1
|
Pavel-Dinu M, Gardner CL, Nakauchi Y, Kawai T, Delmonte OM, Palterer B, Bosticardo M, Pala F, Viel S, Malech HL, Ghanim HY, Bode NM, Kurgan GL, Detweiler AM, Vakulskas CA, Neff NF, Sheikali A, Menezes ST, Chrobok J, Hernández González EM, Majeti R, Notarangelo LD, Porteus MH. Genetically corrected RAG2-SCID human hematopoietic stem cells restore V(D)J-recombinase and rescue lymphoid deficiency. Blood Adv 2024; 8:1820-1833. [PMID: 38096800 PMCID: PMC11006817 DOI: 10.1182/bloodadvances.2023011766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2023] [Accepted: 10/23/2023] [Indexed: 04/10/2024] Open
Abstract
ABSTRACT Recombination-activating genes (RAG1 and RAG2) are critical for lymphoid cell development and function by initiating the variable (V), diversity (D), and joining (J) (V(D)J)-recombination process to generate polyclonal lymphocytes with broad antigen specificity. The clinical manifestations of defective RAG1/2 genes range from immune dysregulation to severe combined immunodeficiencies (SCIDs), causing life-threatening infections and death early in life without hematopoietic cell transplantation (HCT). Despite improvements, haploidentical HCT without myeloablative conditioning carries a high risk of graft failure and incomplete immune reconstitution. The RAG complex is only expressed during the G0-G1 phase of the cell cycle in the early stages of T- and B-cell development, underscoring that a direct gene correction might capture the precise temporal expression of the endogenous gene. Here, we report a feasibility study using the CRISPR/Cas9-based "universal gene-correction" approach for the RAG2 locus in human hematopoietic stem/progenitor cells (HSPCs) from healthy donors and RAG2-SCID patient. V(D)J-recombinase activity was restored after gene correction of RAG2-SCID-derived HSPCs, resulting in the development of T-cell receptor (TCR) αβ and γδ CD3+ cells and single-positive CD4+ and CD8+ lymphocytes. TCR repertoire analysis indicated a normal distribution of CDR3 length and preserved usage of the distal TRAV genes. We confirmed the in vivo rescue of B-cell development with normal immunoglobulin M surface expression and a significant decrease in CD56bright natural killer cells. Together, we provide specificity, toxicity, and efficacy data supporting the development of a gene-correction therapy to benefit RAG2-deficient patients.
Collapse
Affiliation(s)
- Mara Pavel-Dinu
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Cameron L. Gardner
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
- Sir William Dunn School of Pathology, University of Oxford, Oxford, United Kingdom
| | - Yusuke Nakauchi
- Division of Hematology, Department of Medicine, Cancer Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
| | - Tomoki Kawai
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Ottavia M. Delmonte
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Boaz Palterer
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Marita Bosticardo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Francesca Pala
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Sebastien Viel
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
- Service d’immunologie biologique, Hospices Civils de Lyon, Centre International de Recherche en Infectivologie, Centre International de Recheerche in Infectivalogie, INSERM U1111, Université Claude Bernard Lyon 1, Centre National de la Recherge Scientifique, UMR5308, École Normale Supérieure de Lyon, University of Lyon, Lyon, France
| | - Harry L. Malech
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Hana Y. Ghanim
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | | | | | | | | | | | - Adam Sheikali
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Sherah T. Menezes
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Jade Chrobok
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Elaine M. Hernández González
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| | - Ravindra Majeti
- Division of Hematology, Department of Medicine, Cancer Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
| | - Luigi D. Notarangelo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Matthew H. Porteus
- Division of Oncology, Hematology, Stem Cell Transplantation, Department of Pediatrics, Stanford University, Stanford, CA
| |
Collapse
|
2
|
Dudek AM, Feist WN, Sasu EJ, Luna SE, Ben-Efraim K, Bak RO, Cepika AM, Porteus MH. A simultaneous knockout knockin genome editing strategy in HSPCs potently inhibits CCR5- and CXCR4-tropic HIV-1 infection. Cell Stem Cell 2024; 31:499-518.e6. [PMID: 38579682 DOI: 10.1016/j.stem.2024.03.002] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 12/29/2023] [Accepted: 03/06/2024] [Indexed: 04/07/2024]
Abstract
Allogeneic hematopoietic stem and progenitor cell transplant (HSCT) of CCR5 null (CCR5Δ32) cells can be curative for HIV-1-infected patients. However, because allogeneic HSCT poses significant risk, CCR5Δ32 matched bone marrow donors are rare, and CCR5Δ32 transplant does not confer resistance to the CXCR4-tropic virus, it is not a viable option for most patients. We describe a targeted Cas9/AAV6-based genome editing strategy for autologous HSCT resulting in both CCR5- and CXCR4-tropic HIV-1 resistance. Edited human hematopoietic stem and progenitor cells (HSPCs) maintain multi-lineage repopulation capacity in vivo, and edited primary human T cells potently inhibit infection by both CCR5-tropic and CXCR4-tropic HIV-1. Modification rates facilitated complete loss of CCR5-tropic replication and up to a 2,000-fold decrease in CXCR4-tropic replication without CXCR4 locus disruption. This multi-factor editing strategy in HSPCs could provide a broad approach for autologous HSCT as a functional cure for both CCR5-tropic and CXCR4-tropic HIV-1 infections.
Collapse
Affiliation(s)
- Amanda M Dudek
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - William N Feist
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Elena J Sasu
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Sofia E Luna
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kaya Ben-Efraim
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Rasmus O Bak
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biomedicine, Aarhus University, 8000 Aarhus, Denmark; Aarhus Institute of Advanced Studies (AIAS), Aarhus University, 8000 Aarhus, Denmark
| | - Alma-Martina Cepika
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
3
|
Fowler JL, Zheng SL, Nguyen A, Chen A, Xiong X, Chai T, Chen JY, Karigane D, Banuelos AM, Niizuma K, Kayamori K, Nishimura T, Cromer MK, Gonzalez-Perez D, Mason C, Liu DD, Yilmaz L, Miquerol L, Porteus MH, Luca VC, Majeti R, Nakauchi H, Red-Horse K, Weissman IL, Ang LT, Loh KM. Lineage-tracing hematopoietic stem cell origins in vivo to efficiently make human HLF+ HOXA+ hematopoietic progenitors from pluripotent stem cells. Dev Cell 2024:S1534-5807(24)00143-6. [PMID: 38569552 DOI: 10.1016/j.devcel.2024.03.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 12/05/2023] [Accepted: 03/01/2024] [Indexed: 04/05/2024]
Abstract
The developmental origin of blood-forming hematopoietic stem cells (HSCs) is a longstanding question. Here, our non-invasive genetic lineage tracing in mouse embryos pinpoints that artery endothelial cells generate HSCs. Arteries are transiently competent to generate HSCs for 2.5 days (∼E8.5-E11) but subsequently cease, delimiting a narrow time frame for HSC formation in vivo. Guided by the arterial origins of blood, we efficiently and rapidly differentiate human pluripotent stem cells (hPSCs) into posterior primitive streak, lateral mesoderm, artery endothelium, hemogenic endothelium, and >90% pure hematopoietic progenitors within 10 days. hPSC-derived hematopoietic progenitors generate T, B, NK, erythroid, and myeloid cells in vitro and, critically, express hallmark HSC transcription factors HLF and HOXA5-HOXA10, which were previously challenging to upregulate. We differentiated hPSCs into highly enriched HLF+ HOXA+ hematopoietic progenitors with near-stoichiometric efficiency by blocking formation of unwanted lineages at each differentiation step. hPSC-derived HLF+ HOXA+ hematopoietic progenitors could avail both basic research and cellular therapies.
Collapse
Affiliation(s)
- Jonas L Fowler
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Sherry Li Zheng
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Alana Nguyen
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Angela Chen
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Xiaochen Xiong
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Timothy Chai
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Julie Y Chen
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA
| | - Daiki Karigane
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Allison M Banuelos
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Kouta Niizuma
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kensuke Kayamori
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Toshinobu Nishimura
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - M Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA
| | | | - Charlotte Mason
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Daniel Dan Liu
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Leyla Yilmaz
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Lucile Miquerol
- Aix-Marseille Université, CNRS UMR 7288, IBDM, Marseille 13288, France
| | - Matthew H Porteus
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Vincent C Luca
- Department of Drug Discovery, Moffitt Cancer Center, Tampa, FL 33612, USA
| | - Ravindra Majeti
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Division of Hematology, Department of Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Kristy Red-Horse
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biology, Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Irving L Weissman
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Lay Teng Ang
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Kyle M Loh
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
4
|
Vaidyanathan S, Kerschner JL, Paranjapye A, Sinha V, Lin B, Bedrosian TA, Thrasher AJ, Turchiano G, Harris A, Porteus MH. Investigating adverse genomic and regulatory changes caused by replacement of the full-length CFTR cDNA using Cas9 and AAV. Mol Ther Nucleic Acids 2024; 35:102134. [PMID: 38384445 PMCID: PMC10879780 DOI: 10.1016/j.omtn.2024.102134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/22/2023] [Accepted: 01/30/2024] [Indexed: 02/23/2024]
Abstract
A "universal strategy" replacing the full-length CFTR cDNA may treat >99% of people with cystic fibrosis (pwCF), regardless of their specific mutations. Cas9-based gene editing was used to insert the CFTR cDNA and a truncated CD19 (tCD19) enrichment tag at the CFTR locus in airway basal stem cells. This strategy restores CFTR function to non-CF levels. Here, we investigate the safety of this approach by assessing genomic and regulatory changes after CFTR cDNA insertion. Safety was first assessed by quantifying genetic rearrangements using CAST-seq. After validating restored CFTR function in edited and enriched airway cells, the CFTR locus open chromatin profile was characterized using ATAC-seq. The regenerative potential and differential gene expression in edited cells was assessed using scRNA-seq. CAST-seq revealed a translocation in ∼0.01% of alleles primarily occurring at a nononcogenic off-target site and large indels in 1% of alleles. The open chromatin profile of differentiated airway epithelial cells showed no appreciable changes, except in the region corresponding to the CFTR cDNA and tCD19 cassette, indicating no detectable changes in gene regulation. Edited stem cells produced the same types of airway cells as controls with minimal alternations in gene expression. Overall, the universal strategy showed minor undesirable genomic changes.
Collapse
Affiliation(s)
- Sriram Vaidyanathan
- Center for Gene Therapy, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
| | - Jenny L. Kerschner
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Alekh Paranjapye
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | - Vrishti Sinha
- Department of Pediatrics, Stanford University, Palo Alto, CA 94305, USA
| | - Brian Lin
- Department of Developmental, Molecular, and Chemical Biology, Tufts University, Boston, MA 02111, USA
| | - Tracy A. Bedrosian
- Department of Pediatrics, The Ohio State University, Columbus, OH 43210, USA
- Steve and Cindy Rasmussen Institute for Genomic Medicine, Abigail Wexner Research Institute at Nationwide Children’s Hospital, Columbus, OH 43205, USA
| | - Adrian J. Thrasher
- Infection, Immunity, and Inflammation Research and Teaching Department, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Giandomenico Turchiano
- Infection, Immunity, and Inflammation Research and Teaching Department, Zayed Centre for Research Into Rare Disease in Children, Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Ann Harris
- Department of Genetics and Genome Sciences, Case Western Reserve University, Cleveland, OH 44106, USA
| | | |
Collapse
|
5
|
Feist WN, Luna SE, Ben-Efraim K, Filsinger Interrante MV, Amorin NA, Johnston NM, Bruun TUJ, Ghanim HY, Lesch BJ, Dudek AM, Porteus MH. Combining Cell-Intrinsic and -Extrinsic Resistance to HIV-1 By Engineering Hematopoietic Stem Cells for CCR5 Knockout and B Cell Secretion of Therapeutic Antibodies. bioRxiv 2024:2024.03.08.583956. [PMID: 38496600 PMCID: PMC10942466 DOI: 10.1101/2024.03.08.583956] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/19/2024]
Abstract
Autologous transplantation of CCR5 null hematopoietic stem and progenitor cells (HSPCs) is the only known cure for HIV-1 infection. However, this treatment is limited because of the rarity of CCR5 -null matched donors, the morbidities associated with allogeneic transplantation, and the prevalence of HIV-1 strains resistant to CCR5 knockout (KO) alone. Here, we propose a one-time therapy through autologous transplantation of HSPCs genetically engineered ex vivo to produce both CCR5 KO cells and long-term secretion of potent HIV-1 inhibiting antibodies from B cell progeny. CRISPR-Cas9-engineered HSPCs maintain engraftment capacity and multi-lineage potential in vivo and can be engineered to express multiple antibodies simultaneously. Human B cells engineered to express each antibody secrete neutralizing concentrations capable of inhibiting HIV-1 pseudovirus infection in vitro . This work lays the groundwork for a potential one-time functional cure for HIV-1 through combining the long-term delivery of therapeutic antibodies against HIV-1 and the known efficacy of CCR5 KO HSPC transplantation.
Collapse
|
6
|
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] [What about the content of this article? (0)] [Affiliation(s)] [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.
Collapse
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
| |
Collapse
|
7
|
Riepe C, Wąchalska M, Deol KK, Amaya AK, Porteus MH, Olzmann JA, Kopito RR. Small-molecule correctors divert CFTR-F508del from ERAD by stabilizing sequential folding states. Mol Biol Cell 2024; 35:ar15. [PMID: 38019608 PMCID: PMC10881158 DOI: 10.1091/mbc.e23-08-0336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Revised: 11/13/2023] [Accepted: 11/20/2023] [Indexed: 12/01/2023] Open
Abstract
Over 80% of people with cystic fibrosis (CF) carry the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR), a chloride ion channel at the apical plasma membrane (PM) of epithelial cells. F508del impairs CFTR folding causing it to be destroyed by endoplasmic reticulum associated degradation (ERAD). Small-molecule correctors, which act as pharmacological chaperones to divert CFTR-F508del from ERAD, are the primary strategy for treating CF, yet corrector development continues with only a rudimentary understanding of how ERAD targets CFTR-F508del. We conducted genome-wide CRISPR/Cas9 knockout screens to systematically identify the molecular machinery that underlies CFTR-F508del ERAD. Although the ER-resident ubiquitin ligase, RNF5 was the top E3 hit, knocking out RNF5 only modestly reduced CFTR-F508del degradation. Sublibrary screens in an RNF5 knockout background identified RNF185 as a redundant ligase and demonstrated that CFTR-F508del ERAD is robust. Gene-drug interaction experiments illustrated that correctors tezacaftor (VX-661) and elexacaftor (VX-445) stabilize sequential, RNF5-resistant folding states. We propose that binding of correctors to nascent CFTR-F508del alters its folding landscape by stabilizing folding states that are not substrates for RNF5-mediated ubiquitylation.
