patient hematopoietic stem cells (HSCs), mean that curing most patients with SCD could soon be a reality in wealthy countries. In parallel, ongoing research is pursuing more facile treatments, such as in-vivo-delivered genetic therapies and new drugs that can eventually be administered in low- and middle-income countries where most SCD patients reside.
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Affiliation(s)
- Merlin Crossley
- School of Biotechnology and Biomolecular Sciences, University of New South Wales, Sydney, Australia 2052.
| | | | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
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34
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In Vivo Hematopoietic Stem Cell Genome Editing: Perspectives and Limitations. Genes (Basel) 2022; 13:genes13122222. [PMID: 36553489 PMCID: PMC9778055 DOI: 10.3390/genes13122222] [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: 09/16/2022] [Revised: 11/11/2022] [Accepted: 11/22/2022] [Indexed: 11/29/2022] Open
Abstract
The tremendous evolution of genome-editing tools in the last two decades has provided innovative and effective approaches for gene therapy of congenital and acquired diseases. Zinc-finger nucleases (ZFNs), transcription activator- like effector nucleases (TALENs) and CRISPR-Cas9 have been already applied by ex vivo hematopoietic stem cell (HSC) gene therapy in genetic diseases (i.e., Hemoglobinopathies, Fanconi anemia and hereditary Immunodeficiencies) as well as infectious diseases (i.e., HIV), and the recent development of CRISPR-Cas9-based systems using base and prime editors as well as epigenome editors has provided safer tools for gene therapy. The ex vivo approach for gene addition or editing of HSCs, however, is complex, invasive, technically challenging, costly and not free of toxicity. In vivo gene addition or editing promise to transform gene therapy from a highly sophisticated strategy to a "user-friendly' approach to eventually become a broadly available, highly accessible and potentially affordable treatment modality. In the present review article, based on the lessons gained by more than 3 decades of ex vivo HSC gene therapy, we discuss the concept, the tools, the progress made and the challenges to clinical translation of in vivo HSC gene editing.
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35
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Siegner SM, Ugalde L, Clemens A, Garcia-Garcia L, Bueren JA, Rio P, Karasu ME, Corn JE. Adenine base editing efficiently restores the function of Fanconi anemia hematopoietic stem and progenitor cells. Nat Commun 2022; 13:6900. [PMID: 36371486 PMCID: PMC9653444 DOI: 10.1038/s41467-022-34479-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Accepted: 10/26/2022] [Indexed: 11/13/2022] Open
Abstract
Fanconi Anemia (FA) is a debilitating genetic disorder with a wide range of severe symptoms including bone marrow failure and predisposition to cancer. CRISPR-Cas genome editing manipulates genotypes by harnessing DNA repair and has been proposed as a potential cure for FA. But FA is caused by deficiencies in DNA repair itself, preventing the use of editing strategies such as homology directed repair. Recently developed base editing (BE) systems do not rely on double stranded DNA breaks and might be used to target mutations in FA genes, but this remains to be tested. Here we develop a proof of concept therapeutic base editing strategy to address two of the most prevalent FANCA mutations in patient hematopoietic stem and progenitor cells. We find that optimizing adenine base editor construct, vector type, guide RNA format, and delivery conditions leads to very effective genetic modification in multiple FA patient backgrounds. Optimized base editing restored FANCA expression, molecular function of the FA pathway, and phenotypic resistance to crosslinking agents. ABE8e mediated editing in primary hematopoietic stem and progenitor cells from FA patients was both genotypically effective and restored FA pathway function, indicating the potential of base editing strategies for future clinical application in FA.
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Affiliation(s)
- Sebastian M. Siegner
- grid.5801.c0000 0001 2156 2780Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Laura Ugalde
- grid.5515.40000000119578126Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER) and Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Alexandra Clemens
- grid.5801.c0000 0001 2156 2780Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Laura Garcia-Garcia
- grid.5515.40000000119578126Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER) and Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Juan A. Bueren
- grid.5515.40000000119578126Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER) and Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Paula Rio
- grid.5515.40000000119578126Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIEMAT/CIBERER) and Advanced Therapies Unit, Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Madrid, Spain
| | - Mehmet E. Karasu
- grid.5801.c0000 0001 2156 2780Department of Biology, ETH Zurich, Zurich, Switzerland
| | - Jacob E. Corn
- grid.5801.c0000 0001 2156 2780Department of Biology, ETH Zurich, Zurich, Switzerland
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Antoniou P, Hardouin G, Martinucci P, Frati G, Felix T, Chalumeau A, Fontana L, Martin J, Masson C, Brusson M, Maule G, Rosello M, Giovannangeli C, Abramowski V, de Villartay JP, Concordet JP, Del Bene F, El Nemer W, Amendola M, Cavazzana M, Cereseto A, Romano O, Miccio A. Base-editing-mediated dissection of a γ-globin cis-regulatory element for the therapeutic reactivation of fetal hemoglobin expression. Nat Commun 2022; 13:6618. [PMID: 36333351 PMCID: PMC9636226 DOI: 10.1038/s41467-022-34493-1] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Sickle cell disease and β-thalassemia affect the production of the adult β-hemoglobin chain. The clinical severity is lessened by mutations that cause fetal γ-globin expression in adult life (i.e., the hereditary persistence of fetal hemoglobin). Mutations clustering ~200 nucleotides upstream of the HBG transcriptional start sites either reduce binding of the LRF repressor or recruit the KLF1 activator. Here, we use base editing to generate a variety of mutations in the -200 region of the HBG promoters, including potent combinations of four to eight γ-globin-inducing mutations. Editing of patient hematopoietic stem/progenitor cells is safe, leads to fetal hemoglobin reactivation and rescues the pathological phenotype. Creation of a KLF1 activator binding site is the most potent strategy - even in long-term repopulating hematopoietic stem/progenitor cells. Compared with a Cas9-nuclease approach, base editing avoids the generation of insertions, deletions and large genomic rearrangements and results in higher γ-globin levels. Our results demonstrate that base editing of HBG promoters is a safe, universal strategy for treating β-hemoglobinopathies.
