1
|
Bijlani S, Pang KM, Bugga LV, Rangasamy S, Narayanan V, Chatterjee S. Nuclease-free precise genome editing corrects MECP2 mutations associated with Rett syndrome. Front Genome Ed 2024; 6:1346781. [PMID: 38495533 PMCID: PMC10940404 DOI: 10.3389/fgeed.2024.1346781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 02/12/2024] [Indexed: 03/19/2024] Open
Abstract
Rett syndrome is an acquired progressive neurodevelopmental disorder caused by de novo mutations in the X-linked MECP2 gene which encodes a pleiotropic protein that functions as a global transcriptional regulator and a chromatin modifier. Rett syndrome predominantly affects heterozygous females while affected male hemizygotes rarely survive. Gene therapy of Rett syndrome has proven challenging due to a requirement for stringent regulation of expression with either over- or under-expression being toxic. Ectopic expression of MECP2 in conjunction with regulatory miRNA target sequences has achieved some success, but the durability of this approach remains unknown. Here we evaluated a nuclease-free homologous recombination (HR)-based genome editing strategy to correct mutations in the MECP2 gene. The stem cell-derived AAVHSCs have previously been shown to mediate seamless and precise HR-based genome editing. We tested the ability of HR-based genome editing to correct pathogenic mutations in Exons 3 and 4 of the MECP2 gene and restore the wild type sequence while preserving all native genomic regulatory elements associated with MECP2 expression, thus potentially addressing a significant issue in gene therapy for Rett syndrome. Moreover, since the mutations are edited directly at the level of the genome, the corrections are expected to be durable with progeny cells inheriting the edited gene. The AAVHSC MECP2 editing vector was designed to be fully homologous to the target MECP2 region and to insert a promoterless Venus reporter at the end of Exon 4. Evaluation of AAVHSC editing in a panel of Rett cell lines bearing mutations in Exons 3 and 4 demonstrated successful correction and rescue of expression of the edited MECP2 gene. Sequence analysis of edited Rett cells revealed successful and accurate correction of mutations in both Exons 3 and 4 and permitted mapping of HR crossover events. Successful correction was observed only when the mutations were flanked at both the 5' and 3' ends by crossover events, but not when both crossovers occurred either exclusively upstream or downstream of the mutation. Importantly, we concluded that pathogenic mutations were successfully corrected in every Rett line analyzed, demonstrating the therapeutic potential of HR-based genome editing.
Collapse
Affiliation(s)
- Swati Bijlani
- Department of Surgery, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| | - Ka Ming Pang
- Department of Surgery, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| | - Lakshmi V. Bugga
- Department of Surgery, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| | - Sampath Rangasamy
- Center for Rare Childhood Disorders (C4RCD), Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Vinodh Narayanan
- Center for Rare Childhood Disorders (C4RCD), Neurogenomics Division, Translational Genomics Research Institute (TGen), Phoenix, AZ, United States
| | - Saswati Chatterjee
- Department of Surgery, Beckman Research Institute of the City of Hope, Duarte, CA, United States
| |
Collapse
|
2
|
Baruteau J, Brunetti-Pierri N, Gissen P. Liver-directed gene therapy for inherited metabolic diseases. J Inherit Metab Dis 2024; 47:9-21. [PMID: 38171926 DOI: 10.1002/jimd.12709] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/22/2023] [Revised: 12/18/2023] [Accepted: 12/19/2023] [Indexed: 01/05/2024]
Abstract
Gene therapy clinical trials are rapidly expanding for inherited metabolic liver diseases whilst two gene therapy products have now been approved for liver based monogenic disorders. Liver-directed gene therapy has recently become an option for treatment of haemophilias and is likely to become one of the favoured therapeutic strategies for inherited metabolic liver diseases in the near future. In this review, we present the different gene therapy vectors and strategies for liver-targeting, including gene editing. We highlight the current development of viral and nonviral gene therapy for a number of inherited metabolic liver diseases including urea cycle defects, organic acidaemias, Crigler-Najjar disease, Wilson disease, glycogen storage disease Type Ia, phenylketonuria and maple syrup urine disease. We describe the main limitations and open questions for further gene therapy development: immunogenicity, inflammatory response, genotoxicity, gene therapy administration in a fibrotic liver. The follow-up of a constantly growing number of gene therapy treated patients allows better understanding of its benefits and limitations and provides strategies to design safer and more efficacious treatments. Undoubtedly, liver-targeting gene therapy offers a promising avenue for innovative therapies with an unprecedented potential to address the unmet needs of patients suffering from inherited metabolic diseases.