Collapse
Affiliation(s)
- Celeste Riepe
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA 94305
| | - Kirandeep K. Deol
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub Network, San Francisco, CA 94158
| | - Anais K. Amaya
- Department of Pediatrics, Stanford University, Stanford, CA 94305
| | | | - James A. Olzmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA 94720
- Chan Zuckerberg Biohub Network, San Francisco, CA 94158
| | - Ron R. Kopito
- Department of Biology, Stanford University, Stanford, CA 94305
| |
Collapse
|
8
|
Baik R, Cromer MK, Glenn SE, Vakulskas CA, Chmielewski KO, Dudek AM, Feist WN, Klermund J, Shipp S, Cathomen T, Dever DP, Porteus MH. Transient inhibition of 53BP1 increases the frequency of targeted integration in human hematopoietic stem and progenitor cells. Nat Commun 2024; 15:111. [PMID: 38169468 PMCID: PMC10762240 DOI: 10.1038/s41467-023-43413-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 11/08/2023] [Indexed: 01/05/2024] Open
Abstract
Genome editing by homology directed repair (HDR) is leveraged to precisely modify the genome of therapeutically relevant hematopoietic stem and progenitor cells (HSPCs). Here, we present a new approach to increasing the frequency of HDR in human HSPCs by the delivery of an inhibitor of 53BP1 (named "i53") as a recombinant peptide. We show that the use of i53 peptide effectively increases the frequency of HDR-mediated genome editing at a variety of therapeutically relevant loci in HSPCs as well as other primary human cell types. We show that incorporating the use of i53 recombinant protein allows high frequencies of HDR while lowering the amounts of AAV6 needed by 8-fold. HDR edited HSPCs were capable of long-term and bi-lineage hematopoietic reconstitution in NSG mice, suggesting that i53 recombinant protein might be safely integrated into the standard CRISPR/AAV6-mediated genome editing protocol to gain greater numbers of edited cells for transplantation of clinically meaningful cell populations.
Collapse
Affiliation(s)
- Ron Baik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
- Molecular Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - M Kyle Cromer
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Steve E Glenn
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | - Kay O Chmielewski
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
- Ph.D. Program, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Amanda M Dudek
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - William N Feist
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Julia Klermund
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Suzette Shipp
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, 79106, Freiburg, Germany
- Center for Chronic Immunodeficiency, University of Freiburg, 79106, Freiburg, Germany
| | - Daniel P Dever
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew H Porteus
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
9
|
Riepe C, Wąchalska M, Deol KK, Amaya AK, Porteus MH, Olzmann JA, Kopito RR. Small molecule correctors divert CFTR-F508del from ERAD by stabilizing sequential folding states. bioRxiv 2023:2023.09.15.556420. [PMID: 37745470 PMCID: PMC10515913 DOI: 10.1101/2023.09.15.556420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Over 80% of people with cystic fibrosis (CF) carry the F508del mutation in the cystic fibrosis transmembrane conductance regulator (CFTR), a chloride ion channel at the apical plasma membrane (PM) of epithelial cells. F508del impairs CFTR folding causing it to be destroyed by endoplasmic reticulum associated degradation (ERAD). Small molecule correctors, which act as pharmacological chaperones to divert CFTR-F508del from ERAD, are the primary strategy for treating CF, yet corrector development continues with only a rudimentary understanding of how ERAD targets CFTR-F508del. We conducted genome-wide CRISPR/Cas9 knockout screens to systematically identify the molecular machinery that underlies CFTR-F508del ERAD. Although the ER-resident ubiquitin ligase, RNF5 was the top E3 hit, knocking out RNF5 only modestly reduced CFTR-F508del degradation. Sublibrary screens in an RNF5 knockout background identified RNF185 as a redundant ligase, demonstrating that CFTR-F508del ERAD is highly buffered. Gene-drug interaction experiments demonstrated that correctors tezacaftor (VX-661) and elexacaftor (VX-445) stabilize sequential, RNF5-resistant folding states. We propose that binding of correctors to nascent CFTR-F508del alters its folding landscape by stabilizing folding states that are not substrates for RNF5-mediated ubiquitylation.
Collapse
Affiliation(s)
- Celeste Riepe
- Department of Biology, Stanford University, Stanford, CA, USA 94305
| | - Magda Wąchalska
- Department of Biology, Stanford University, Stanford, CA, USA 94305
| | - Kirandeep K. Deol
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA USA 94720
- Chan Zuckerberg Biohub, San Francisco, CA, USA 94158
| | - Anais K. Amaya
- Department of Pediatrics, Stanford University, Stanford, CA, USA 94305
| | | | - James A. Olzmann
- Department of Molecular and Cell Biology, University of California, Berkeley, CA USA 94720
- Department of Nutritional Sciences and Toxicology, University of California, Berkeley, CA USA 94720
- Chan Zuckerberg Biohub, San Francisco, CA, USA 94158
| | - Ron R. Kopito
- Department of Biology, Stanford University, Stanford, CA, USA 94305
| |
Collapse
|
10
|
Xu L, Lahiri P, Skowronski J, Bhatia N, Lattanzi A, Porteus MH. Molecular dynamics of genome editing with CRISPR-Cas9 and rAAV6 virus in human HSPCs to treat sickle cell disease. Mol Ther Methods Clin Dev 2023; 30:317-331. [PMID: 37637384 PMCID: PMC10447934 DOI: 10.1016/j.omtm.2023.07.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
Ex vivo gene correction with CRISPR-Cas9 and a recombinant adeno-associated virus serotype 6 (rAAV6) in autologous hematopoietic stem/progenitor cells (HSPCs) to treat sickle cell disease (SCD) has now entered early-phase clinical investigation. To facilitate the progress of CRISPR-Cas9/rAAV6 genome editing technology, we analyzed the molecular changes in key reagents and cellular responses during and after the genome editing procedure in human HSPCs. We demonstrated the high stability of rAAV6 to serve as the donor DNA template. We assessed the benefit of longer HSPC pre-stimulation in terms of increased numbers of edited cells. We observed that the p53 pathway was transiently activated, peaking at 6 h, and resolved over time. Notably, we revealed a strong correlation between p21 mRNA level and rAAV6 genome number in cells and beneficial effects of transient inhibition of p53 with siRNA on genome editing, cell proliferation, and cell survival. In terms of potential immunogenicity, we found that rAAV6 capsid protein was not detectable, while a trace amount of residual Cas9 protein was still detected at 48 h post-genome editing. We believe this information will provide important insights for future improvements of gene correction protocols in HSPCs.
Collapse
Affiliation(s)
- Liwen Xu
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Premanjali Lahiri
- Stanford Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Jason Skowronski
- Stanford Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Neehar Bhatia
- Stanford Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Annalisa Lattanzi
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | |
Collapse
|
11
|
Selvaraj S, Feist WN, Viel S, Vaidyanathan S, Dudek AM, Gastou M, Rockwood SJ, Ekman FK, Oseghale AR, Xu L, Pavel-Dinu M, Luna SE, Cromer MK, Sayana R, Gomez-Ospina N, Porteus MH. High-efficiency transgene integration by homology-directed repair in human primary cells using DNA-PKcs inhibition. Nat Biotechnol 2023:10.1038/s41587-023-01888-4. [PMID: 37537500 DOI: 10.1038/s41587-023-01888-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2022] [Accepted: 06/28/2023] [Indexed: 08/05/2023]
Abstract
Therapeutic applications of nuclease-based genome editing would benefit from improved methods for transgene integration via homology-directed repair (HDR). To improve HDR efficiency, we screened six small-molecule inhibitors of DNA-dependent protein kinase catalytic subunit (DNA-PKcs), a key protein in the alternative repair pathway of non-homologous end joining (NHEJ), which generates genomic insertions/deletions (INDELs). From this screen, we identified AZD7648 as the most potent compound. The use of AZD7648 significantly increased HDR (up to 50-fold) and concomitantly decreased INDELs across different genomic loci in various therapeutically relevant primary human cell types. In all cases, the ratio of HDR to INDELs markedly increased, and, in certain situations, INDEL-free high-frequency (>50%) targeted integration was achieved. This approach has the potential to improve the therapeutic efficacy of cell-based therapies and broaden the use of targeted integration as a research tool.
Collapse
Affiliation(s)
- Sridhar Selvaraj
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - William N Feist
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sebastien Viel
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Immunology Department, Lyon Sud University Hospital, Pierre-Bénite, France
- International Center of Research in Infectiology, Lyon University, INSERM U1111, CNRS UMR 5308, ENS, UCBL, Lyon, France
| | - Sriram Vaidyanathan
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Center for Gene Therapy, Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH, USA
- Department of Pediatrics, The Ohio State University, Columbus, OH, USA
| | - Amanda M Dudek
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Marc Gastou
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sarah J Rockwood
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Freja K Ekman
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Aluya R Oseghale
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Liwen Xu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Sofia E Luna
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
| | - Ruhi Sayana
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University, Stanford, CA, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| |
Collapse
|
12
|
Galdos FX, Lee C, Lee S, Paige S, Goodyer W, Xu S, Samad T, Escobar GV, Darsha A, Beck A, Bak RO, Porteus MH, Wu S. Combined lineage tracing and scRNA-seq reveals unexpected first heart field predominance of human iPSC differentiation. eLife 2023; 12:80075. [PMID: 37284748 DOI: 10.7554/elife.80075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 05/27/2023] [Indexed: 06/08/2023] Open
Abstract
During mammalian development, the left and right ventricles arise from early populations of cardiac progenitors known as the first and second heart fields, respectively. While these populations have been extensively studied in non-human model systems, their identification and study in vivo human tissues have been limited due to the ethical and technical limitations of accessing gastrulation stage human embryos. Human induced pluripotent stem cells (hiPSCs) present an exciting alternative for modeling early human embryogenesis due to their well-established ability to differentiate into all embryonic germ layers. Here, we describe the development of a TBX5/MYL2 lineage tracing reporter system that allows for the identification of FHF- progenitors and their descendants including left ventricular cardiomyocytes. Furthermore, using single cell RNA sequencing (scRNA-seq) with oligonucleotide-based sample multiplexing, we extensively profiled differentiating hiPSCs across 12 timepoints in two independent iPSC lines. Surprisingly, our reporter system and scRNA-seq analysis revealed a predominance of FHF differentiation using the small molecule Wnt-based 2D differentiation protocol. We compared this data with existing murine and 3D cardiac organoid scRNA-seq data and confirmed the dominance of left ventricular cardiomyocytes (>90%) in our hiPSC-derived progeny. Together, our work provides the scientific community with a powerful new genetic lineage tracing approach as well as a single cell transcriptomic atlas of hiPSCs undergoing cardiac differentiation.
Collapse
Affiliation(s)
| | - Carissa Lee
- Stanford Cardiovascular Institute, Stanford University, Stanford, United States
| | - Soah Lee
- Department of Pharmacy, Sungkyunkwan University, Seoul, Republic of Korea
| | - Sharon Paige
- Stanford Cardiovascular Institute, Stanford University, Stanford, United States
| | - William Goodyer
- Stanford Cardiovascular Institute, Stanford University, Stanford, United States
| | - Sidra Xu
- Stanford Cardiovascular Institute, Stanford University, Stanford, United States
| | - Tahmina Samad
- Stanford Cardiovascular Institute, Stanford University, Stanford, United States
| | - Gabriela V Escobar
- Stanford Cardiovascular Institute, Stanford University, Stanford, United States
| | - Adrija Darsha
- School of Medicine, University of California, San Diego, Stanford, United States
| | - Aimee Beck
- Stanford Cardiovascular Institute, Stanford University, Stanford, United States
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, United States
| | - Sean Wu
- Stanford Cardiovascular Institute, Stanford University, Stanford, United States
| |
Collapse
|
13
|
Cromer MK, Majeti KR, Rettig GR, Murugan K, Kurgan GL, Bode NM, Hampton JP, Vakulskas CA, Behlke MA, Porteus MH. Comparative analysis of CRISPR off-target discovery tools following ex vivo editing of CD34 + hematopoietic stem and progenitor cells. Mol Ther 2023; 31:1074-1087. [PMID: 36793210 PMCID: PMC10124080 DOI: 10.1016/j.ymthe.2023.02.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2022] [Revised: 01/11/2023] [Accepted: 02/09/2023] [Indexed: 02/17/2023] Open
Abstract
While a number of methods exist to investigate CRISPR off-target (OT) editing, few have been compared head-to-head in primary cells after clinically relevant editing processes. Therefore, we compared in silico tools (COSMID, CCTop, and Cas-OFFinder) and empirical methods (CHANGE-Seq, CIRCLE-Seq, DISCOVER-Seq, GUIDE-Seq, and SITE-Seq) after ex vivo hematopoietic stem and progenitor cell (HSPC) editing. We performed editing using 11 different gRNAs complexed with Cas9 protein (high-fidelity [HiFi] or wild-type versions), then performed targeted next-generation sequencing of nominated OT sites identified by in silico and empirical methods. We identified an average of less than one OT site per guide RNA (gRNA) and all OT sites generated using HiFi Cas9 and a 20-nt gRNA were identified by all OT detection methods with the exception of SITE-seq. This resulted in high sensitivity for the majority of OT nomination tools and COSMID, DISCOVER-Seq, and GUIDE-Seq attained the highest positive predictive value (PPV). We found that empirical methods did not identify OT sites that were not also identified by bioinformatic methods. This study supports that refined bioinformatic algorithms could be developed that maintain both high sensitivity and PPV, thereby enabling more efficient identification of potential OT sites without compromising a thorough examination for any given gRNA.