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Affiliation(s)
- Panagiotis Antoniou
- Université Paris Cité, Imagine Institute, Laboratory of chromatin and gene regulation during development, INSERM UMR 1163, 75015, Paris, France
| | - Giulia Hardouin
- Université Paris Cité, Imagine Institute, Laboratory of chromatin and gene regulation during development, INSERM UMR 1163, 75015, Paris, France
- Université Paris Cité, Imagine Institute, Laboratory of Human Lymphohematopoiesis, INSERM UMR 1163, 75015, Paris, France
- Biotherapy Department and Clinical Investigation Center, Assistance Publique Hopitaux de Paris, INSERM, 75015, Paris, France
| | - Pierre Martinucci
- Université Paris Cité, Imagine Institute, Laboratory of chromatin and gene regulation during development, INSERM UMR 1163, 75015, Paris, France
| | - Giacomo Frati
- Université Paris Cité, Imagine Institute, Laboratory of chromatin and gene regulation during development, INSERM UMR 1163, 75015, Paris, France
| | - Tristan Felix
- Université Paris Cité, Imagine Institute, Laboratory of chromatin and gene regulation during development, INSERM UMR 1163, 75015, Paris, France
| | - Anne Chalumeau
- Université Paris Cité, Imagine Institute, Laboratory of chromatin and gene regulation during development, INSERM UMR 1163, 75015, Paris, France
| | - Letizia Fontana
- Université Paris Cité, Imagine Institute, Laboratory of chromatin and gene regulation during development, INSERM UMR 1163, 75015, Paris, France
| | - Jeanne Martin
- Université Paris Cité, Imagine Institute, Laboratory of chromatin and gene regulation during development, INSERM UMR 1163, 75015, Paris, France
| | - Cecile Masson
- Bioinformatics Platform, Imagine Institute, 75015, Paris, France
| | - Megane Brusson
- Université Paris Cité, Imagine Institute, Laboratory of chromatin and gene regulation during development, INSERM UMR 1163, 75015, Paris, France
| | - Giulia Maule
- CIBIO, University of Trento, 38100, Trento, Italy
| | - Marion Rosello
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75015, Paris, France
| | | | - Vincent Abramowski
- Université Paris Cité, Imagine Institute, Laboratory of genome dynamics in the immune system, INSERM UMR 1163, 75015, Paris, France
| | - Jean-Pierre de Villartay
- Université Paris Cité, Imagine Institute, Laboratory of genome dynamics in the immune system, INSERM UMR 1163, 75015, Paris, France
| | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris, France
| | - Filippo Del Bene
- Sorbonne Université, INSERM, CNRS, Institut de la Vision, 75015, Paris, France
| | - Wassim El Nemer
- Établissement Français du Sang, UMR 7268, 13005, Marseille, France
- Laboratoire d'Excellence GR-Ex, 75015, Paris, France
| | - Mario Amendola
- Genethon, 91000, Evry, France
- Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000, Evry, France
| | - Marina Cavazzana
- Biotherapy Department and Clinical Investigation Center, Assistance Publique Hopitaux de Paris, INSERM, 75015, Paris, France
- Université Paris Cité, 75015, Paris, France
- Imagine Institute, 75015, Paris, France
| | | | - Oriana Romano
- Department of Life Sciences, University of Modena and Reggio Emilia, 41125, Modena, Italy
| | - Annarita Miccio
- Université Paris Cité, Imagine Institute, Laboratory of chromatin and gene regulation during development, INSERM UMR 1163, 75015, Paris, France.