Collapse
Affiliation(s)
- Julien Baruteau
- Department of Paediatric Metabolic Medicine, Great Ormond Street Hospital for Children NHS Trust, London, UK
- University College London Great Ormond Street Institute of Child Health, London, UK
- National Institute of Health Research Great Ormond Street Biomedical Research Centre, London, UK
| | - Nicola Brunetti-Pierri
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
- Department of Translational Medicine, Federico II University, Naples, Italy
- Scuola Superiore Meridionale (SSM, School of Advanced Studies), Genomics and Experimental Medicine Program, University of Naples Federico II, Naples, Italy
| | - Paul Gissen
- Department of Paediatric Metabolic Medicine, Great Ormond Street Hospital for Children NHS Trust, London, UK
- University College London Great Ormond Street Institute of Child Health, London, UK
- National Institute of Health Research Great Ormond Street Biomedical Research Centre, London, UK
| |
Collapse
|
3
|
Martinez M, Harding CO, Schwank G, Thöny B. State-of-the-art 2023 on gene therapy for phenylketonuria. J Inherit Metab Dis 2024; 47:80-92. [PMID: 37401651 PMCID: PMC10764640 DOI: 10.1002/jimd.12651] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 06/13/2023] [Accepted: 06/30/2023] [Indexed: 07/05/2023]
Abstract
Phenylketonuria (PKU) or hyperphenylalaninemia is considered a paradigm for an inherited (metabolic) liver defect and is, based on murine models that replicate all human pathology, an exemplar model for experimental studies on liver gene therapy. Variants in the PAH gene that lead to hyperphenylalaninemia are never fatal (although devastating if untreated), newborn screening has been available for two generations, and dietary treatment has been considered for a long time as therapeutic and satisfactory. However, significant shortcomings of contemporary dietary treatment of PKU remain. A long list of various gene therapeutic experimental approaches using the classical model for human PKU, the homozygous enu2/2 mouse, witnesses the value of this model to develop treatment for a genetic liver defect. The list of experiments for proof of principle includes recombinant viral (AdV, AAV, and LV) and non-viral (naked DNA or LNP-mRNA) vector delivery methods, combined with gene addition, genome, gene or base editing, and gene insertion or replacement. In addition, a list of current and planned clinical trials for PKU gene therapy is included. This review summarizes, compares, and evaluates the various approaches for the sake of scientific understanding and efficacy testing that may eventually pave the way for safe and efficient human application.
Collapse
Affiliation(s)
- Michael Martinez
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Cary O. Harding
- Department of Molecular and Medical Genetics, Oregon Health & Science University, Portland, OR, USA
| | - Gerald Schwank
- Institute of Pharmacology and Toxicology, University of Zurich, Zurich, Switzerland
| | - Beat Thöny
- Division of Metabolism, University Children’s Hospital Zurich and Children’s Research Centre, Zurich, Switzerland
| |
Collapse
|
4
|
Duff C, Alexander IE, Baruteau J. Gene therapy for urea cycle defects: An update from historical perspectives to future prospects. J Inherit Metab Dis 2024; 47:50-62. [PMID: 37026568 PMCID: PMC10953416 DOI: 10.1002/jimd.12609] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/19/2023] [Revised: 03/31/2023] [Accepted: 04/04/2023] [Indexed: 04/08/2023]
Abstract
Urea cycle defects (UCDs) are severe inherited metabolic diseases with high unmet needs which present a permanent risk of hyperammonaemic decompensation and subsequent acute death or neurological sequelae, when treated with conventional dietetic and medical therapies. Liver transplantation is currently the only curative option, but has the potential to be supplanted by highly effective gene therapy interventions without the attendant need for life-long immunosuppression or limitations imposed by donor liver supply. Over the last three decades, pioneering genetic technologies have been explored to circumvent the consequences of UCDs, improve quality of life and long-term outcomes: adenoviral vectors, adeno-associated viral vectors, gene editing, genome integration and non-viral technology with messenger RNA. In this review, we present a summarised view of this historical path, which includes some seminal milestones of the gene therapy's epic. We provide an update about the state of the art of gene therapy technologies for UCDs and the current advantages and pitfalls driving future directions for research and development.