Collapse
Affiliation(s)
- M Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Bioengineering and Therapeutic Sciences, University of California, San Francisco, San Francisco, CA 94143, USA; Eli and Edythe Broad Center for Regeneration Medicine, University of California, San Francisco, San Francisco, CA 94143, USA.
| | - Kiran R Majeti
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Karthik Murugan
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Gavin L Kurgan
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Nicole M Bode
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Jessica P Hampton
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA 52241, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
14
|
Kunte N, Din H, Saini G, Istomina E, Dougall K, MacDonald B, Bartolome R, Olsen AB, Bouge A, Czechowicz A, Agarwal R, Porteus MH. Implementation of a Phase 1b/2a Clinical Trial for Fanconi Anemia Patients Using JSP191 Antibody Conditioning and TCRαβ+ T-Cell/CD19+ B-Cell Depleted Grafts: A Center Experience. Transplant Cell Ther 2023. [DOI: 10.1016/s2666-6367(23)00649-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
|
15
|
Brault J, Liu T, Liu S, Lawson A, Choi U, Kozhushko N, Bzhilyanskaya V, Pavel-Dinu M, Meis RJ, Eckhaus MA, Burkett SS, Bosticardo M, Kleinstiver BP, Notarangelo LD, Lazzarotto CR, Tsai SQ, Wu X, Dahl GA, Porteus MH, Malech HL, De Ravin SS. CRISPR-Cas9-AAV versus lentivector transduction for genome modification of X-linked severe combined immunodeficiency hematopoietic stem cells. Front Immunol 2023; 13:1067417. [PMID: 36685559 PMCID: PMC9846165 DOI: 10.3389/fimmu.2022.1067417] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 12/06/2022] [Indexed: 01/05/2023] Open
Abstract
Introduction Ex vivo gene therapy for treatment of Inborn errors of Immunity (IEIs) have demonstrated significant clinical benefit in multiple Phase I/II clinical trials. Current approaches rely on engineered retroviral vectors to randomly integrate copy(s) of gene-of-interest in autologous hematopoietic stem/progenitor cells (HSPCs) genome permanently to provide gene function in transduced HSPCs and their progenies. To circumvent concerns related to potential genotoxicities due to the random vector integrations in HSPCs, targeted correction with CRISPR-Cas9-based genome editing offers improved precision for functional correction of multiple IEIs. Methods We compare the two approaches for integration of IL2RG transgene for functional correction of HSPCs from patients with X-linked Severe Combined Immunodeficiency (SCID-X1 or XSCID); delivery via current clinical lentivector (LV)-IL2RG versus targeted insertion (TI) of IL2RG via homology-directed repair (HDR) when using an adeno-associated virus (AAV)-IL2RG donor following double-strand DNA break at the endogenous IL2RG locus. Results and discussion In vitro differentiation of LV- or TI-treated XSCID HSPCs similarly overcome differentiation block into Pre-T-I and Pre-T-II lymphocytes but we observed significantly superior development of NK cells when corrected by TI (40.7% versus 4.1%, p = 0.0099). Transplants into immunodeficient mice demonstrated robust engraftment (8.1% and 23.3% in bone marrow) for LV- and TI-IL2RG HSPCs with efficient T cell development following TI-IL2RG in all four patients' HSPCs. Extensive specificity analysis of CRISPR-Cas9 editing with rhAmpSeq covering 82 predicted off-target sites found no evidence of indels in edited cells before (in vitro) or following transplant, in stark contrast to LV's non-targeted vector integration sites. Together, the improved efficiency and safety of IL2RG correction via CRISPR-Cas9-based TI approach provides a strong rationale for a clinical trial for treatment of XSCID patients.
Collapse
Affiliation(s)
- Julie Brault
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Taylor Liu
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Siyuan Liu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick, MD, United States
| | - Amanda Lawson
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Uimook Choi
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Nikita Kozhushko
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Vera Bzhilyanskaya
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Mara Pavel-Dinu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Palo Alto, CA, United States
| | | | - Michael A. Eckhaus
- Division of Veterinary Resources, Office of Research Services, National Institutes of Health, Bethesda, MD, United States
| | - Sandra S. Burkett
- Molecular Cytogenetic Core Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD, United States
| | - Marita Bosticardo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Benjamin P. Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA, United States
- Department of Pathology, Harvard Medical School, Boston, MA, United States
| | - Luigi D. Notarangelo
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Cicera R. Lazzarotto
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Shengdar Q. Tsai
- Department of Hematology, St. Jude Children’s Research Hospital, Memphis, TN, United States
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick, MD, United States
| | | | - Matthew H. Porteus
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Palo Alto, CA, United States
| | - Harry L. Malech
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| | - Suk See De Ravin
- Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases (NIAID), National Institutes of Health (NIH), Bethesda, MD, United States
| |
Collapse
|
16
|
Cromer MK, Barsan VV, Jaeger E, Wang M, Hampton JP, Chen F, Kennedy D, Xiao J, Khrebtukova I, Granat A, Truong T, Porteus MH. Ultra-deep sequencing validates safety of CRISPR/Cas9 genome editing in human hematopoietic stem and progenitor cells. Nat Commun 2022; 13:4724. [PMID: 35953477 PMCID: PMC9372057 DOI: 10.1038/s41467-022-32233-z] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 07/22/2022] [Indexed: 12/25/2022] Open
Abstract
As CRISPR-based therapies enter the clinic, evaluation of safety remains a critical and active area of study. Here, we employ a clinical next generation sequencing (NGS) workflow to achieve high sequencing depth and detect ultra-low frequency variants across exons of genes associated with cancer, all exons, and genome wide. In three separate primary human hematopoietic stem and progenitor cell (HSPC) donors assessed in technical triplicates, we electroporated high-fidelity Cas9 protein targeted to three loci (AAVS1, HBB, and ZFPM2) and harvested genomic DNA at days 4 and 10. Our results demonstrate that clinically relevant delivery of high-fidelity Cas9 to primary HSPCs and ex vivo culture up to 10 days does not introduce or enrich for tumorigenic variants and that even a single SNP in a gRNA spacer sequence is sufficient to eliminate Cas9 off-target activity in primary, repair-competent human HSPCs.
Collapse
Affiliation(s)
- M Kyle Cromer
- Department of Surgery, University of California, San Francisco, San Francisco, CA, USA
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Hnatiuk AP, Bruyneel AA, Tailor D, Pandrala M, Dheeraj A, Li W, Serrano R, Feyen DA, Vu MM, Amatya P, Gupta S, Nakauchi Y, Morgado I, Wiebking V, Liao R, Porteus MH, Majeti R, Malhotra SV, Mercola M. Reengineering Ponatinib to Minimize Cardiovascular Toxicity. Cancer Res 2022; 82:2777-2791. [PMID: 35763671 PMCID: PMC9620869 DOI: 10.1158/0008-5472.can-21-3652] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 03/29/2022] [Accepted: 05/24/2022] [Indexed: 01/07/2023]
Abstract
Small molecule tyrosine kinase inhibitors (TKI) have revolutionized cancer treatment and greatly improved patient survival. However, life-threatening cardiotoxicity of many TKIs has become a major concern. Ponatinib (ICLUSIG) was developed as an inhibitor of the BCR-ABL oncogene and is among the most cardiotoxic of TKIs. Consequently, use of ponatinib is restricted to the treatment of tumors carrying T315I-mutated BCR-ABL, which occurs in chronic myeloid leukemia (CML) and confers resistance to first- and second-generation inhibitors such as imatinib and nilotinib. Through parallel screening of cardiovascular toxicity and antitumor efficacy assays, we engineered safer analogs of ponatinib that retained potency against T315I BCR-ABL kinase activity and suppressed T315I mutant CML tumor growth. The new compounds were substantially less toxic in human cardiac vasculogenesis and cardiomyocyte contractility assays in vitro. The compounds showed a larger therapeutic window in vivo, leading to regression of human T315I mutant CML xenografts without cardiotoxicity. Comparison of the kinase inhibition profiles of ponatinib and the new compounds suggested that ponatinib cardiotoxicity is mediated by a few kinases, some of which were previously unassociated with cardiovascular disease. Overall, the study develops an approach using complex phenotypic assays to reduce the high risk of cardiovascular toxicity that is prevalent among small molecule oncology therapeutics. SIGNIFICANCE Newly developed ponatinib analogs retain antitumor efficacy but elicit significantly decreased cardiotoxicity, representing a therapeutic opportunity for safer CML treatment.
Collapse
MESH Headings
- Antineoplastic Agents/adverse effects
- Cardiotoxicity/drug therapy
- Cardiotoxicity/etiology
- Cardiotoxicity/prevention & control
- Drug Resistance, Neoplasm
- Fusion Proteins, bcr-abl/genetics
- Humans
- Imidazoles
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/drug therapy
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/genetics
- Leukemia, Myelogenous, Chronic, BCR-ABL Positive/pathology
- Protein Kinase Inhibitors/adverse effects
- Pyridazines/pharmacology
- Pyridazines/therapeutic use
Collapse
Affiliation(s)
- Anna P. Hnatiuk
- Stanford Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, California
| | - Arne A.N. Bruyneel
- Stanford Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, California
| | - Dhanir Tailor
- Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health Sciences University School of Medicine, Portland, Oregon
| | - Mallesh Pandrala
- Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health Sciences University School of Medicine, Portland, Oregon
| | - Arpit Dheeraj
- Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health Sciences University School of Medicine, Portland, Oregon
| | - Wenqi Li
- Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health Sciences University School of Medicine, Portland, Oregon
| | - Ricardo Serrano
- Stanford Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, California
| | - Dries A.M. Feyen
- Stanford Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, California
| | - Michelle M. Vu
- Stanford Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, California
| | - Prashila Amatya
- Stanford Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, California
| | - Saloni Gupta
- Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health Sciences University School of Medicine, Portland, Oregon
| | - Yusuke Nakauchi
- Division of Hematology Institute for Stem cell Biology and Regenerative Medicine, Stanford School of Medicine, California
| | - Isabel Morgado
- Stanford Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, California
| | - Volker Wiebking
- Department of Pediatrics, Stanford School of Medicine, Stanford, California
| | - Ronglih Liao
- Stanford Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, California
| | - Matthew H. Porteus
- Department of Pediatrics, Stanford School of Medicine, Stanford, California
| | - Ravindra Majeti
- Division of Hematology Institute for Stem cell Biology and Regenerative Medicine, Stanford School of Medicine, California
| | - Sanjay V. Malhotra
- Center for Experimental Therapeutics, Knight Cancer Institute, Oregon Health Sciences University School of Medicine, Portland, Oregon
| | - Mark Mercola
- Stanford Cardiovascular Institute and Department of Medicine, Stanford University, Stanford, California
| |
Collapse
|
18
|
Porteus MH, Pavel-Dinu M, Pai SY. A Curative DNA Code for Hematopoietic Defects: Novel Cell Therapies for Monogenic Diseases of the Blood and Immune System. Hematol Oncol Clin North Am 2022; 36:647-665. [PMID: 35773054 PMCID: PMC9365196 DOI: 10.1016/j.hoc.2022.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Matthew H Porteus
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford Medical School, Lokey Stem Cell Research Building, G3040B, MC 5462, 265 Campus Drive, Stanford, CA 94305, USA.
| | - Mara Pavel-Dinu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford Medical School, Lokey Stem Cell Research Building, G3045, MC 5175, 265 Campus Drive, Stanford, CA 94305, USA.
| | - Sung-Yun Pai
- Immune Deficiency Cellular Therapy Program, Center for Cancer Research, National Cancer Institute, 10 Center Drive, MSC 1102, Bethesda, MD 20892, USA
| |
Collapse
|
19
|
Ang LT, Nguyen AT, Liu KJ, Chen A, Xiong X, Curtis M, Martin RM, Raftry BC, Ng CY, Vogel U, Lander A, Lesch BJ, Fowler JL, Holman AR, Chai T, Vijayakumar S, Suchy FP, Nishimura T, Bhadury J, Porteus MH, Nakauchi H, Cheung C, George SC, Red-Horse K, Prescott JB, Loh KM. Generating human artery and vein cells from pluripotent stem cells highlights the arterial tropism of Nipah and Hendra viruses. Cell 2022; 185:2523-2541.e30. [PMID: 35738284 DOI: 10.1016/j.cell.2022.05.024] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Revised: 03/26/2022] [Accepted: 05/26/2022] [Indexed: 02/07/2023]
Abstract
Stem cell research endeavors to generate specific subtypes of classically defined "cell types." Here, we generate >90% pure human artery or vein endothelial cells from pluripotent stem cells within 3-4 days. We specified artery cells by inhibiting vein-specifying signals and vice versa. These cells modeled viral infection of human vasculature by Nipah and Hendra viruses, which are extraordinarily deadly (∼57%-59% fatality rate) and require biosafety-level-4 containment. Generating pure populations of artery and vein cells highlighted that Nipah and Hendra viruses preferentially infected arteries; arteries expressed higher levels of their viral-entry receptor. Virally infected artery cells fused into syncytia containing up to 23 nuclei, which rapidly died. Despite infecting arteries and occupying ∼6%-17% of their transcriptome, Nipah and Hendra largely eluded innate immune detection, minimally eliciting interferon signaling. We thus efficiently generate artery and vein cells, introduce stem-cell-based toolkits for biosafety-level-4 virology, and explore the arterial tropism and cellular effects of Nipah and Hendra viruses.
Collapse
Affiliation(s)
- Lay Teng Ang
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Alana T Nguyen
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Kevin J Liu
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Angela Chen
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Xiaochen Xiong
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Matthew Curtis
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
| | - Renata M Martin
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Brian C Raftry
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Chun Yi Ng
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore
| | - Uwe Vogel
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany
| | - Angelika Lander
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany
| | - Benjamin J Lesch
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Jonas L Fowler
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Alyssa R Holman
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Timothy Chai
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Siva Vijayakumar
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA
| | - Fabian P Suchy
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Toshinobu Nishimura
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Joydeep Bhadury
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Hiromitsu Nakauchi
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA
| | - Christine Cheung
- Lee Kong Chian School of Medicine, Nanyang Technological University, Singapore 308232, Singapore; Institute of Molecular and Cell Biology, A(∗)STAR, Singapore 138673, Singapore
| | - Steven C George
- Department of Biomedical Engineering, University of California, Davis, Davis, CA 95616, USA
| | - Kristy Red-Horse
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University, Stanford, CA 94305, USA
| | - Joseph B Prescott
- Center for Biological Threats and Special Pathogens, Robert Koch Institute, Berlin 13353, Germany.
| | - Kyle M Loh
- Stanford Institute for Stem Cell Biology & Regenerative Medicine, Stanford University, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford Cardiovascular Institute, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
20
|
Toral MA, Charlesworth CT, Ng B, Chemudupati T, Homma S, Nakauchi H, Bassuk AG, Porteus MH, Mahajan VB. Investigation of Cas9 antibodies in the human eye. Nat Commun 2022; 13:1053. [PMID: 35217666 PMCID: PMC8881612 DOI: 10.1038/s41467-022-28674-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2021] [Accepted: 02/04/2022] [Indexed: 12/04/2022] Open
Abstract
Preexisting immunity against Cas9 proteins in humans represents a safety risk for CRISPR–Cas9 technologies. However, it is unclear to what extent preexisting Cas9 immunity is relevant to the eye as it is targeted for early in vivo CRISPR–Cas9 clinical trials. While the eye lacks T-cells, it contains antibodies, cytokines, and resident immune cells. Although precise mechanisms are unclear, intraocular inflammation remains a major cause of vision loss. Here, we used immunoglobulin isotyping and ELISA platforms to profile antibodies in serum and vitreous fluid biopsies from human adult subjects and Cas9-immunized mice. We observed high prevalence of preexisting Cas9-reactive antibodies in serum but not in the eye. However, we detected intraocular antibodies reactive to S. pyogenes-derived Cas9 after S. pyogenes intraocular infection. Our data suggest that serum antibody concentration may determine whether specific intraocular antibodies develop, but preexisting immunity to Cas9 may represent a lower risk in human eyes than systemically. Pre-existing antibodies against Cas9 proteins represent a potential issue for gene therapies, including those targeting the eye. Here the authors assess the presence of intraocular antibodies, and show that Cas9 antibodies were prevalent in human serum but not the eye, unless prior bacterial infection occurred.