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Li C, Georgakopoulou A, Newby GA, Everette KA, Nizamis E, Paschoudi K, Vlachaki E, Gil S, Anderson AK, Koob T, Huang L, Wang H, Kiem HP, Liu DR, Yannaki E, Lieber A. In vivo base editing by a single i.v. vector injection for treatment of hemoglobinopathies. JCI Insight 2022; 7:e162939. [PMID: 36006707 PMCID: PMC9675455 DOI: 10.1172/jci.insight.162939] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2022] [Accepted: 08/19/2022] [Indexed: 11/17/2022] Open
Abstract
Individuals with β-thalassemia or sickle cell disease and hereditary persistence of fetal hemoglobin (HPFH) possessing 30% fetal hemoglobin (HbF) appear to be symptom free. Here, we used a nonintegrating HDAd5/35++ vector expressing a highly efficient and accurate version of an adenine base editor (ABE8e) to install, in vivo, a -113 A>G HPFH mutation in the γ-globin promoters in healthy CD46/β-YAC mice carrying the human β-globin locus. Our in vivo hematopoietic stem cell (HSC) editing/selection strategy involves only s.c. and i.v. injections and does not require myeloablation and HSC transplantation. In vivo HSC base editing in CD46/β-YAC mice resulted in > 60% -113 A>G conversion, with 30% γ-globin of β-globin expressed in 70% of erythrocytes. Importantly, no off-target editing at sites predicted by CIRCLE-Seq or in silico was detected. Furthermore, no critical alterations in the transcriptome of in vivo edited mice were found by RNA-Seq. In vitro, in HSCs from β-thalassemia and patients with sickle cell disease, transduction with the base editor vector mediated efficient -113 A>G conversion and reactivation of γ-globin expression with subsequent phenotypic correction of erythroid cells. Because our in vivo base editing strategy is safe and technically simple, it has the potential for clinical application in developing countries where hemoglobinopathies are prevalent.
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Affiliation(s)
- Chang Li
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Aphrodite Georgakopoulou
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
| | - Gregory A. Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Chemistry and Chemical Biology and
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Kelcee A. Everette
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Chemistry and Chemical Biology and
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Evangelos Nizamis
- Department of Computer Science and Biomedical Informatics, University of Thessaly, Lamia, Greece
| | - Kiriaki Paschoudi
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
- School of Biology, Aristotle University of Thessaloniki, Thessaloniki, Greece
| | - Efthymia Vlachaki
- Hematological Laboratory, Second Department of Internal Medicine, Faculty of Health Sciences, School of Medicine, Aristotle University of Thessaloniki, Hippokration General Hospital, Thessaloniki, Greece
| | - Sucheol Gil
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Anna K. Anderson
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Theodore Koob
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Lishan Huang
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Hongjie Wang
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
| | - Hans-Peter Kiem
- Stem and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, Washington, USA
| | - David R. Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, Massachusetts, USA
- Department of Chemistry and Chemical Biology and
- Howard Hughes Medical Institute, Harvard University, Cambridge, Massachusetts, USA
| | - Evangelia Yannaki
- Gene and Cell Therapy Center, Hematology Department, George Papanicolaou Hospital, Thessaloniki, Greece
| | - André Lieber
- Department of Medicine, Division of Medical Genetics, University of Washington, Seattle, Washington, USA
- Department of Pathology, University of Washington, Seattle, Washington, USA
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Reshetnikov VV, Chirinskaite AV, Sopova JV, Ivanov RA, Leonova EI. Translational potential of base-editing tools for gene therapy of monogenic diseases. Front Bioeng Biotechnol 2022; 10:942440. [PMID: 36032737 PMCID: PMC9399415 DOI: 10.3389/fbioe.2022.942440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2022] [Accepted: 07/14/2022] [Indexed: 12/26/2022] Open
Abstract
Millions of people worldwide have rare genetic diseases that are caused by various mutations in DNA sequence. Classic treatments of rare genetic diseases are often ineffective, and therefore great hopes are placed on gene-editing methods. A DNA base-editing system based on nCas9 (Cas9 with a nickase activity) or dCas9 (a catalytically inactive DNA-targeting Cas9 enzyme) enables editing without double-strand breaks. These tools are constantly being improved, which increases their potential usefulness for therapies. In this review, we describe the main types of base-editing systems and their application to the treatment of monogenic diseases in experiments in vitro and in vivo. Additionally, to understand the therapeutic potential of these systems, the advantages and disadvantages of base-editing systems are examined.