Collapse
Affiliation(s)
- Claire Duff
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
| | - Ian E. Alexander
- Gene Therapy Research Unit, Children's Medical Research Institute, Faculty of Medicine and HealthThe University of Sydney and Sydney Children's Hospitals NetworkWestmeadNew South WalesAustralia
- Discipline of Child and Adolescent HealthThe University of SydneyWestmeadNew South WalesAustralia
| | - Julien Baruteau
- Genetics and Genomic Medicine Department, Great Ormond Street Institute of Child HealthUniversity College LondonLondonUK
- National Institute of Health Research Great Ormond Street Biomedical Research CentreLondonUK
- Metabolic Medicine DepartmentGreat Ormond Street Hospital for Children NHS Foundation TrustLondonUK
| |
Collapse
|
5
|
Chandler RJ, Venditti CP. Gene therapy for organic acidemias: Lessons learned from methylmalonic and propionic acidemia. J Inherit Metab Dis 2024; 47:63-79. [PMID: 37530705 DOI: 10.1002/jimd.12665] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 07/26/2023] [Accepted: 07/31/2023] [Indexed: 08/03/2023]
Abstract
Organic acidemias (OA) are a group of rare autosomal recessive disorders of intermediary metabolism that result in a systemic elevation of organic acid. Despite optimal dietary and cofactor therapy, OA patients still suffer from potentially lethal metabolic instability and experience long-term multisystemic complications. Severely affected patients can benefit from elective liver transplantation, which restores hepatic enzymatic activity, improves metabolic stability, and provides the theoretical basis for the pursuit of gene therapy as a new treatment for patients. Because of the poor outcomes reported in those with OA, especially methylmalonic and propionic acidemia, multiple gene therapy approaches have been explored in relevant animal models. Here, we review the results of gene therapy experiments performed using MMA and PA mouse models to illustrate experimental paradigms that could be applicable for all forms of OA.
Collapse
Affiliation(s)
- Randy J Chandler
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Charles P Venditti
- National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
6
|
Padula A, Spinelli M, Nusco E, Bujanda Cundin X, Capolongo F, Campione S, Perna C, Bastille A, Ericson M, Wang CC, Zhang S, Amoresano A, Nacht M, Piccolo P. Genome editing without nucleases confers proliferative advantage to edited hepatocytes and corrects Wilson disease. JCI Insight 2023; 8:e171281. [PMID: 37707949 PMCID: PMC10721260 DOI: 10.1172/jci.insight.171281] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Accepted: 09/12/2023] [Indexed: 09/16/2023] Open
Abstract
Application of classic liver-directed gene replacement strategies is limited in genetic diseases characterized by liver injury due to hepatocyte proliferation, resulting in decline of therapeutic transgene expression and potential genotoxic risk. Wilson disease (WD) is a life-threatening autosomal disorder of copper homeostasis caused by pathogenic variants in copper transporter ATP7B and characterized by toxic copper accumulation, resulting in severe liver and brain diseases. Genome editing holds promise for the treatment of WD; nevertheless, to rescue copper homeostasis, ATP7B function must be restored in at least 25% of the hepatocytes, which surpasses by far genome-editing correction rates. We applied a liver-directed, nuclease-free genome editing approach, based on adeno-associated viral vector-mediated (AAV-mediated) targeted integration of a promoterless mini-ATP7B cDNA into the albumin (Alb) locus. Administration of AAV-Alb-mini-ATP7B in 2 WD mouse models resulted in extensive liver repopulation by genome-edited hepatocytes holding a proliferative advantage over nonedited ones, and ameliorated liver injury and copper metabolism. Furthermore, combination of genome editing with a copper chelator, currently used for WD treatment, achieved greater disease improvement compared with chelation therapy alone. Nuclease-free genome editing provided therapeutic efficacy and may represent a safer and longer-lasting alternative to classic gene replacement strategies for WD.
Collapse
Affiliation(s)
- Agnese Padula
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Michele Spinelli
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Edoardo Nusco
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | | | | | | | - Claudia Perna
- Telethon Institute of Genetics and Medicine, Pozzuoli, Italy
| | - Amy Bastille
- LogicBio Therapeutics, Lexington, Massachusetts, USA
| | - Megan Ericson
- LogicBio Therapeutics, Lexington, Massachusetts, USA
| | | | | | - Angela Amoresano
- Department of Chemical Sciences, University of Naples Federico II, Naples, Italy
| | - Mariana Nacht
- LogicBio Therapeutics, Lexington, Massachusetts, USA
| | | |
Collapse
|
7
|
Vos EN, Demirbas D, Mangel M, Gozalbo MER, Levy HL, Berry GT. The treatment of biochemical genetic diseases: From substrate reduction to nucleic acid therapies. Mol Genet Metab 2023; 140:107693. [PMID: 37716025 DOI: 10.1016/j.ymgme.2023.107693] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/07/2023] [Revised: 08/29/2023] [Accepted: 08/29/2023] [Indexed: 09/18/2023]
Abstract
Newborn screening (NBS) began a revolution in the management of biochemical genetic diseases, greatly increasing the number of patients for whom dietary therapy would be beneficial in preventing complications in phenylketonuria as well as in a few similar disorders. The advent of next generation sequencing and expansion of NBS have markedly increased the number of biochemical genetic diseases as well as the number of patients identified each year. With the avalanche of new and proposed therapies, a second wave of options for the treatment of biochemical genetic disorders has emerged. These therapies range from simple substrate reduction to enzyme replacement, and now ex vivo gene therapy with autologous cell transplantation. In some instances, it may be optimal to introduce nucleic acid therapy during the prenatal period to avoid fetopathy. However, as with any new therapy, complications may occur. It is important for physicians and other caregivers, along with ethicists, to determine what new therapies might be beneficial to the patient, and which therapies have to be avoided for those individuals who have less severe problems and for which standard treatments are available. The purpose of this review is to discuss the "Standard" treatment plans that have been in place for many years and to identify the newest and upcoming therapies, to assist the physician and other healthcare workers in making the right decisions regarding the initiation of both the "Standard" and new therapies. We have utilized several diseases to illustrate the applications of these different modalities and discussed for which disorders they may be suitable. The future is bright, but optimal care of the patient, including and especially the newborn infant, requires a deep knowledge of the disease process and careful consideration of the necessary treatment plan, not just based on the different genetic defects but also with regards to different variants within a gene itself.