Collapse
Affiliation(s)
- Marcus A Toral
- Molecular Surgery Program, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA.,Medical Scientist Training Program and Graduate Program in Molecular Medicine, University of Iowa, Iowa City, IA, USA
| | | | - Benjamin Ng
- Molecular Surgery Program, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA.,Medical Sciences Division, University of Oxford, Oxford, UK
| | - Teja Chemudupati
- Molecular Surgery Program, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA
| | - Shota Homma
- Department of Genetics, Stanford University, Palo Alto, CA, USA
| | - Hiromitsu Nakauchi
- Department of Genetics, Stanford University, Palo Alto, CA, USA.,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Palo Alto, CA, USA.,Division of Stem Cell Therapy, Distinguished Professor Unit, Institute of Medical Science, University of Tokyo, Tokyo, Japan
| | - Alexander G Bassuk
- Departments of Pediatrics and Neurology and The Iowa Neuroscience Institute (INI), University of Iowa, Iowa City, IA, USA
| | | | - Vinit B Mahajan
- Molecular Surgery Program, Department of Ophthalmology, Byers Eye Institute, Stanford University, Palo Alto, CA, USA. .,Veterans Affairs Palo Alto Health Care System, Palo Alto, CA, Palo Alto, CA, USA.
| |
Collapse
|
21
|
Vaidyanathan S, Baik R, Chen L, Bravo DT, Suarez CJ, Abazari SM, Salahudeen AA, Dudek AM, Teran CA, Davis TH, Lee CM, Bao G, Randell SH, Artandi SE, Wine JJ, Kuo CJ, Desai TJ, Nayak JV, Sellers ZM, Porteus MH. Targeted replacement of full-length CFTR in human airway stem cells by CRISPR-Cas9 for pan-mutation correction in the endogenous locus. Mol Ther 2022; 30:223-237. [PMID: 33794364 PMCID: PMC8753290 DOI: 10.1016/j.ymthe.2021.03.023] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2020] [Revised: 02/23/2021] [Accepted: 03/25/2021] [Indexed: 01/07/2023] Open
Abstract
Cystic fibrosis (CF) is a monogenic disease caused by impaired production and/or function of the CF transmembrane conductance regulator (CFTR) protein. Although we have previously shown correction of the most common pathogenic mutation, there are many other pathogenic mutations throughout the CF gene. An autologous airway stem cell therapy in which the CFTR cDNA is precisely inserted into the CFTR locus may enable the development of a durable cure for almost all CF patients, irrespective of the causal mutation. Here, we use CRISPR-Cas9 and two adeno-associated viruses (AAVs) carrying the two halves of the CFTR cDNA to sequentially insert the full CFTR cDNA along with a truncated CD19 (tCD19) enrichment tag in upper airway basal stem cells (UABCs) and human bronchial epithelial cells (HBECs). The modified cells were enriched to obtain 60%-80% tCD19+ UABCs and HBECs from 11 different CF donors with a variety of mutations. Differentiated epithelial monolayers cultured at air-liquid interface showed restored CFTR function that was >70% of the CFTR function in non-CF controls. Thus, our study enables the development of a therapy for almost all CF patients, including patients who cannot be treated using recently approved modulator therapies.
Collapse
Affiliation(s)
| | - Ron Baik
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Lu Chen
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Dawn T Bravo
- Department of Otolaryngology-Head and Neck Surgery, Stanford, CA 94305, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University, Stanford, CA 94305, USA
| | - Shayda M Abazari
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Ameen A Salahudeen
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Amanda M Dudek
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Timothy H Davis
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Scott H Randell
- Department of Cell Biology and Physiology, The University of North Carolina at Chapel Hill, Chapel Hill, NC 27599, USA
| | - Steven E Artandi
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA; Department of Biochemistry, Stanford University School of Medicine, Stanford, CA 94305, USA; Stanford Cancer Institute, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jeffrey J Wine
- Department of Psychology, Stanford University, Stanford, CA 94305, USA
| | - Calvin J Kuo
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Tushar J Desai
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford, CA 94305, USA
| | - Zachary M Sellers
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
22
|
Lattanzi A, Camarena J, Lahiri P, Segal H, Srifa W, Vakulskas CA, Frock RL, Kenrick J, Lee C, Talbott N, Skowronski J, Cromer MK, Charlesworth CT, Bak RO, Mantri S, Bao G, DiGiusto D, Tisdale J, Wright JF, Bhatia N, Roncarolo MG, Dever DP, Porteus MH. Development of β-globin gene correction in human hematopoietic stem cells as a potential durable treatment for sickle cell disease. Sci Transl Med 2021; 13:13/598/eabf2444. [PMID: 34135108 DOI: 10.1126/scitranslmed.abf2444] [Citation(s) in RCA: 74] [Impact Index Per Article: 24.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 05/25/2021] [Indexed: 12/11/2022]
Abstract
Sickle cell disease (SCD) is the most common serious monogenic disease with 300,000 births annually worldwide. SCD is an autosomal recessive disease resulting from a single point mutation in codon six of the β-globin gene (HBB). Ex vivo β-globin gene correction in autologous patient-derived hematopoietic stem and progenitor cells (HSPCs) may potentially provide a curative treatment for SCD. We previously developed a CRISPR-Cas9 gene targeting strategy that uses high-fidelity Cas9 precomplexed with chemically modified guide RNAs to induce recombinant adeno-associated virus serotype 6 (rAAV6)-mediated HBB gene correction of the SCD-causing mutation in HSPCs. Here, we demonstrate the preclinical feasibility, efficacy, and toxicology of HBB gene correction in plerixafor-mobilized CD34+ cells from healthy and SCD patient donors (gcHBB-SCD). We achieved up to 60% HBB allelic correction in clinical-scale gcHBB-SCD manufacturing. After transplant into immunodeficient NSG mice, 20% gene correction was achieved with multilineage engraftment. The long-term safety, tumorigenicity, and toxicology study demonstrated no evidence of abnormal hematopoiesis, genotoxicity, or tumorigenicity from the engrafted gcHBB-SCD drug product. Together, these preclinical data support the safety, efficacy, and reproducibility of this gene correction strategy for initiation of a phase 1/2 clinical trial in patients with SCD.
Collapse
Affiliation(s)
- Annalisa Lattanzi
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Premanjali Lahiri
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Helen Segal
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Waracharee Srifa
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Richard L Frock
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Josefin Kenrick
- Department of Radiation Oncology, Stanford University, Stanford, CA 94305, USA
| | - Ciaran Lee
- APC Microbiome Ireland, University College Cork, T12 YN60 Cork, Ireland
| | - Narae Talbott
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - Jason Skowronski
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, DK-8000 Aarhus, Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, DK-8000 Aarhus, Denmark
| | - Sruthi Mantri
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77006, USA
| | - David DiGiusto
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA
| | - John Tisdale
- Molecular and Clinical Hematology Branch, NHLBI, Bethesda, MD 20814, USA
| | - J Fraser Wright
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Neehar Bhatia
- Laboratory for Cell and Gene Medicine, Stanford University, Stanford, CA 94304, USA.,Deceased
| | - Maria Grazia Roncarolo
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA. .,Center for Definitive and Curative Medicine, Stanford University, Stanford, CA 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| |
Collapse
|
23
|
Sweeney CL, Pavel-Dinu M, Choi U, Brault J, Liu T, Koontz S, Li L, Theobald N, Lee J, Bello EA, Wu X, Meis RJ, Dahl GA, Porteus MH, Malech HL, De Ravin SS. Correction of X-CGD patient HSPCs by targeted CYBB cDNA insertion using CRISPR/Cas9 with 53BP1 inhibition for enhanced homology-directed repair. Gene Ther 2021; 28:373-390. [PMID: 33712802 PMCID: PMC8232036 DOI: 10.1038/s41434-021-00251-z] [Citation(s) in RCA: 34] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2020] [Revised: 02/09/2021] [Accepted: 02/24/2021] [Indexed: 01/31/2023]
Abstract
X-linked chronic granulomatous disease is an immunodeficiency characterized by defective production of microbicidal reactive oxygen species (ROS) by phagocytes. Causative mutations occur throughout the 13 exons and splice sites of the CYBB gene, resulting in loss of gp91phox protein. Here we report gene correction by homology-directed repair in patient hematopoietic stem/progenitor cells (HSPCs) using CRISPR/Cas9 for targeted insertion of CYBB exon 1-13 or 2-13 cDNAs from adeno-associated virus donors at endogenous CYBB exon 1 or exon 2 sites. Targeted insertion of exon 1-13 cDNA did not restore physiologic gp91phox levels, consistent with a requirement for intron 1 in CYBB expression. However, insertion of exon 2-13 cDNA fully restored gp91phox and ROS production upon phagocyte differentiation. Addition of a woodchuck hepatitis virus post-transcriptional regulatory element did not further enhance gp91phox expression in exon 2-13 corrected cells, indicating that retention of intron 1 was sufficient for optimal CYBB expression. Targeted correction was increased ~1.5-fold using i53 mRNA to transiently inhibit nonhomologous end joining. Following engraftment in NSG mice, corrected HSPCs generated phagocytes with restored gp91phox and ROS production. Our findings demonstrate the utility of tailoring donor design and targeting strategies to retain regulatory elements needed for optimal expression of the target gene.
Collapse
Affiliation(s)
- Colin L Sweeney
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Uimook Choi
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Julie Brault
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Taylor Liu
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Sherry Koontz
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | | | - Narda Theobald
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Janet Lee
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Ezekiel A Bello
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick, MD, USA
| | | | | | - Matthew H Porteus
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Harry L Malech
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA
| | - Suk See De Ravin
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD, USA.
| |
Collapse
|
24
|
De Ravin SS, Brault J, Meis RJ, Liu S, Li L, Pavel-Dinu M, Lazzarotto CR, Liu T, Koontz SM, Choi U, Sweeney CL, Theobald N, Lee G, Clark AB, Burkett SS, Kleinstiver BP, Porteus MH, Tsai S, Kuhns DB, Dahl GA, Headey S, Wu X, Malech HL. Enhanced homology-directed repair for highly efficient gene editing in hematopoietic stem/progenitor cells. Blood 2021; 137:2598-2608. [PMID: 33623984 PMCID: PMC8120141 DOI: 10.1182/blood.2020008503] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 01/28/2021] [Indexed: 12/21/2022] Open
Abstract
Lentivector gene therapy for X-linked chronic granulomatous disease (X-CGD) has proven to be a viable approach, but random vector integration and subnormal protein production from exogenous promoters in transduced cells remain concerning for long-term safety and efficacy. A previous genome editing-based approach using Streptococcus pyogenes Cas9 mRNA and an oligodeoxynucleotide donor to repair genetic mutations showed the capability to restore physiological protein expression but lacked sufficient efficiency in quiescent CD34+ hematopoietic cells for clinical translation. Here, we report that transient inhibition of p53-binding protein 1 (53BP1) significantly increased (2.3-fold) long-term homology-directed repair to achieve highly efficient (80% gp91phox+ cells compared with healthy donor control subjects) long-term correction of X-CGD CD34+ cells.
Collapse
Affiliation(s)
- Suk See De Ravin
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Julie Brault
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | - Siyuan Liu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick, MD
| | | | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University, School of Medicine, Stanford, CA
| | - Cicera R Lazzarotto
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN
| | - Taylor Liu
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Sherry M Koontz
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Uimook Choi
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Colin L Sweeney
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Narda Theobald
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - GaHyun Lee
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN
| | - Aaron B Clark
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick, MD
| | - Sandra S Burkett
- Molecular Cytogenetic Core Facility, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Frederick, MD
| | - Benjamin P Kleinstiver
- Center for Genomic Medicine and Department of Pathology, Massachusetts General Hospital, Boston, MA
- Department of Pathology, Harvard Medical School, Boston, MA; and
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, School of Medicine, Stanford, CA
| | - Shengdar Tsai
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN
| | - Douglas B Kuhns
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | | | - Stephen Headey
- School of Science, RMIT University, Melbourne, VIC, Australia
| | - Xiaolin Wu
- Cancer Research Technology Program, Leidos Biomedical Research Inc., Frederick, MD
| | - Harry L Malech
- Genetic Immunotherapy Section, Laboratory of Clinical Immunology and Microbiology, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| |
Collapse
|
25
|
Gardner CL, Pavel-Dinu M, Dobbs K, Bosticardo M, Reardon PK, Lack J, DeRavin SS, Le K, Bello E, Pala F, Delmonte OM, Malech H, Montel-Hagen A, Crooks G, Acuto O, Porteus MH, Notarangelo LD. Correction to: Gene Editing Rescues in Vitro T Cell Development of RAG2-Deficient Induced Pluripotent Stem Cells in an Artificial Thymic Organoid System. J Clin Immunol 2021; 41:863. [PMID: 33821398 DOI: 10.1007/s10875-021-01030-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- Cameron L Gardner
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX14RE, UK
| | - Mara Pavel-Dinu
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Kerry Dobbs
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Marita Bosticardo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Paul K Reardon
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX14RE, UK
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource, NIAID, NIH, Bethesda, MD, USA
- Advanced Biomedical Computational Science (ABCS), Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Suk See DeRavin
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Kent Le
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Ezekiel Bello
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Francesca Pala
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Ottavia M Delmonte
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Harry Malech
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Amelie Montel-Hagen
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gay Crooks
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX14RE, UK.
| | - Matthew H Porteus
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
| | - Luigi D Notarangelo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA.
| |
Collapse
|
26
|
Cromer MK, Camarena J, Martin RM, Lesch BJ, Vakulskas CA, Bode NM, Kurgan G, Collingwood MA, Rettig GR, Behlke MA, Lemgart VT, Zhang Y, Goyal A, Zhao F, Ponce E, Srifa W, Bak RO, Uchida N, Majeti R, Sheehan VA, Tisdale JF, Dever DP, Porteus MH. Gene replacement of α-globin with β-globin restores hemoglobin balance in β-thalassemia-derived hematopoietic stem and progenitor cells. Nat Med 2021; 27:677-687. [PMID: 33737751 PMCID: PMC8265212 DOI: 10.1038/s41591-021-01284-y] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Accepted: 02/09/2021] [Indexed: 12/12/2022]
Abstract
β-Thalassemia pathology is due not only to loss of β-globin (HBB), but also to erythrotoxic accumulation and aggregation of the β-globin-binding partner, α-globin (HBA1/2). Here we describe a Cas9/AAV6-mediated genome editing strategy that can replace the entire HBA1 gene with a full-length HBB transgene in β-thalassemia-derived hematopoietic stem and progenitor cells (HSPCs), which is sufficient to normalize β-globin:α-globin messenger RNA and protein ratios and restore functional adult hemoglobin tetramers in patient-derived red blood cells. Edited HSPCs were capable of long-term and bilineage hematopoietic reconstitution in mice, establishing proof of concept for replacement of HBA1 with HBB as a novel therapeutic strategy for curing β-thalassemia.