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Affiliation(s)
- Vasiliy V. Reshetnikov
- Department of Biotechnology, Sirius University of Science and Technology, Sochi, Russia
- Department of Molecular Genetics, Institute of Cytology and Genetics, Novosibirsk, Russia
| | - Angelina V. Chirinskaite
- Сenter of Transgenesis and Genome Editing, St. Petersburg State University, St. Petersburg, Russia
| | - Julia V. Sopova
- Сenter of Transgenesis and Genome Editing, St. Petersburg State University, St. Petersburg, Russia
- Laboratory of Amyloid Biology, St. Petersburg State University, St. Petersburg, Russia
| | - Roman A. Ivanov
- Department of Biotechnology, Sirius University of Science and Technology, Sochi, Russia
| | - Elena I. Leonova
- Сenter of Transgenesis and Genome Editing, St. Petersburg State University, St. Petersburg, Russia
- Scientific Center for Genetics and Life Sciences, Sirius University of Science and Technology, Sochi, Russia
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Wang H, Germond A, Li C, Gil S, Kim J, Kiem HP, Lieber A. In vivo HSC transduction in rhesus macaques with an HDAd5/3+ vector targeting desmoglein 2 and transiently overexpressing cxcr4. Blood Adv 2022; 6:4360-4372. [PMID: 35679480 PMCID: PMC9636333 DOI: 10.1182/bloodadvances.2022007975] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Accepted: 06/01/2022] [Indexed: 11/20/2022] Open
Abstract
We developed a new in vivo hematopoietic stem cell (HSC) gene therapy approach that involves only IV injections and does not require myeloablation/conditioning and HSC transplantation. In this approach, HSCs are mobilized from the bone marrow into the peripheral bloodstream and transduced with IV injected helper-dependent adenovirus (HDAd) vectors. A fraction of transduced HSCs returns to the bone marrow and persists there long term. Here, we report desmoglein 2 (DSG2) as a new receptor that can be used for in vivo HSC transduction. HDAd5/3+ vectors were developed that use DSG2 as a high-affinity attachment receptor, and in vivo HSC transduction and safety after IV injection of an HDAd5/3+ vector expressing green fluorescent protein (GFP) in granulocyte colony-stimulating factor/AMD3100 (plerixafor)-mobilized rhesus macaques were studied. Unlike previously used CD46-targeting HDAd5/35++ vectors, HDAd5/3+ virions were not sequestered by rhesus erythrocytes and therefore mediated ∼10-fold higher GFP marking rates in primitive HSCs (CD34+/CD45RA-/CD90+ cells) in the bone marrow at day 7 after vector injection. To further increase the return of in vivo transduced, mobilized HSCs to the bone marrow, we transiently expressed cxcr4 in mobilized HSCs from the HDAd5/3+ vector. In vivo transduction with an HDAd5/3+GFP/cxcr4 vector at a low dose of 0.4 × 1012 viral particles/kg resulted in up to 7% of GFP-positive CD34+/CD45RA-/CD90+ cells in the bone marrow. This transduction rate is a solid basis for in vivo base or prime editing in combination with natural or drug-induced expansion of edited HSCs. Furthermore, our study provides new insights into HSC biology and trafficking after mobilization in nonhuman primates.
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Affiliation(s)
- Hongjie Wang
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Audrey Germond
- Washington National Primate Research Center, Seattle, WA
| | - Chang Li
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Sucheol Gil
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
| | - Jiho Kim
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
- PAI Life Sciences, Seattle, WA
| | - Hans-Peter Kiem
- Stem and Gene Therapy Program, Fred Hutchinson Cancer Research Center, Seattle, WA
- Division of Medical Oncology, Department of Medicine
| | - André Lieber
- Division of Medical Genetics, Department of Medicine, University of Washington, Seattle, WA
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA
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40
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Sipe CJ, Kluesner MG, Bingea SP, Lahr WS, Andrew AA, Wang M, DeFeo AP, Hinkel TL, Laoharawee K, Wagner JE, MacMillan ML, Vercellotti GM, Tolar J, Osborn MJ, McIvor RS, Webber BR, Moriarity BS. Correction of Fanconi Anemia Mutations Using Digital Genome Engineering. Int J Mol Sci 2022; 23:8416. [PMID: 35955545 PMCID: PMC9369391 DOI: 10.3390/ijms23158416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2022] [Revised: 07/20/2022] [Accepted: 07/25/2022] [Indexed: 12/10/2022] Open
Abstract
Fanconi anemia (FA) is a rare genetic disease in which genes essential for DNA repair are mutated. Both the interstrand crosslink (ICL) and double-strand break (DSB) repair pathways are disrupted in FA, leading to patient bone marrow failure (BMF) and cancer predisposition. The only curative therapy for the hematological manifestations of FA is an allogeneic hematopoietic cell transplant (HCT); however, many (>70%) patients lack a suitable human leukocyte antigen (HLA)-matched donor, often resulting in increased rates of graft-versus-host disease (GvHD) and, potentially, the exacerbation of cancer risk. Successful engraftment of gene-corrected autologous hematopoietic stem cells (HSC) circumvents the need for an allogeneic HCT and has been achieved in other genetic diseases using targeted nucleases to induce site specific DSBs and the correction of mutated genes through homology-directed repair (HDR). However, this process is extremely inefficient in FA cells, as they are inherently deficient in DNA repair. Here, we demonstrate the correction of FANCA mutations in primary patient cells using ‘digital’ genome editing with the cytosine and adenine base editors (BEs). These Cas9-based tools allow for C:G > T:A or A:T > C:G base transitions without the induction of a toxic DSB or the need for a DNA donor molecule. These genetic corrections or conservative codon substitution strategies lead to phenotypic rescue as illustrated by a resistance to the alkylating crosslinking agent Mitomycin C (MMC). Further, FANCA protein expression was restored, and an intact FA pathway was demonstrated by downstream FANCD2 monoubiquitination induction. This BE digital correction strategy will enable the use of gene-corrected FA patient hematopoietic stem and progenitor cells (HSPCs) for autologous HCT, obviating the risks associated with allogeneic HCT and DSB induction during autologous HSC gene therapy.