Collapse
Affiliation(s)
- M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Renata M Martin
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Benjamin J Lesch
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Nicole M Bode
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Gavin Kurgan
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | | | | | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Viktor T Lemgart
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Yankai Zhang
- Division of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Ankush Goyal
- Division of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - Feifei Zhao
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Ezequiel Ponce
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Waracharee Srifa
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark
- Aarhus Institute of Advanced Studies, Aarhus University, Aarhus, Denmark
| | - Naoya Uchida
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Vivien A Sheehan
- Division of Hematology/Oncology, Department of Pediatrics, Baylor College of Medicine, Houston, TX, USA
| | - John F Tisdale
- Cellular and Molecular Therapeutics Branch, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, USA.
- Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA.
| |
Collapse
|
27
|
de Alencastro G, Puzzo F, Pavel-Dinu M, Zhang F, Pillay S, Majzoub K, Tiffany M, Jang H, Sheikali A, Cromer MK, Meetei R, Carette JE, Porteus MH, Pekrun K, Kay MA. Improved Genome Editing through Inhibition of FANCM and Members of the BTR Dissolvase Complex. Mol Ther 2021; 29:1016-1027. [PMID: 33678249 DOI: 10.1016/j.ymthe.2020.10.020] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/27/2020] [Accepted: 10/19/2020] [Indexed: 11/16/2022] Open
Abstract
Recombinant adeno-associated virus (rAAV) vectors have the unique property of being able to perform genomic targeted integration (TI) without inducing a double-strand break (DSB). In order to improve our understanding of the mechanism behind TI mediated by AAV and improve its efficiency, we performed an unbiased genetic screen in human cells using a promoterless AAV-homologous recombination (AAV-HR) vector system. We identified that the inhibition of the Fanconi anemia complementation group M (FANCM) protein enhanced AAV-HR-mediated TI efficiencies in different cultured human cells by ∼6- to 9-fold. The combined knockdown of the FANCM and two proteins also associated with the FANCM complex, RecQ-mediated genome instability 1 (RMI1) and Bloom DNA helicase (BLM) from the BLM-topoisomerase IIIα (TOP3A)-RMI (BTR) dissolvase complex (RMI1, having also been identified in our screen), led to the enhancement of AAV-HR-mediated TI up to ∼17 times. AAV-HR-mediated TI in the presence of a nuclease (CRISPR-Cas9) was also increased by ∼1.5- to 2-fold in FANCM and RMI1 knockout cells, respectively. Furthermore, knockdown of FANCM in human CD34+ hematopoietic stem and progenitor cells (HSPCs) increased AAV-HR-mediated TI by ∼3.5-fold. This study expands our knowledge on the mechanisms related to AAV-mediated TI, and it highlights new pathways that might be manipulated for future improvements in AAV-HR-mediated TI.
Collapse
Affiliation(s)
| | - Francesco Puzzo
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Mara Pavel-Dinu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford, CA, USA
| | - Feijie Zhang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Sirika Pillay
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Karim Majzoub
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Matthew Tiffany
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Hagoon Jang
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Adam Sheikali
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford, CA, USA
| | - M Kyle Cromer
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford, CA, USA
| | - Ruhikanta Meetei
- Division of Experimental Hematology and Cancer Biology, Cincinnati Children's Hospital Medical Center, Cincinnati, OH, USA
| | - Jan E Carette
- Department of Microbiology and Immunology, Stanford University, Stanford, CA, USA
| | - Matthew H Porteus
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford, CA, USA
| | - Katja Pekrun
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA
| | - Mark A Kay
- Departments of Pediatrics and Genetics, Stanford University, Stanford, CA, USA.
| |
Collapse
|
28
|
Wiebking V, Lee CM, Mostrel N, Lahiri P, Bak R, Bao G, Roncarolo MG, Bertaina A, Porteus MH. Genome editing of donor-derived T-cells to generate allogenic chimeric antigen receptor-modified T cells: Optimizing αβ T cell-depleted haploidentical hematopoietic stem cell transplantation. Haematologica 2021; 106:847-858. [PMID: 32241852 PMCID: PMC7928014 DOI: 10.3324/haematol.2019.233882] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2019] [Indexed: 12/11/2022] Open
Abstract
Allogeneic hematopoietic stem cell transplantation is an effective therapy for high-risk leukemias. In children, graft manipulation based on the selective removal of αβT cells and B cells has been shown to reduce the risk of acute and chronic graft-versus-host disease, thus allowing the use of haploidentical donors which expands the population of recipients in whom allogeneic hematopoietic stem cell transplantation can be used. Leukemic relapse, however, remains a challenge. T cells expressing chimeric antigen receptors can potently eliminate leukemia, including those in the central nervous system. We hypothesized that by engineering the donor αβT cells that are removed from the graft by genome editing to express a CD19-specific chimeric antigen receptor, while simultaneously inactivating the T-cell receptor, we could create a therapy that enhances the anti-leukemic efficacy of the stem cell transplant without increasing the risk of graft-versus-host disease. Using genome editing with Cas9 ribonucleoprotein and adeno-associated virus serotype 6, we integrated a CD19-specific chimeric antigen receptor inframe into the TRAC locus. More than 90% of cells lost T-cell receptor expression, while >75% expressed the chimeric antigen receptor. The initial product was further purified with less than 0.05% T-cell receptorpositive cells remaining. In vitro, the chimeric antigen receptor T cells efficiently eliminated target cells and produced high cytokine levels when challenged with CD19+ leukemia cells. In vivo, the gene-modified T cells eliminated leukemia without causing graft-versus-host disease in a xenograft model. Gene editing was highly specific with no evidence of off-target effects. These data support the concept that the addition of αβ T-cell-derived, genome-edited T cells expressing CD19-specific chimeric antigen receptors could enhance the anti-leukemic efficacy of αβT-celldepleted haploidentical hematopoietic stem cell transplantation without increasing the risk of graft-versus-host disease.
Collapse
Affiliation(s)
- Volker Wiebking
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Nathalie Mostrel
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Premanjali Lahiri
- Laboratory for Cell and Gene Medicine, Stanford University School of Medicine, Stanford, CA, USA
| | - Rasmus Bak
- Department of Biomedicine, Aarhus University, Aarhus, Denmark,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, Aarhus, Denmark
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Maria Grazia Roncarolo
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Alice Bertaina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA,Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| |
Collapse
|
29
|
Gardner CL, Pavel-Dinu M, Dobbs K, Bosticardo M, Reardon PK, Lack J, DeRavin SS, Le K, Bello E, Pala F, Delmonte OM, Malech H, Montel-Hagan A, Crooks G, Acuto O, Porteus MH, Notarangelo LD. Gene Editing Rescues In vitro T Cell Development of RAG2-Deficient Induced Pluripotent Stem Cells in an Artificial Thymic Organoid System. J Clin Immunol 2021; 41:852-862. [PMID: 33650026 DOI: 10.1007/s10875-021-00989-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Accepted: 02/03/2021] [Indexed: 12/12/2022]
Abstract
Severe combined immune deficiency (SCID) caused by RAG1 or RAG2 deficiency is a genetically determined immune deficiency characterized by the virtual absence of T and B lymphocytes. Unless treated with hematopoietic stem cell transplantation (HSCT), patients with RAG deficiency succumb to severe infections early in life. However, HSCT carries the risk of graft-versus-host disease. Moreover, a high rate of graft failure and poor immune reconstitution have been reported after unconditioned HSCT. Expression of the RAG genes is tightly regulated, and preclinical attempts of gene therapy with heterologous promoters have led to controversial results. Using patient-derived induced pluripotent stem cells (iPSCs) and an in vitro artificial thymic organoid system as a model, here we demonstrate that gene editing rescues the progressive T cell differentiation potential of RAG2-deficient cells to normal levels, with generation of a diversified T cell repertoire. These results suggest that targeted gene editing may represent a novel therapeutic option for correction of this immunodeficiency.
Collapse
Affiliation(s)
- Cameron L Gardner
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA.,Sir William Dunn School of Pathology, University of Oxford, Oxford, OX14RE, UK
| | - Mara Pavel-Dinu
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA
| | - Kerry Dobbs
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Marita Bosticardo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Paul K Reardon
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX14RE, UK
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource, NIAID, NIH, Bethesda, MD, USA.,Advanced Biomedical Computational Science (ABCS), Frederick National Laboratory for Cancer Research, Frederick, MD, USA
| | - Suk See DeRavin
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Kent Le
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Ezekiel Bello
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Francesca Pala
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Ottavia M Delmonte
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Harry Malech
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA
| | - Amelie Montel-Hagan
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Gay Crooks
- Department of Pathology and Laboratory Medicine, David Geffen School of Medicine, University of California, Los Angeles, Los Angeles, CA, USA
| | - Oreste Acuto
- Sir William Dunn School of Pathology, University of Oxford, Oxford, OX14RE, UK.
| | - Matthew H Porteus
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford School of Medicine, Stanford University, Stanford, CA, USA.
| | - Luigi D Notarangelo
- Immune Deficiency Genetics Section, Laboratory of Clinical Immunology and Microbiology, DIR, NIAID, NIH, 10 Center Drive, Bldg. 10 CRC, Room 5-3950, Bethesda, MD, 20892-1456, USA.
| |
Collapse
|
30
|
Bonafont J, Mencía A, Chacón-Solano E, Srifa W, Vaidyanathan S, Romano R, Garcia M, Hervás-Salcedo R, Ugalde L, Duarte B, Porteus MH, Del Rio M, Larcher F, Murillas R. Correction of recessive dystrophic epidermolysis bullosa by homology-directed repair-mediated genome editing. Mol Ther 2021; 29:2008-2018. [PMID: 33609734 PMCID: PMC8178438 DOI: 10.1016/j.ymthe.2021.02.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2020] [Revised: 02/09/2021] [Accepted: 02/11/2021] [Indexed: 12/15/2022] Open
Abstract
Genome-editing technologies that enable the introduction of precise changes in DNA sequences have the potential to lead to a new class of treatments for genetic diseases. Epidermolysis bullosa (EB) is a group of rare genetic disorders characterized by extreme skin fragility. The recessive dystrophic subtype of EB (RDEB), which has one of the most severe phenotypes, is caused by mutations in COL7A1. In this study, we report a gene-editing approach for ex vivo homology-directed repair (HDR)-based gene correction that uses the CRISPR-Cas9 system delivered as a ribonucleoprotein (RNP) complex in combination with donor DNA templates delivered by adeno-associated viral vectors (AAVs). We demonstrate sufficient mutation correction frequencies to achieve therapeutic benefit in primary RDEB keratinocytes containing different COL7A1 mutations as well as efficient HDR-mediated COL7A1 modification in healthy cord blood-derived CD34+ cells and mesenchymal stem cells (MSCs). These results are a proof of concept for HDR-mediated gene correction in different cell types with therapeutic potential for RDEB.
Collapse
Affiliation(s)
- Jose Bonafont
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| | - Angeles Mencía
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), 28040 Madrid, Spain
| | - Esteban Chacón-Solano
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| | - Wai Srifa
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Rosa Romano
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Marta Garcia
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain
| | - Rosario Hervás-Salcedo
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - Laura Ugalde
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Division of Hematopoietic Innovative Therapies, Centro de Investigaciones Energéticas, Medioambientales y Tecnológicas (CIEMAT), Madrid, Spain
| | - Blanca Duarte
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), 28040 Madrid, Spain
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Marcela Del Rio
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), 28040 Madrid, Spain
| | - Fernando Larcher
- Department of Biomedical Engineering, Carlos III University (UC3M), Madrid, Spain; Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), 28040 Madrid, Spain.
| | - Rodolfo Murillas
- Centro de Investigación Biomédica en Red en Enfermedades Raras (CIBERER), Madrid, Spain; Fundación Instituto de Investigación Sanitaria de la Fundación Jiménez Díaz, Madrid, Spain; Epithelial Biomedicine Division, Centro de Investigaciones Energéticas Medioambientales y Tecnológicas (CIEMAT), 28040 Madrid, Spain.
| |
Collapse
|
31
|
Wilkinson AC, Dever DP, Baik R, Camarena J, Hsu I, Charlesworth CT, Morita C, Nakauchi H, Porteus MH. Cas9-AAV6 gene correction of beta-globin in autologous HSCs improves sickle cell disease erythropoiesis in mice. Nat Commun 2021; 12:686. [PMID: 33514718 PMCID: PMC7846836 DOI: 10.1038/s41467-021-20909-x] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2020] [Accepted: 12/23/2020] [Indexed: 12/12/2022] Open
Abstract
CRISPR/Cas9-mediated beta-globin (HBB) gene correction of sickle cell disease (SCD) patient-derived hematopoietic stem cells (HSCs) in combination with autologous transplantation represents a recent paradigm in gene therapy. Although several Cas9-based HBB-correction approaches have been proposed, functional correction of in vivo erythropoiesis has not been investigated previously. Here, we use a humanized globin-cluster SCD mouse model to study Cas9-AAV6-mediated HBB-correction in functional HSCs within the context of autologous transplantation. We discover that long-term multipotent HSCs can be gene corrected ex vivo and stable hemoglobin-A production can be achieved in vivo from HBB-corrected HSCs following autologous transplantation. We observe a direct correlation between increased HBB-corrected myeloid chimerism and normalized in vivo red blood cell (RBC) features, but even low levels of chimerism resulted in robust hemoglobin-A levels. Moreover, this study offers a platform for gene editing of mouse HSCs for both basic and translational research.
Collapse
Affiliation(s)
- Adam C Wilkinson
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
| | - Daniel P Dever
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ron Baik
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Joab Camarena
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Ian Hsu
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Carsten T Charlesworth
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Chika Morita
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Hiromitsu Nakauchi
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA.
- Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA.
- Division of Stem Cell Therapy, Distinguished Professor Unit, The Institute of Medical Science, The University of Tokyo, Tokyo, 108-8639, Japan.
| | - Matthew H Porteus
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Lorry I. Lokey Stem Cell Research Building, 265 Campus Drive, Stanford, CA, USA.
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
32
|
Sharma R, Dever DP, Lee CM, Azizi A, Pan Y, Camarena J, Köhnke T, Bao G, Porteus MH, Majeti R. The TRACE-Seq method tracks recombination alleles and identifies clonal reconstitution dynamics of gene targeted human hematopoietic stem cells. Nat Commun 2021; 12:472. [PMID: 33473139 PMCID: PMC7817666 DOI: 10.1038/s41467-020-20792-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 12/16/2020] [Indexed: 12/12/2022] Open
Abstract
Targeted DNA correction of disease-causing mutations in hematopoietic stem and progenitor cells (HSPCs) may enable the treatment of genetic diseases of the blood and immune system. It is now possible to correct mutations at high frequencies in HSPCs by combining CRISPR/Cas9 with homologous DNA donors. Because of the precision of gene correction, these approaches preclude clonal tracking of gene-targeted HSPCs. Here, we describe Tracking Recombination Alleles in Clonal Engraftment using sequencing (TRACE-Seq), a methodology that utilizes barcoded AAV6 donor template libraries, carrying in-frame silent mutations or semi-randomized nucleotides outside the coding region, to track the in vivo lineage contribution of gene-targeted HSPC clones. By targeting the HBB gene with an AAV6 donor template library consisting of ~20,000 possible unique exon 1 in-frame silent mutations, we track the hematopoietic reconstitution of HBB targeted myeloid-skewed, lymphoid-skewed, and balanced multi-lineage repopulating human HSPC clones in mice. We anticipate this methodology could potentially be used for HSPC clonal tracking of Cas9 RNP and AAV6-mediated gene targeting outcomes in translational and basic research settings.
Collapse
Affiliation(s)
- Rajiv Sharma
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Armon Azizi
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Yidan Pan
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - Thomas Köhnke
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA.
| | - Ravindra Majeti
- Department of Medicine, Division of Hematology, Cancer Institute, and Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
33
|
Khan TA, Revah O, Gordon A, Yoon SJ, Krawisz AK, Goold C, Sun Y, Kim CH, Tian Y, Li MY, Schaepe JM, Ikeda K, Amin ND, Sakai N, Yazawa M, Kushan L, Nishino S, Porteus MH, Rapoport JL, Bernstein JA, O'Hara R, Bearden CE, Hallmayer JF, Huguenard JR, Geschwind DH, Dolmetsch RE, Paşca SP. Neuronal defects in a human cellular model of 22q11.2 deletion syndrome. Nat Med 2020; 26:1888-1898. [PMID: 32989314 PMCID: PMC8525897 DOI: 10.1038/s41591-020-1043-9] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 07/30/2020] [Indexed: 11/09/2022]
Abstract
22q11.2 deletion syndrome (22q11DS) is a highly penetrant and common genetic cause of neuropsychiatric disease. Here we generated induced pluripotent stem cells from 15 individuals with 22q11DS and 15 control individuals and differentiated them into three-dimensional (3D) cerebral cortical organoids. Transcriptional profiling across 100 days showed high reliability of differentiation and revealed changes in neuronal excitability-related genes. Using electrophysiology and live imaging, we identified defects in spontaneous neuronal activity and calcium signaling in both organoid- and 2D-derived cortical neurons. The calcium deficit was related to resting membrane potential changes that led to abnormal inactivation of voltage-gated calcium channels. Heterozygous loss of DGCR8 recapitulated the excitability and calcium phenotypes and its overexpression rescued these defects. Moreover, the 22q11DS calcium abnormality could also be restored by application of antipsychotics. Taken together, our study illustrates how stem cell derived models can be used to uncover and rescue cellular phenotypes associated with genetic forms of neuropsychiatric disease.
Collapse
Affiliation(s)
- Themasap A Khan
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
- Program in Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA, USA
| | - Omer Revah
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Aaron Gordon
- Program in Neurogenetics, Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
| | - Se-Jin Yoon
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Anna K Krawisz
- Department of Neurobiology, Stanford University, Stanford, CA, USA
- Division of Cardiology, Department of Medicine, Beth Israel Deaconess Medical Center, Boston, MA, USA
| | - Carleton Goold
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Yishan Sun
- Department of Neurobiology, Stanford University, Stanford, CA, USA
| | - Chul Hoon Kim
- Department of Neurobiology, Stanford University, Stanford, CA, USA
- Department of Pharmacology, Yonsei University College of Medicine, Seoul, Republic of Korea
| | - Yuan Tian
- Program in Neurogenetics, Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
- Interdepartmental PhD Program in Bioinformatics, University of California Los Angeles, Los Angeles, CA, USA
| | - Min-Yin Li
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Julia M Schaepe
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Kazuya Ikeda
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Neal D Amin
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Noriaki Sakai
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Masayuki Yazawa
- Department of Neurobiology, Stanford University, Stanford, CA, USA
- Columbia Stem Cell Initiative, Department of Rehabilitation and Regenerative Medicine, Department of Molecular Pharmacology and Therapeutics, Vagelos College of Physicians and Surgeons, Columbia University, New York, NY, USA
| | - Leila Kushan
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA, USA
| | - Seiji Nishino
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | | | - Judith L Rapoport
- National Institute of Mental Health, Child Psychiatry Branch, Bethesda, MD, USA
| | | | - Ruth O'Hara
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - Carrie E Bearden
- Department of Psychiatry and Biobehavioral Sciences, University of California Los Angeles, Los Angeles, CA, USA
- Department of Psychology, University of California Los Angeles, Los Angeles, CA, USA
- Center for Neurobehavioral Genetics, Semel Institute for Neuroscience and Human Behavior, University of California Los Angeles, Los Angeles, CA, USA
| | - Joachim F Hallmayer
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA
| | - John R Huguenard
- Department of Neurology and Neurological Sciences, Stanford University, Stanford, CA, USA
| | - Daniel H Geschwind
- Program in Neurogenetics, Department of Neurology, University of California Los Angeles, Los Angeles, CA, USA
- Department of Human Genetics, David Geffen School of Medicine, University of California Los Angeles, Los Angeles, CA, USA
- Center for Autism Research and Treatment, Semel Institute, University of California Los Angeles, Los Angeles, CA, USA
- Institute of Precision Health, University of California Los Angeles, Los Angeles, CA, USA
| | | | - Sergiu P Paşca
- Department of Psychiatry and Behavioral Sciences, Stanford University, Stanford, CA, USA.
- Stanford Brain Organogenesis Program, Wu Tsai Neurosciences Institute, Stanford University, Stanford, CA, USA.
| |
Collapse
|
34
|
Long HK, Osterwalder M, Welsh IC, Hansen K, Davies JOJ, Liu YE, Koska M, Adams AT, Aho R, Arora N, Ikeda K, Williams RM, Sauka-Spengler T, Porteus MH, Mohun T, Dickel DE, Swigut T, Hughes JR, Higgs DR, Visel A, Selleri L, Wysocka J. Loss of Extreme Long-Range Enhancers in Human Neural Crest Drives a Craniofacial Disorder. Cell Stem Cell 2020; 27:765-783.e14. [PMID: 32991838 PMCID: PMC7655526 DOI: 10.1016/j.stem.2020.09.001] [Citation(s) in RCA: 72] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2020] [Revised: 06/09/2020] [Accepted: 09/02/2020] [Indexed: 01/09/2023]
Abstract
Non-coding mutations at the far end of a large gene desert surrounding the SOX9 gene result in a human craniofacial disorder called Pierre Robin sequence (PRS). Leveraging a human stem cell differentiation model, we identify two clusters of enhancers within the PRS-associated region that regulate SOX9 expression during a restricted window of facial progenitor development at distances up to 1.45 Mb. Enhancers within the 1.45 Mb cluster exhibit highly synergistic activity that is dependent on the Coordinator motif. Using mouse models, we demonstrate that PRS phenotypic specificity arises from the convergence of two mechanisms: confinement of Sox9 dosage perturbation to developing facial structures through context-specific enhancer activity and heightened sensitivity of the lower jaw to Sox9 expression reduction. Overall, we characterize the longest-range human enhancers involved in congenital malformations, directly demonstrate that PRS is an enhanceropathy, and illustrate how small changes in gene expression can lead to morphological variation.
Collapse
Affiliation(s)
- Hannah K Long
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Marco Osterwalder
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Ian C Welsh
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Karissa Hansen
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - James O J Davies
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Yiran E Liu
- Cancer Biology Program, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Mervenaz Koska
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alexander T Adams
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Biology, Stanford University, Stanford, CA 94305, USA
| | - Robert Aho
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Neha Arora
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Kazuya Ikeda
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Ruth M Williams
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Tatjana Sauka-Spengler
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Tim Mohun
- The Francis Crick Institute, Mill Hill Laboratory, The Ridgeway, Mill Hill, London NW7 1AA, UK
| | - Diane E Dickel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
| | - Tomek Swigut
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Jim R Hughes
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Douglas R Higgs
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK; Laboratory of Gene Regulation, MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Axel Visel
- Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA; School of Natural Sciences, University of California, Merced, Merced, CA 95343, USA
| | - Licia Selleri
- Program in Craniofacial Biology, Department of Orofacial Sciences and Department of Anatomy, Institute of Human Genetics, Eli and Edythe Broad Center of Regeneration Medicine and Stem Cell Research, University of California, San Francisco, San Francisco, CA, USA
| | - Joanna Wysocka
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Department of Developmental Biology, Stanford University School of Medicine, Stanford, CA 94305, USA; Institute of Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA 94305, USA; Howard Hughes Medical Institute, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
35
|
Mantri S, Sheikali A, Binns C, Lyell DJ, DiGiusto DL, Porteus MH, Agarwal-Hashmi R. The Binns Program for Cord Blood Research: A novel model of cord blood banking for academic biomedical research. Placenta 2020; 103:50-52. [PMID: 33075720 DOI: 10.1016/j.placenta.2020.10.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/04/2020] [Accepted: 10/12/2020] [Indexed: 10/23/2022]
Abstract
Umbilical cord blood is an important graft source in the treatment of many genetic, hematologic, and immunologic disorders by hematopoietic stem cell transplantation. Millions of cord blood units have been collected and stored for clinical use since the inception of cord blood banking in 1989. However, the use of cord blood in biomedical research has been limited by access to viable samples. Here, we present a cost-effective, self-sustaining model for the procurement of fresh umbilical cord blood components for research purposes within hospital-affiliated academic institutions.
Collapse
Affiliation(s)
- Sruthi Mantri
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA.
| | - Adam Sheikali
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA.
| | - Corey Binns
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA.
| | - Deirdre J Lyell
- Division of Maternal-Fetal Medicine and Obstetrics, Department of Obstetrics and Gynecology, Stanford University School of Medicine, 300 Pasteur Drive, Stanford, CA 94305, USA.
| | - David L DiGiusto
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA.
| | - Matthew H Porteus
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA.
| | - Rajni Agarwal-Hashmi
- Division of Stem Cell Transplantation and Regenerative Medicine, Department of Pediatrics, Stanford University School of Medicine, 265 Campus Drive, Stanford, CA, 94305, USA.
| |
Collapse
|
36
|
Martin RM, Ikeda K, Cromer MK, Uchida N, Nishimura T, Romano R, Tong AJ, Lemgart VT, Camarena J, Pavel-Dinu M, Sindhu C, Wiebking V, Vaidyanathan S, Dever DP, Bak RO, Laustsen A, Lesch BJ, Jakobsen MR, Sebastiano V, Nakauchi H, Porteus MH. Highly Efficient and Marker-free Genome Editing of Human Pluripotent Stem Cells by CRISPR-Cas9 RNP and AAV6 Donor-Mediated Homologous Recombination. Cell Stem Cell 2020; 24:821-828.e5. [PMID: 31051134 DOI: 10.1016/j.stem.2019.04.001] [Citation(s) in RCA: 119] [Impact Index Per Article: 29.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2018] [Revised: 10/08/2018] [Accepted: 03/29/2019] [Indexed: 11/25/2022]
Abstract
Genome editing of human pluripotent stem cells (hPSCs) provides powerful opportunities for in vitro disease modeling, drug discovery, and personalized stem cell-based therapeutics. Currently, only small edits can be engineered with high frequency, while larger modifications suffer from low efficiency and a resultant need for selection markers. Here, we describe marker-free genome editing in hPSCs using Cas9 ribonucleoproteins (RNPs) in combination with AAV6-mediated DNA repair template delivery. We report highly efficient and bi-allelic integration frequencies across multiple loci and hPSC lines, achieving mono-allelic editing frequencies of up to 94% at the HBB locus. Using this method, we show robust bi-allelic correction of homozygous sickle cell mutations in a patient-derived induced PSC (iPSC) line. Thus, this strategy shows significant utility for generating hPSCs with large gene integrations and/or single-nucleotide changes at high frequency and without the need for introducing selection genes, enhancing the applicability of hPSC editing for research and translational uses.
Collapse
Affiliation(s)
- Renata M Martin
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Kazuya Ikeda
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Nobuko Uchida
- ReGen Med Division, BOCO Silicon Valley, Palo Alto, CA 94303, USA
| | | | - Rosa Romano
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Andrew J Tong
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Viktor T Lemgart
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Camille Sindhu
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Volker Wiebking
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | | | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Rasmus O Bak
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Anders Laustsen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus C, Denmark; Aarhus Research Centre of Innate Immunology, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus C, Denmark
| | - Benjamin J Lesch
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Martin R Jakobsen
- Department of Biomedicine, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus C, Denmark; Aarhus Research Centre of Innate Immunology, Aarhus University, Wilhelm Meyers Alle 4, 8000 Aarhus C, Denmark
| | - Vittorio Sebastiano
- Department of Obstetrics & Gynecology, Stanford University, Stanford, CA 94305, USA
| | | | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
37
|
Wilkes MC, Siva K, Chen J, Varetti G, Youn MY, Chae H, Ek F, Olsson R, Lundbäck T, Dever DP, Nishimura T, Narla A, Glader B, Nakauchi H, Porteus MH, Repellin CE, Gazda HT, Lin S, Serrano M, Flygare J, Sakamoto KM. Diamond Blackfan anemia is mediated by hyperactive Nemo-like kinase. Nat Commun 2020; 11:3344. [PMID: 32620751 PMCID: PMC7334220 DOI: 10.1038/s41467-020-17100-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2018] [Accepted: 05/26/2020] [Indexed: 01/30/2023] Open
Abstract
Diamond Blackfan Anemia (DBA) is a congenital bone marrow failure syndrome associated with ribosomal gene mutations that lead to ribosomal insufficiency. DBA is characterized by anemia, congenital anomalies, and cancer predisposition. Treatment for DBA is associated with significant morbidity. Here, we report the identification of Nemo-like kinase (NLK) as a potential target for DBA therapy. To identify new DBA targets, we screen for small molecules that increase erythroid expansion in mouse models of DBA. This screen identified a compound that inhibits NLK. Chemical and genetic inhibition of NLK increases erythroid expansion in mouse and human progenitors, including bone marrow cells from DBA patients. In DBA models and patient samples, aberrant NLK activation is initiated at the Megakaryocyte/Erythroid Progenitor (MEP) stage of differentiation and is not observed in non-erythroid hematopoietic lineages or healthy erythroblasts. We propose that NLK mediates aberrant erythropoiesis in DBA and is a potential target for therapy. Diamond Blackfan Anemia (DBA) is a congenital bone marrow failure syndrome that is associated with anemia. Here, the authors examine the role of Nemo-like kinase (NLK) in erythroid cells in the pathogenesis of DBA and as a potential target for therapy.