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Affiliation(s)
- Christopher J. Sipe
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mitchell G. Kluesner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Medical Scientist Training Program, University of Washington, Seattle, WA 98195, USA
| | - Samuel P. Bingea
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Walker S. Lahr
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Aneesha A. Andrew
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Minjing Wang
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Anthony P. DeFeo
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Timothy L. Hinkel
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Kanut Laoharawee
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - John E. Wagner
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Margaret L. MacMillan
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Gregory M. Vercellotti
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA;
| | - Jakub Tolar
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
- Division of Blood and Marrow Transplantation, University of Minnesota, Minneapolis, MN 55455, USA
| | - Mark J. Osborn
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Division of Hematology, Oncology and Transplantation, University of Minnesota, Minneapolis, MN 55455, USA;
| | - R. Scott McIvor
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Beau R. Webber
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
| | - Branden S. Moriarity
- Department of Pediatrics, University of Minnesota, Minneapolis, MN 55455, USA; (C.J.S.); (M.G.K.); (S.P.B.); (W.S.L.); (A.A.A.); (M.W.); (A.P.D.); (T.L.H.); (K.L.); (J.E.W.); (M.L.M.); (J.T.); (M.J.O.); (R.S.M.)
- Masonic Cancer Center, University of Minnesota, Minneapolis, MN 55455, USA
- Center for Genome Engineering, University of Minnesota, Minneapolis, MN 55455, USA
- Stem Cell Institute, University of Minnesota, Minneapolis, MN 55455, USA
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Raguram A, Banskota S, Liu DR. Therapeutic in vivo delivery of gene editing agents. Cell 2022; 185:2806-2827. [PMID: 35798006 PMCID: PMC9454337 DOI: 10.1016/j.cell.2022.03.045] [Citation(s) in RCA: 165] [Impact Index Per Article: 82.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/26/2022] [Accepted: 03/30/2022] [Indexed: 12/18/2022]
Abstract
In vivo gene editing therapies offer the potential to treat the root causes of many genetic diseases. Realizing the promise of therapeutic in vivo gene editing requires the ability to safely and efficiently deliver gene editing agents to relevant organs and tissues in vivo. Here, we review current delivery technologies that have been used to enable therapeutic in vivo gene editing, including viral vectors, lipid nanoparticles, and virus-like particles. Since no single delivery modality is likely to be appropriate for every possible application, we compare the benefits and drawbacks of each method and highlight opportunities for future improvements.
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Affiliation(s)
- Aditya Raguram
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - Samagya Banskota
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of MIT and Harvard, Cambridge, MA, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA, USA.
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Li M, Morse B, Kassim S. Development and clinical translation considerations for the next wave of gene modified hematopoietic stem and progenitor cells therapies. Expert Opin Biol Ther 2022; 22:1177-1191. [PMID: 35833356 DOI: 10.1080/14712598.2022.2101361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
Abstract
INTRODUCTION Consistent and reliable manufacture of gene modified hematopoietic stem and progenitor cell (HPSC) therapies will be of the utmost importance as they become more mainstream and address larger populations. Robust development campaigns will be needed to ensure that these products will be delivered to patients with the highest quality standards. AREAS COVERED Through publicly available manuscripts, press releases, and news articles - this review touches on aspects related to HSPC therapy, development, and manufacturing. EXPERT OPINION Recent advances in genome modification technology coupled with the longstanding clinical success of HSPCs warrants great optimism for the next generation of engineered HSPC-based therapies. Treatments for some diseases that have thus far been intractable now appear within reach. Reproducible manufacturing will be of critical importance in delivering these therapies but will be challenging due to the need for bespoke materials and methods in combination with the lack of off-the-shelf solutions. Continued progress in the field will manifest in the form of industrialization which currently requires attention and resources directed toward the custom reagents, a focus on closed and automated processes, and safer and more precise genome modification technologies that will enable broader, faster, and safer access to these life-changing therapies.
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Affiliation(s)
| | - Brent Morse
- Dark Horse Consulting Group, Walnut Creek, CA, USA
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Torres LS, Asada N, Weiss MJ, Trumpp A, Suda T, Scadden DT, Ito K. Recent advances in "sickle and niche" research - Tribute to Dr. Paul S Frenette. Stem Cell Reports 2022; 17:1509-1535. [PMID: 35830837 PMCID: PMC9287685 DOI: 10.1016/j.stemcr.2022.06.004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Revised: 06/08/2022] [Accepted: 06/09/2022] [Indexed: 10/27/2022] Open
Abstract
In this retrospective, we review the two research topics that formed the basis of the outstanding career of Dr. Paul S. Frenette. In the first part, we focus on sickle cell disease (SCD). The defining feature of SCD is polymerization of the deoxygenated mutant hemoglobin, which leads to a vicious cycle of hemolysis and vaso-occlusion. We survey important discoveries in SCD pathophysiology that have led to recent advances in treatment of SCD. The second part focuses on the hematopoietic stem cell (HSC) niche, the complex microenvironment within the bone marrow that controls HSC function and homeostasis. We detail the cells that constitute this niche, and the factors that these cells use to exert control over hematopoiesis. Here, we trace the scientific paths of Dr. Frenette, highlight key aspects of his research, and identify his most important scientific contributions in both fields.
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Affiliation(s)
- Lidiane S Torres
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA
| | - Noboru Asada
- Department of Hematology and Oncology, Okayama University Hospital, Okayama 700-8558, Japan
| | - Mitchell J Weiss
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Andreas Trumpp
- Division of Stem Cells and Cancer, German Cancer Research Center (DKFZ) and DKFZ-ZMBH Alliance, 69120 Heidelberg, Germany; Heidelberg Institute for Stem Cell Technology and Experimental Medicine (HI-STEM gGmbH), 69120 Heidelberg, Germany; Faculty of Biosciences, Heidelberg University, 69117 Heidelberg, Germany; German Cancer Consortium (DKTK), 69120 Heidelberg, Germany
| | - Toshio Suda
- Cancer Science Institute of Singapore, National University of Singapore, Singapore, Singapore; International Research Center for Medical Sciences, Kumamoto University, Kumamoto, Japan
| | - David T Scadden
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA; Harvard Stem Cell Institute, Harvard University, Cambridge, MA, USA; Center for Regenerative Medicine, Massachusetts General Hospital, Boston, MA, USA
| | - Keisuke Ito
- Ruth L. and David S. Gottesman Institute for Stem Cell and Regenerative Medicine Research, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Cell Biology, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Department of Medicine, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, New York, NY 10461, USA; Einstein Diabetes Research Center, Albert Einstein College of Medicine, Bronx, NY, USA.
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Lederer CW, Koniali L, Buerki-Thurnherr T, Papasavva PL, La Grutta S, Licari A, Staud F, Bonifazi D, Kleanthous M. Catching Them Early: Framework Parameters and Progress for Prenatal and Childhood Application of Advanced Therapies. Pharmaceutics 2022; 14:pharmaceutics14040793. [PMID: 35456627 PMCID: PMC9031205 DOI: 10.3390/pharmaceutics14040793] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 03/29/2022] [Accepted: 04/01/2022] [Indexed: 01/19/2023] Open
Abstract
Advanced therapy medicinal products (ATMPs) are medicines for human use based on genes, cells or tissue engineering. After clear successes in adults, the nascent technology now sees increasing pediatric application. For many still untreatable disorders with pre- or perinatal onset, timely intervention is simply indispensable; thus, prenatal and pediatric applications of ATMPs hold great promise for curative treatments. Moreover, for most inherited disorders, early ATMP application may substantially improve efficiency, economy and accessibility compared with application in adults. Vindicating this notion, initial data for cell-based ATMPs show better cell yields, success rates and corrections of disease parameters for younger patients, in addition to reduced overall cell and vector requirements, illustrating that early application may resolve key obstacles to the widespread application of ATMPs for inherited disorders. Here, we provide a selective review of the latest ATMP developments for prenatal, perinatal and pediatric use, with special emphasis on its comparison with ATMPs for adults. Taken together, we provide a perspective on the enormous potential and key framework parameters of clinical prenatal and pediatric ATMP application.
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Affiliation(s)
- Carsten W. Lederer
- The Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology & Genetics, Nicosia 2371, Cyprus; (L.K.); (P.L.P.); (M.K.)
- Correspondence: ; Tel.: +357-22-392764
| | - Lola Koniali
- The Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology & Genetics, Nicosia 2371, Cyprus; (L.K.); (P.L.P.); (M.K.)
| | - Tina Buerki-Thurnherr
- Empa, Swiss Federal Laboratories for Materials Science and Technology, 9014 St. Gallen, Switzerland;
| | - Panayiota L. Papasavva
- The Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology & Genetics, Nicosia 2371, Cyprus; (L.K.); (P.L.P.); (M.K.)
| | - Stefania La Grutta
- Institute of Translational Pharmacology, IFT National Research Council, 90146 Palermo, Italy;
| | - Amelia Licari
- Pediatric Clinic, Department of Clinical, Surgical, Diagnostic and Pediatric Sciences, Fondazione IRCCS Policlinico San Matteo, University of Pavia, 27100 Pavia, Italy;
| | - Frantisek Staud
- Department of Pharmacology and Toxicology, Faculty of Pharmacy in Hradec Králové, Charles University, 50005 Hradec Králové, Czech Republic;
| | - Donato Bonifazi
- Consorzio per Valutazioni Biologiche e Farmacologiche (CVBF) and European Paediatric Translational Research Infrastructure (EPTRI), 70122 Bari, Italy;
| | - Marina Kleanthous
- The Molecular Genetics Thalassemia Department, The Cyprus Institute of Neurology & Genetics, Nicosia 2371, Cyprus; (L.K.); (P.L.P.); (M.K.)