Collapse
Affiliation(s)
- M C Wilkes
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - K Siva
- Department of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, 22184, Sweden
| | - J Chen
- Department of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, 22184, Sweden
| | - G Varetti
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028, Spain.,Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08028, Spain
| | - M Y Youn
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - H Chae
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - F Ek
- Chemical Biology and Therapeutics Group, Department of Medical Science, Lund University, Lund, 22184, Sweden
| | - R Olsson
- Chemical Biology and Therapeutics Group, Department of Medical Science, Lund University, Lund, 22184, Sweden
| | - T Lundbäck
- Chemical Biology Consortium Sweden (CBCS), Science for Life Laboratory, Department for Medical Biochemistry and Biophysics, Karolinska Institutet, 17177, Stockholm, Sweden
| | - D P Dever
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - T Nishimura
- Department of Genetics, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - A Narla
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - B Glader
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - H Nakauchi
- Department of Genetics, Institute for Stem Cell Biology and Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Division of Stem Cell Therapy, Center for Stem Cell Biology and Regenerative Medicine, Institute of Medical Science, University of Tokyo, Tokyo, 108-8639, Japan
| | - M H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA
| | - C E Repellin
- Biosciences Division, SRI International, Menlo Park, CA, 94025, USA
| | - H T Gazda
- Broad Institute of MIT and Harvard, Cambridge, MA, 02142, USA.,Division of Genetics and Genomics, Manton Center for Orphan Disease Research, Boston Children's Hospital, Harvard Medical School, Boston, MA, 02115, USA
| | - S Lin
- Department of Molecular, Cell and Development Biology, University of California, Los Angeles, CA, 90095, USA
| | - M Serrano
- Institute for Research in Biomedicine (IRB Barcelona), Barcelona, 08028, Spain.,Barcelona Institute of Science and Technology (BIST), Barcelona, 08028, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, 08028, Spain
| | - J Flygare
- Department of Molecular Medicine and Gene Therapy, Lund Stem Cell Center, Lund University, Lund, 22184, Sweden
| | - K M Sakamoto
- Division of Hematology/Oncology, Department of Pediatrics, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
38
|
Martin RM, Fowler JL, Cromer MK, Lesch BJ, Ponce E, Uchida N, Nishimura T, Porteus MH, Loh KM. Improving the safety of human pluripotent stem cell therapies using genome-edited orthogonal safeguards. Nat Commun 2020; 11:2713. [PMID: 32483127 PMCID: PMC7264334 DOI: 10.1038/s41467-020-16455-7] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Accepted: 04/16/2020] [Indexed: 02/06/2023] Open
Abstract
Despite their rapidly-expanding therapeutic potential, human pluripotent stem cell (hPSC)-derived cell therapies continue to have serious safety risks. Transplantation of hPSC-derived cell populations into preclinical models has generated teratomas (tumors arising from undifferentiated hPSCs), unwanted tissues, and other types of adverse events. Mitigating these risks is important to increase the safety of such therapies. Here we use genome editing to engineer a general platform to improve the safety of future hPSC-derived cell transplantation therapies. Specifically, we develop hPSC lines bearing two drug-inducible safeguards, which have distinct functionalities and address separate safety concerns. In vitro administration of one small molecule depletes undifferentiated hPSCs >106-fold, thus preventing teratoma formation in vivo. Administration of a second small molecule kills all hPSC-derived cell-types, thus providing an option to eliminate the entire hPSC-derived cell product in vivo if adverse events arise. These orthogonal safety switches address major safety concerns with pluripotent cell-derived therapies. Human pluripotent stem cell derived therapies can have serious safety risks. Here the authors design two drug inducible genetic safeguards to deplete undifferentiated hPSCs and hPSC-derived cell types.
Collapse
Affiliation(s)
- Renata M Martin
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Jonas L Fowler
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Developmental Biology, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - M Kyle Cromer
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Benjamin J Lesch
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Ezequiel Ponce
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Nobuko Uchida
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA.,ReGen Med Division, BOCO Silicon Valley, Palo Alto, CA, 94303, USA
| | - Toshinobu Nishimura
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Matthew H Porteus
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| | - Kyle M Loh
- Institute for Stem Cell Biology & Regenerative Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA. .,Department of Developmental Biology, Stanford-UC Berkeley Siebel Stem Cell Institute, Stanford Ludwig Center for Cancer Stem Cell Research and Medicine, Stanford University School of Medicine, Stanford, CA, 94305, USA.
| |
Collapse
|
39
|
Adair JE, Enstrom MR, Haworth KG, Schefter LE, Shahbazi R, Humphrys DR, Porter S, Tam K, Porteus MH, Kiem HP. DNA Barcoding in Nonhuman Primates Reveals Important Limitations in Retrovirus Integration Site Analysis. Mol Ther Methods Clin Dev 2020; 17:796-809. [PMID: 32355868 PMCID: PMC7184234 DOI: 10.1016/j.omtm.2020.03.021] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Accepted: 03/24/2020] [Indexed: 12/25/2022]
Abstract
In vivo tracking of retrovirus-tagged blood stem and progenitor cells is used to study hematopoiesis. Two techniques are used most frequently: sequencing the locus of retrovirus insertion, termed integration site analysis, or retrovirus DNA barcode sequencing. Of these, integration site analysis is currently the only available technique for monitoring clonal pools in patients treated with retrovirus-modified blood cells. A key question is how these two techniques compare in their ability to detect and quantify clonal contributions. In this study, we assessed both methods simultaneously in a clinically relevant nonhuman primate model of autologous, myeloablative transplantation. Our data demonstrate that both methods track abundant clones; however, DNA barcode sequencing is at least 5-fold more efficient than integration site analysis. Using computational simulation to identify the sources of low efficiency, we identify sampling depth as the major factor. We show that the sampling required for integration site analysis to achieve minimal coverage of the true clonal pool is likely prohibitive, especially in cases of low gene-modified cell engraftment. We also show that early subsampling of different blood cell lineages adds value to clone tracking information in terms of safety and hematopoietic biology. Our analysis demonstrates DNA barcode sequencing as a useful guide to maximize integration site analysis interpretation in gene therapy patients.
Collapse
Affiliation(s)
- Jennifer E Adair
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,School of Medicine, University of Washington, Seattle, WA 98195, USA
| | - Mark R Enstrom
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Kevin G Haworth
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Lauren E Schefter
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Reza Shahbazi
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Daniel R Humphrys
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA
| | - Shaina Porter
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Kenric Tam
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.,Institute of Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA 94305, USA
| | - Hans-Peter Kiem
- Clinical Research Division, Fred Hutchinson Cancer Research Center, Seattle, WA 98109, USA.,School of Medicine, University of Washington, Seattle, WA 98195, USA
| |
Collapse
|
40
|
Vaidyanathan S, Salahudeen AA, Sellers ZM, Bravo DT, Choi SS, Batish A, Le W, Baik R, de la O S, Kaushik MP, Galper N, Lee CM, Teran CA, Yoo JH, Bao G, Chang EH, Patel ZM, Hwang PH, Wine JJ, Milla CE, Desai TJ, Nayak JV, Kuo CJ, Porteus MH. High-Efficiency, Selection-free Gene Repair in Airway Stem Cells from Cystic Fibrosis Patients Rescues CFTR Function in Differentiated Epithelia. Cell Stem Cell 2020; 26:161-171.e4. [PMID: 31839569 PMCID: PMC10908575 DOI: 10.1016/j.stem.2019.11.002] [Citation(s) in RCA: 73] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Revised: 07/29/2019] [Accepted: 11/11/2019] [Indexed: 12/19/2022]
Abstract
Cystic fibrosis (CF) is a monogenic disorder caused by mutations in the Cystic Fibrosis Transmembrane Conductance Regulator (CFTR) gene. Mortality in CF patients is mostly due to respiratory sequelae. Challenges with gene delivery have limited attempts to treat CF using in vivo gene therapy, and low correction levels have hindered ex vivo gene therapy efforts. We have used Cas9 and adeno-associated virus 6 to correct the ΔF508 mutation in readily accessible upper-airway basal stem cells (UABCs) obtained from CF patients. On average, we achieved 30%-50% allelic correction in UABCs and bronchial epithelial cells (HBECs) from 10 CF patients and observed 20%-50% CFTR function relative to non-CF controls in differentiated epithelia. Furthermore, we successfully embedded the corrected UABCs on an FDA-approved porcine small intestinal submucosal membrane (pSIS), and they retained differentiation capacity. This study supports further development of genetically corrected autologous airway stem cell transplant as a treatment for CF.
Collapse
Affiliation(s)
| | - Ameen A Salahudeen
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Zachary M Sellers
- Department of Pediatrics, Stanford University, Stanford, CA 94304, USA
| | - Dawn T Bravo
- Department of Otolaryngology-Head and Neck Surgery, Stanford, CA 94305, USA
| | - Shannon S Choi
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Arpit Batish
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Wei Le
- Department of Otolaryngology-Head and Neck Surgery, Stanford, CA 94305, USA
| | - Ron Baik
- Department of Pediatrics, Stanford University, Stanford, CA 94304, USA
| | - Sean de la O
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Milan P Kaushik
- Department of Pediatrics, Stanford University, Stanford, CA 94304, USA
| | - Noah Galper
- Department of Pediatrics, Stanford University, Stanford, CA 94304, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | | | - Jessica H Yoo
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Eugene H Chang
- Department of Otolaryngology, University of Arizona, Tucson, Tucson, AZ 85724, USA
| | - Zara M Patel
- Department of Otolaryngology-Head and Neck Surgery, Stanford, CA 94305, USA
| | - Peter H Hwang
- Department of Otolaryngology-Head and Neck Surgery, Stanford, CA 94305, USA
| | - Jeffrey J Wine
- Department of Psychology, Stanford University, Stanford, CA 94305, USA
| | - Carlos E Milla
- Department of Pediatrics, Stanford University, Stanford, CA 94304, USA
| | - Tushar J Desai
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Jayakar V Nayak
- Department of Otolaryngology-Head and Neck Surgery, Stanford, CA 94305, USA.
| | - Calvin J Kuo
- Department of Internal Medicine, Stanford University, Stanford, CA 94305, USA.
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94304, USA.
| |
Collapse
|
41
|
Esfahani MS, Lee LJ, Jeon YJ, Flynn RA, Stehr H, Hui AB, Ishisoko N, Kildebeck E, Newman AM, Bratman SV, Porteus MH, Chang HY, Alizadeh AA, Diehn M. Functional significance of U2AF1 S34F mutations in lung adenocarcinomas. Nat Commun 2019; 10:5712. [PMID: 31836708 PMCID: PMC6911043 DOI: 10.1038/s41467-019-13392-y] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 11/07/2019] [Indexed: 12/23/2022] Open
Abstract
The functional role of U2AF1 mutations in lung adenocarcinomas (LUADs) remains incompletely understood. Here, we report a significant co-occurrence of U2AF1 S34F mutations with ROS1 translocations in LUADs. To characterize this interaction, we profiled effects of S34F on the transcriptome-wide distribution of RNA binding and alternative splicing in cells harboring the ROS1 translocation. Compared to its wild-type counterpart, U2AF1 S34F preferentially binds and modulates splicing of introns containing CAG trinucleotides at their 3' splice junctions. The presence of S34F caused a shift in cross-linking at 3' splice sites, which was significantly associated with alternative splicing of skipped exons. U2AF1 S34F induced expression of genes involved in the epithelial-mesenchymal transition (EMT) and increased tumor cell invasion. Finally, S34F increased splicing of the long over the short SLC34A2-ROS1 isoform, which was also associated with enhanced invasiveness. Taken together, our results suggest a mechanistic interaction between mutant U2AF1 and ROS1 in LUAD.
Collapse
Affiliation(s)
- Mohammad S Esfahani
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Division of Oncology, Department of Medicine, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Luke J Lee
- Stanford Cancer Institute, Stanford University, Stanford, USA
| | - Young-Jun Jeon
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, USA
| | - Henning Stehr
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Pathology, Stanford University, Stanford, CA, USA
| | - Angela B Hui
- Stanford Cancer Institute, Stanford University, Stanford, USA
- Department of Radiation Oncology, Stanford University, Stanford, USA
| | - Noriko Ishisoko
- Department of Bioengineering, Stanford University, Stanford, USA
| | - Eric Kildebeck
- Department of Pediatrics, Stanford University, Stanford, USA
| | - Aaron M Newman
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA
- Department of Biomedical Data Science, Stanford University, Stanford, USA
| | - Scott V Bratman
- Department of Radiation Oncology, Stanford University, Stanford, USA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA
- Department of Radiation Oncology, University of Toronto, Toronto, CA, USA
| | | | - Howard Y Chang
- Howard Hughes Medical Institute, Stanford University, Stanford, CA, USA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, USA
| | - Ash A Alizadeh
- Stanford Cancer Institute, Stanford University, Stanford, USA.
- Division of Oncology, Department of Medicine, Stanford University, Stanford, USA.
- Division of Hematology, Department of Medicine, Stanford University, Stanford, USA.
| | - Maximilian Diehn
- Stanford Cancer Institute, Stanford University, Stanford, USA.
- Department of Radiation Oncology, Stanford University, Stanford, USA.
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, USA.
| |
Collapse
|
42
|
Pavel-Dinu M, Wiebking V, Dejene BT, Srifa W, Mantri S, Nicolas CE, Lee C, Bao G, Kildebeck EJ, Punjya N, Sindhu C, Inlay MA, Saxena N, DeRavin SS, Malech H, Roncarolo MG, Weinberg KI, Porteus MH. Author Correction: Gene correction for SCID-X1 in long-term hematopoietic stem cells. Nat Commun 2019; 10:5624. [PMID: 31796738 PMCID: PMC6890644 DOI: 10.1038/s41467-019-13620-5] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
Affiliation(s)
- Mara Pavel-Dinu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Volker Wiebking
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Beruh T Dejene
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Waracharee Srifa
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Sruthi Mantri
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Carmencita E Nicolas
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Ciaran Lee
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Eric J Kildebeck
- Center for Engineering Innovation, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Niraj Punjya
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.,University of California Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Camille Sindhu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Matthew A Inlay
- Department of Cellular and Molecular Biosciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Nivedita Saxena
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Suk See DeRavin
- Laboratory of Host Defenses, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, 20892, USA
| | - Harry Malech
- Laboratory of Host Defenses, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, 20892, USA
| | - Maria Grazia Roncarolo
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Kenneth I Weinberg
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
43
|
Dudek AM, Porteus MH. AAV6 Is Superior to Clade F AAVs in Stimulating Homologous Recombination-Based Genome Editing in Human HSPCs. Mol Ther 2019; 27:1701-1705. [PMID: 31537456 DOI: 10.1016/j.ymthe.2019.09.005] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Affiliation(s)
- Amanda M Dudek
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA.
| |
Collapse
|
44
|
Gomez-Ospina N, Scharenberg SG, Mostrel N, Bak RO, Mantri S, Quadros RM, Gurumurthy CB, Lee C, Bao G, Suarez CJ, Khan S, Sawamoto K, Tomatsu S, Raj N, Attardi LD, Aurelian L, Porteus MH. Human genome-edited hematopoietic stem cells phenotypically correct Mucopolysaccharidosis type I. Nat Commun 2019; 10:4045. [PMID: 31492863 PMCID: PMC6731271 DOI: 10.1038/s41467-019-11962-8] [Citation(s) in RCA: 77] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 08/09/2019] [Indexed: 12/26/2022] Open
Abstract
Lysosomal enzyme deficiencies comprise a large group of genetic disorders that generally lack effective treatments. A potential treatment approach is to engineer the patient’s own hematopoietic system to express high levels of the deficient enzyme, thereby correcting the biochemical defect and halting disease progression. Here, we present an efficient ex vivo genome editing approach using CRISPR-Cas9 that targets the lysosomal enzyme iduronidase to the CCR5 safe harbor locus in human CD34+ hematopoietic stem and progenitor cells. The modified cells secrete supra-endogenous enzyme levels, maintain long-term repopulation and multi-lineage differentiation potential, and can improve biochemical and phenotypic abnormalities in an immunocompromised mouse model of Mucopolysaccharidosis type I. These studies provide support for the development of genome-edited CD34+ hematopoietic stem and progenitor cells as a potential treatment for Mucopolysaccharidosis type I. The safe harbor approach constitutes a flexible platform for the expression of lysosomal enzymes making it applicable to other lysosomal storage disorders. Mucopolysaccharidosis type I (MPSI) is a lysosomal storage disease caused by insufficient iduronidase (IDUA) activity. Here, the authors use an ex vivo genome editing approach to overexpress IDUA in human hematopoietic stem and progenitor cells and show it can phenotypically correct MSPI in mouse model.