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Quintana-Bustamante O, Fañanas-Baquero S, Dessy-Rodriguez M, Ojeda-Pérez I, Segovia JC. Gene Editing for Inherited Red Blood Cell Diseases. Front Physiol 2022; 13:848261. [PMID: 35418876 PMCID: PMC8995967 DOI: 10.3389/fphys.2022.848261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/28/2022] [Indexed: 11/24/2022] Open
Abstract
Today gene therapy is a real therapeutic option to address inherited hematological diseases that could be beneficial for thousands of patients worldwide. Currently, gene therapy is used to treat different monogenic hematological pathologies, including several red blood cell diseases such as β-thalassemia, sickle cell disease and pyruvate kinase deficiency. This approach is based on addition gene therapy, which consists of the correction of hematopoietic stem cells (HSCs) using lentiviral vectors, which integrate a corrected version of the altered gene. Lentivirally-corrected HSCs generate healthy cells that compensate for the deficiency caused by genetic mutations. Despite its successful results, this approach lacks both control of the integration of the transgene into the genome and endogenous regulation of the therapeutic gene, both of which are important aspects that might be a cause for concern. To overcome these limitations, gene editing is able to correct the altered gene through more precise and safer approaches. Cheap and easy-to-design gene editing tools, such as the CRISPR/Cas9 system, allow the specific correction of the altered gene without affecting the rest of the genome. Inherited erythroid diseases, such as thalassemia, sickle cell disease and Pyruvate Kinase Deficiency, have been the test bed for these gene editing strategies, and promising results are currently being seen. CRISPR/Cas9 system has been successfully used to manipulate globin regulation to re-activate fetal globin chains in adult red blood cells and to compensate for hemoglobin defects. Knock-in at the mutated locus to express the therapeutic gene under the endogenous gene regulatory region has also been accomplished successfully. Thanks to the lessons learned from previous lentiviral gene therapy research and trials, gene editing for red blood cell diseases is rapidly moving from its proof-of-concept to its first exciting results in the clinic. Indeed, patients suffering from β-thalassemia and sickle cell disease have already been successfully treated with gene editing, which will hopefully inspire the use of gene editing to cure erythroid disorders and many other inherited diseases in the near future.
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Affiliation(s)
- Oscar Quintana-Bustamante
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Unidad Mixta de Terapias Avanzadas, Madrid, Spain
| | - Sara Fañanas-Baquero
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Unidad Mixta de Terapias Avanzadas, Madrid, Spain
| | - Mercedes Dessy-Rodriguez
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Unidad Mixta de Terapias Avanzadas, Madrid, Spain
| | - Isabel Ojeda-Pérez
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Unidad Mixta de Terapias Avanzadas, Madrid, Spain
| | - Jose-Carlos Segovia
- Hematopoietic Innovative Therapies Division, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT) and Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Madrid, Spain
- Instituto de Investigación Sanitaria Fundación Jiménez Díaz (IIS-FJD, UAM), Unidad Mixta de Terapias Avanzadas, Madrid, Spain
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Safe and efficient in vivo hematopoietic stem cell transduction in nonhuman primates using HDAd5/35++ vectors. MOLECULAR THERAPY - METHODS & CLINICAL DEVELOPMENT 2022; 24:127-141. [PMID: 35036470 PMCID: PMC8741415 DOI: 10.1016/j.omtm.2021.12.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Accepted: 12/04/2021] [Indexed: 12/11/2022]
Abstract
We tested a new in vivo hematopoietic stem cell (HSC) transduction/selection approach in rhesus macaques using HSC-tropic, integrating, helper-dependent adenovirus vectors (HDAd5/35++) designed for the expression of human γ-globin in red blood cells (RBCs) to treat hemoglobinopathies. We show that HDAd5/35++ vectors preferentially transduce HSCs in vivo after intravenous injection into granulocyte colony-stimulating factor (G-CSF)/AMD3100-mobilized animals and that transduced cells return to the bone marrow and spleen. The approach was well tolerated, and the activation of proinflammatory cytokines that are usually associated with intravenous adenovirus vector injection was successfully blunted by pre-treatment with dexamethasone in combination with interleukin (IL)-1 and IL-6 receptor blockers. Using our MGMTP140K-based in vivo selection approach, γ-globin+ RBCs increased in all animals with levels up to 90%. After selection, the percentage of γ-globin+ RBCs declined, most likely due to an immune response against human transgene products. Our biodistribution data indicate that γ-globin+ RBCs in the periphery were mostly derived from mobilized HSCs that homed to the spleen. Integration site analysis revealed a polyclonal pattern and no genotoxicity related to transgene integrations. This is the first proof-of-concept study in nonhuman primates to show that in vivo HSC gene therapy could be feasible in humans without the need for high-dose chemotherapy conditioning and HSC transplantation.
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Radtke S, Kiem HP. Bringing gene therapy to where it’s needed. Trends Mol Med 2022; 28:171-172. [DOI: 10.1016/j.molmed.2022.01.005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2022] [Accepted: 01/12/2022] [Indexed: 01/14/2023]
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Samuelson C, Radtke S, Zhu H, Llewellyn M, Fields E, Cook S, Huang MLW, Jerome KR, Kiem HP, Humbert O. Multiplex CRISPR/Cas9 genome editing in hematopoietic stem cells for fetal hemoglobin reinduction generates chromosomal translocations. Mol Ther Methods Clin Dev 2021; 23:507-523. [PMID: 34853798 PMCID: PMC8605315 DOI: 10.1016/j.omtm.2021.10.008] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 10/20/2021] [Accepted: 10/26/2021] [Indexed: 12/26/2022]
Abstract
Sickle cell disease and β-thalassemia are common monogenic disorders that cause significant morbidity and mortality globally. The only curative treatment currently is allogeneic hematopoietic stem cell transplantation, which is unavailable to many patients due to a lack of matched donors and carries risks including graft-versus-host disease. Genome editing therapies targeting either the BCL11A erythroid enhancer or the HBG promoter are already demonstrating success in reinducing fetal hemoglobin. However, where a single locus is targeted, reliably achieving levels high enough to deliver an effective cure remains a challenge. We investigated the application of a CRISPR/Cas9 multiplex genome editing approach, in which both the BCL11A erythroid enhancer and HBG promoter are disrupted within human hematopoietic stem cells. We demonstrate superior fetal hemoglobin reinduction with this dual-editing approach without compromising engraftment or lineage differentiation potential of edited cells post-xenotransplantation. However, multiplex editing consistently resulted in the generation of chromosomal rearrangement events that persisted in vivo following transplantation into immunodeficient mice. The risk of oncogenic events resulting from such translocations therefore currently prohibits its clinical translation, but it is anticipated that, in the future, alternative editing platforms will help alleviate this risk.
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Affiliation(s)
- Clare Samuelson
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Stefan Radtke
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Haiying Zhu
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Mallory Llewellyn
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Emily Fields
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Savannah Cook
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
| | - Meei-Li W. Huang
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
| | - Keith R. Jerome
- Department of Laboratory Medicine and Pathology, University of Washington, Seattle, WA 98195, USA
- Vaccine and Infectious Disease Division, Fred Hutchinson Cancer Research Center, Seattle WA 98109-1024, USA
| | - Hans-Peter Kiem
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
- Department of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Olivier Humbert
- Stem Cell and Gene Therapy Program, Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109-1024, USA
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Demirci S, Leonard A, Essawi K, Tisdale JF. CRISPR-Cas9 to induce fetal hemoglobin for the treatment of sickle cell disease. Mol Ther Methods Clin Dev 2021; 23:276-285. [PMID: 34729375 PMCID: PMC8526756 DOI: 10.1016/j.omtm.2021.09.010] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
Genome editing is potentially a curative technique available to all individuals with β-hemoglobinopathies, including sickle cell disease (SCD). Fetal hemoglobin (HbF) inhibits sickle hemoglobin (HbS) polymerization, and it is well described that naturally occurring hereditary persistence of HbF (HPFH) alleviates disease symptoms; therefore, reawakening of developmentally silenced HbF in adult red blood cells (RBCs) has long been of interest as a therapeutic strategy. Recent advances in genome editing platforms, particularly with the use of CRISPR-Cas9, have paved the way for efficient HbF induction through the creation of artificial HPFH mutations, editing of transcriptional HbF silencers, and modulating epigenetic intermediates that govern HbF expression. Clinical trials investigating BCL11A enhancer editing in patients with β-hemoglobinopathies have demonstrated promising results, although follow-up is short and the number of patients treated to date is low. While practical, economic, and clinical challenges of genome editing are well recognized by the scientific community, potential solutions to overcome these hurdles are in development. Here, we review the recent progress and obstacles yet to be overcome for the most effective and feasible HbF reactivation practice using CRISPR-Cas9 genome editing as a curative strategy for patients with SCD.
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Affiliation(s)
- Selami Demirci
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
| | - Alexis Leonard
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
| | - Khaled Essawi
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
- Department of Medical Laboratory Science, College of Applied Medical Sciences, Jazan University, Jazan 45142, Saudi Arabia
| | - John F. Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung, and Blood Institute (NHLBI), National Institutes of Health (NIH), Bethesda, MD 20814, USA
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Newby GA, Liu DR. In vivo somatic cell base editing and prime editing. Mol Ther 2021; 29:3107-3124. [PMID: 34509669 PMCID: PMC8571176 DOI: 10.1016/j.ymthe.2021.09.002] [Citation(s) in RCA: 72] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 08/26/2021] [Accepted: 09/06/2021] [Indexed: 12/16/2022] Open
Abstract
Recent advances in genome editing technologies have magnified the prospect of single-dose cures for many genetic diseases. For most genetic disorders, precise DNA correction is anticipated to best treat patients. To install desired DNA changes with high precision, our laboratory developed base editors (BEs), which can correct the four most common single-base substitutions, and prime editors, which can install any substitution, insertion, and/or deletion over a stretch of dozens of base pairs. Compared to nuclease-dependent editing approaches that involve double-strand DNA breaks (DSBs) and often result in a large percentage of uncontrolled editing outcomes, such as mixtures of insertions and deletions (indels), larger deletions, and chromosomal rearrangements, base editors and prime editors often offer greater efficiency with fewer byproducts in slowly dividing or non-dividing cells, such as those that make up most of the cells in adult animals. Both viral and non-viral in vivo delivery methods have now been used to deliver base editors and prime editors in animal models, establishing that base editors and prime editors can serve as effective agents for in vivo therapeutic genome editing in animals. This review summarizes examples of in vivo somatic cell (post-natal) base editing and prime editing and prospects for future development.
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Affiliation(s)
- Gregory A Newby
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02142 USA.
| | - David R Liu
- Merkin Institute of Transformative Technologies in Healthcare, Broad Institute of Harvard and MIT, Cambridge, MA 02142, USA; Department of Chemistry and Chemical Biology, Harvard University, Cambridge, MA 02138, USA; Howard Hughes Medical Institute, Harvard University, Cambridge, MA 02142 USA.
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