Collapse
Affiliation(s)
- Natalia Gomez-Ospina
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| | | | - Nathalie Mostrel
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rasmus O Bak
- Department of Biomedicine, Aarhus University, DK-8000, Aarhus C., Denmark.,Aarhus Institute of Advanced Studies (AIAS), Aarhus University, DK-8000, Aarhus C., Denmark
| | - Sruthi Mantri
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA
| | - Rolen M Quadros
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA
| | - Channabasavaiah B Gurumurthy
- Mouse Genome Engineering Core Facility, Vice Chancellor for Research Office, University of Nebraska Medical Center, Omaha, NE, USA.,Department of Pharmacology and Experimental Neuroscience, College of Medicine, University of Nebraska Medical Center, Omaha, NE, USA
| | - Ciaran Lee
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Carlos J Suarez
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Shaukat Khan
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Kazuki Sawamoto
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Shunji Tomatsu
- Nemours/ Alfred I. duPont Hospital for Children, Wilmington, DE, 19803, USA
| | - Nitin Raj
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laura D Attardi
- Department of Radiation Oncology, Stanford University School of Medicine, Stanford, CA, 94305, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, 94305, USA
| | - Laure Aurelian
- Stanford University School of Medicine, Stanford, CA, 94305, USA.,University of Maryland School of Medicine, Baltimore, MD, 21201, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University School of Medicine, Stanford, CA, USA.
| |
Collapse
|
45
|
Park SH, Lee CM, Dever DP, Davis TH, Camarena J, Srifa W, Zhang Y, Paikari A, Chang AK, Porteus MH, Sheehan VA, Bao G. Highly efficient editing of the β-globin gene in patient-derived hematopoietic stem and progenitor cells to treat sickle cell disease. Nucleic Acids Res 2019; 47:7955-7972. [PMID: 31147717 PMCID: PMC6735704 DOI: 10.1093/nar/gkz475] [Citation(s) in RCA: 91] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 04/14/2019] [Accepted: 05/17/2019] [Indexed: 12/14/2022] Open
Abstract
Sickle cell disease (SCD) is a monogenic disorder that affects millions worldwide. Allogeneic hematopoietic stem cell transplantation is the only available cure. Here, we demonstrate the use of CRISPR/Cas9 and a short single-stranded oligonucleotide template to correct the sickle mutation in the β-globin gene in hematopoietic stem and progenitor cells (HSPCs) from peripheral blood or bone marrow of patients with SCD, with 24.5 ± 7.6% efficiency without selection. Erythrocytes derived from gene-edited cells showed a marked reduction of sickle cells, with the level of normal hemoglobin (HbA) increased to 25.3 ± 13.9%. Gene-corrected SCD HSPCs retained the ability to engraft when transplanted into non-obese diabetic (NOD)-SCID-gamma (NSG) mice with detectable levels of gene correction 16-19 weeks post-transplantation. We show that, by using a high-fidelity SpyCas9 that maintained the same level of on-target gene modification, the off-target effects including chromosomal rearrangements were significantly reduced. Taken together, our results demonstrate efficient gene correction of the sickle mutation in both peripheral blood and bone marrow-derived SCD HSPCs, a significant reduction in sickling of red blood cells, engraftment of gene-edited SCD HSPCs in vivo and the importance of reducing off-target effects; all are essential for moving genome editing based SCD treatment into clinical practice.
Collapse
Affiliation(s)
- So Hyun Park
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ciaran M Lee
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Timothy H Davis
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Waracharee Srifa
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Yankai Zhang
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alireza Paikari
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Alicia K Chang
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Vivien A Sheehan
- Texas Children’s Hematology Center, Department of Pediatrics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| |
Collapse
|
46
|
Pavel-Dinu M, Wiebking V, Dejene BT, Srifa W, Mantri S, Nicolas CE, Lee C, Bao G, Kildebeck EJ, Punjya N, Sindhu C, Inlay MA, Saxena N, DeRavin SS, Malech H, Roncarolo MG, Weinberg KI, Porteus MH. Author Correction: Gene correction for SCID-X1 in long-term hematopoietic stem cells. Nat Commun 2019; 10:2021. [PMID: 31028274 PMCID: PMC6486578 DOI: 10.1038/s41467-019-10080-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article omitted the following from the Acknowledgements: "G.B. acknowledges the support from the Cancer Prevention and Research Institute of Texas (RR140081 and RR170721)."This has now been corrected in both the PDF and HTML versions of the Article.
Collapse
Affiliation(s)
- Mara Pavel-Dinu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Volker Wiebking
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Beruh T Dejene
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Waracharee Srifa
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Sruthi Mantri
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Carmencita E Nicolas
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Ciaran Lee
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Eric J Kildebeck
- Center for Engineering Innovation, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Niraj Punjya
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.,University of California Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Camille Sindhu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Matthew A Inlay
- Department of Cellular and Molecular Biosciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Nivedita Saxena
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Suk See DeRavin
- Laboratory of Host Defenses, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, 20892, USA
| | - Harry Malech
- Laboratory of Host Defenses, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, 20892, USA
| | - Maria Grazia Roncarolo
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Kenneth I Weinberg
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
47
|
Pavel-Dinu M, Wiebking V, Dejene BT, Srifa W, Mantri S, Nicolas CE, Lee C, Bao G, Kildebeck EJ, Punjya N, Sindhu C, Inlay MA, Saxena N, DeRavin SS, Malech H, Roncarolo MG, Weinberg KI, Porteus MH. Gene correction for SCID-X1 in long-term hematopoietic stem cells. Nat Commun 2019; 10:1634. [PMID: 30967552 PMCID: PMC6456568 DOI: 10.1038/s41467-019-09614-y] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2018] [Accepted: 03/12/2019] [Indexed: 12/28/2022] Open
Abstract
Gene correction in human long-term hematopoietic stem cells (LT-HSCs) could be an effective therapy for monogenic diseases of the blood and immune system. Here we describe an approach for X-linked sSevere cCombined iImmunodeficiency (SCID-X1) using targeted integration of a cDNA into the endogenous start codon to functionally correct disease-causing mutations throughout the gene. Using a CRISPR-Cas9/AAV6 based strategy, we achieve up to 20% targeted integration frequencies in LT-HSCs. As measures of the lack of toxicity we observe no evidence of abnormal hematopoiesis following transplantation and no evidence of off-target mutations using a high-fidelity Cas9 as a ribonucleoprotein complex. We achieve high levels of targeting frequencies (median 45%) in CD34+ HSPCs from six SCID-X1 patients and demonstrate rescue of lymphopoietic defect in a patient derived HSPC population in vitro and in vivo. In sum, our study provides specificity, toxicity and efficacy data supportive of clinical development of genome editing to treat SCID-Xl.
Collapse
Affiliation(s)
- Mara Pavel-Dinu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Volker Wiebking
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Beruh T Dejene
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Waracharee Srifa
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Sruthi Mantri
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Carmencita E Nicolas
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Ciaran Lee
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX, 77030, USA
| | - Eric J Kildebeck
- Center for Engineering Innovation, University of Texas at Dallas, Richardson, TX, 75080, USA
| | - Niraj Punjya
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
- University of California Davis, School of Medicine, Sacramento, CA, 95817, USA
| | - Camille Sindhu
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Matthew A Inlay
- Department of Cellular and Molecular Biosciences, University of California Irvine, Irvine, CA, 92697, USA
| | - Nivedita Saxena
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Suk See DeRavin
- Laboratory of Host Defenses, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, 20892, USA
| | - Harry Malech
- Laboratory of Host Defenses, National Institutes of Allergy and Infectious Diseases, National Institute of Health, Bethesda, MD, 20892, USA
| | - Maria Grazia Roncarolo
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Kenneth I Weinberg
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA
| | - Matthew H Porteus
- Department of Pediatrics, Division of Stem Cell Transplantation and Regenerative Medicine, Stanford University, Stanford, CA, 94305, USA.
| |
Collapse
|
48
|
Affiliation(s)
- Matthew H Porteus
- From the Department of Pediatrics-Stem Cell Transplantation, Stanford University, Stanford, CA
| |
Collapse
|
49
|
Charlesworth CT, Deshpande PS, Dever DP, Camarena J, Lemgart VT, Cromer MK, Vakulskas CA, Collingwood MA, Zhang L, Bode NM, Behlke MA, Dejene B, Cieniewicz B, Romano R, Lesch BJ, Gomez-Ospina N, Mantri S, Pavel-Dinu M, Weinberg KI, Porteus MH. Identification of preexisting adaptive immunity to Cas9 proteins in humans. Nat Med 2019; 25:249-254. [PMID: 30692695 PMCID: PMC7199589 DOI: 10.1038/s41591-018-0326-x] [Citation(s) in RCA: 517] [Impact Index Per Article: 103.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2018] [Accepted: 12/07/2018] [Indexed: 12/22/2022]
Abstract
The CRISPR-Cas9 system is a powerful tool for genome editing, which allows the precise modification of specific DNA sequences. Many efforts are underway to use the CRISPR-Cas9 system to therapeutically correct human genetic diseases1-6. The most widely used orthologs of Cas9 are derived from Staphylococcus aureus and Streptococcus pyogenes5,7. Given that these two bacterial species infect the human population at high frequencies8,9, we hypothesized that humans may harbor preexisting adaptive immune responses to the Cas9 orthologs derived from these bacterial species, SaCas9 (S. aureus) and SpCas9 (S. pyogenes). By probing human serum for the presence of anti-Cas9 antibodies using an enzyme-linked immunosorbent assay, we detected antibodies against both SaCas9 and SpCas9 in 78% and 58% of donors, respectively. We also found anti-SaCas9 T cells in 78% and anti-SpCas9 T cells in 67% of donors, which demonstrates a high prevalence of antigen-specific T cells against both orthologs. We confirmed that these T cells were Cas9-specific by demonstrating a Cas9-specific cytokine response following isolation, expansion, and antigen restimulation. Together, these data demonstrate that there are preexisting humoral and cell-mediated adaptive immune responses to Cas9 in humans, a finding that should be taken into account as the CRISPR-Cas9 system moves toward clinical trials.
Collapse
Affiliation(s)
| | | | - Daniel P Dever
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Joab Camarena
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Viktor T Lemgart
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - M Kyle Cromer
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | | | - Liyang Zhang
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Nicole M Bode
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Mark A Behlke
- Integrated DNA Technologies, Inc., Coralville, IA, USA
| | - Beruh Dejene
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Rosa Romano
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Benjamin J Lesch
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | - Sruthi Mantri
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | - Mara Pavel-Dinu
- Department of Pediatrics, Stanford University, Stanford, CA, USA
| | | | | |
Collapse
|
50
|
Lattanzi A, Meneghini V, Pavani G, Amor F, Ramadier S, Felix T, Antoniani C, Masson C, Alibeu O, Lee C, Porteus MH, Bao G, Amendola M, Mavilio F, Miccio A. Optimization of CRISPR/Cas9 Delivery to Human Hematopoietic Stem and Progenitor Cells for Therapeutic Genomic Rearrangements. Mol Ther 2019; 27:137-150. [PMID: 30424953 PMCID: PMC6318785 DOI: 10.1016/j.ymthe.2018.10.008] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2018] [Revised: 10/10/2018] [Accepted: 10/11/2018] [Indexed: 12/21/2022] Open
Abstract
Editing the β-globin locus in hematopoietic stem cells is an alternative therapeutic approach for gene therapy of β-thalassemia and sickle cell disease. Using the CRISPR/Cas9 system, we genetically modified human hematopoietic stem and progenitor cells (HSPCs) to mimic the large rearrangements in the β-globin locus associated with hereditary persistence of fetal hemoglobin (HPFH), a condition that mitigates the clinical phenotype of patients with β-hemoglobinopathies. We optimized and compared the efficiency of plasmid-, lentiviral vector (LV)-, RNA-, and ribonucleoprotein complex (RNP)-based methods to deliver the CRISPR/Cas9 system into HSPCs. Plasmid delivery of Cas9 and gRNA pairs targeting two HPFH-like regions led to high frequency of genomic rearrangements and HbF reactivation in erythroblasts derived from sorted, Cas9+ HSPCs but was associated with significant cell toxicity. RNA-mediated delivery of CRISPR/Cas9 was similarly toxic but much less efficient in editing the β-globin locus. Transduction of HSPCs by LVs expressing Cas9 and gRNA pairs was robust and minimally toxic but resulted in poor genome-editing efficiency. Ribonucleoprotein (RNP)-based delivery of CRISPR/Cas9 exhibited a good balance between cytotoxicity and efficiency of genomic rearrangements as compared to the other delivery systems and resulted in HbF upregulation in erythroblasts derived from unselected edited HSPCs.
Collapse
Affiliation(s)
| | - Vasco Meneghini
- Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris 75015, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France
| | | | | | - Sophie Ramadier
- Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris 75015, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France
| | - Tristan Felix
- Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris 75015, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France
| | - Chiara Antoniani
- Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris 75015, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France
| | - Cecile Masson
- Paris-Descartes Bioinformatics Platform, Imagine Institute, Paris 75015, France
| | - Olivier Alibeu
- Genomic Platform, Imagine Institute, Paris 75015, France
| | - Ciaran Lee
- Department of Bioengineering, Rice University, Houston, TX 77006, USA
| | - Matthew H Porteus
- Department of Pediatrics, Stanford University, Stanford, CA 94305, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77006, USA
| | | | - Fulvio Mavilio
- Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France; Department of Life Sciences, University of Modena and Reggio Emilia, 41125 Modena, Italy
| | - Annarita Miccio
- Genethon, INSERM UMR951, Evry 91000, France; Laboratory of Chromatin and Gene Regulation During Development, Imagine Institute, INSERM UMR1163, Paris 75015, France; Paris Descartes, Sorbonne Paris Cité University, Imagine Institute, Paris 75015, France.
| |
Collapse
|