Collapse
Affiliation(s)
- E Naomi Vos
- Division of Genetics & Genomics, Boston Children's Hospital; and Department of Pediatrics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, United States of America; Manton Center for Orphan Disease Research, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, United States of America.
| | - Didem Demirbas
- Division of Genetics & Genomics, Boston Children's Hospital; and Department of Pediatrics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, United States of America; Manton Center for Orphan Disease Research, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, United States of America.
| | - Matthew Mangel
- Division of Genetics & Genomics, Boston Children's Hospital; and Department of Pediatrics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, United States of America.
| | - M Estela Rubio Gozalbo
- Department of Pediatrics and Clinical Genetics, Maastricht University Medical Centre+, P. Debyelaan 25, 6229 HX Maastricht, the Netherlands; GROW, Maastricht University, Minderbroedersberg 4-6, 6211 LK Maastricht, the Netherlands; MetabERN: European Reference Network for Hereditary Metabolic Disorders, Udine, Italy; UMD: United for Metabolic Diseases Member, Amsterdam, the Netherlands.
| | - Harvey L Levy
- Division of Genetics & Genomics, Boston Children's Hospital; and Department of Pediatrics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, United States of America.
| | - Gerard T Berry
- Division of Genetics & Genomics, Boston Children's Hospital; and Department of Pediatrics, Harvard Medical School, 300 Longwood Avenue, Boston, MA 02115, United States of America; Manton Center for Orphan Disease Research, Boston Children's Hospital, 300 Longwood Avenue, Boston, MA 02115, United States of America.
| |
Collapse
|
8
|
Gardin A, Ronzitti G. Current limitations of gene therapy for rare pediatric diseases: Lessons learned from clinical experience with AAV vectors. Arch Pediatr 2023; 30:8S46-8S52. [PMID: 38043983 DOI: 10.1016/s0929-693x(23)00227-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2023]
Abstract
Gene therapy using adeno-associated viral (AAV) vectors is a promising therapeutic strategy for multiple inherited diseases. Following intravenous injection, AAV vectors carrying a copy of the missing gene or the genome-editing machinery reach their target cells and deliver the genetic material. Several clinical trials are currently ongoing and significant success has already been achieved with at least six AAV gene therapy products with market approval in Europe and the United States. Nonetheless, clinical trials and preclinical studies have uncovered several limitations of AAV gene transfer, which need to be addressed in order to improve the safety and enable the treatment of the largest patient population. Limitations include the occurrence of immune-mediated toxicities, the potential loss of correction in the long run, and the development of neutralizing antibodies against AAV vectors preventing re-administration. In this review, we summarize these limitations and discuss the potential technological developments to overcome them. © 2023 Published by Elsevier Masson SAS on behalf of French Society of Pediatrics.
Collapse
Affiliation(s)
- Antoine Gardin
- Genethon, 91000 Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000 Evry, France; Hépatologie et Transplantation Hépatique Pédiatriques, Centre de référence de l'atrésie des voies biliaires et des cholestases génétiques, FSMR FILFOIE, Health Care Provider of the European Reference Network on Rare Liver Disorders (ERN RARE LIVER), Hôpital Bicêtre, AP-HP, Université Paris-Saclay, Le Kremlin-Bicêtre, France
| | - Giuseppe Ronzitti
- Genethon, 91000 Evry, France; Université Paris-Saclay, Univ Evry, Inserm, Genethon, Integrare research unit UMR_S951, 91000 Evry, France.
| |
Collapse
|
9
|
Tammam MA, Pereira F, Aly O, Sebak M, Diab YM, Mahdy A, El-Demerdash A. Investigating the hepatoprotective potentiality of marine-derived steroids as promising inhibitors of liver fibrosis. RSC Adv 2023; 13:27477-27490. [PMID: 37711373 PMCID: PMC10498675 DOI: 10.1039/d3ra04843h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 08/27/2023] [Indexed: 09/16/2023] Open
Abstract
It has been reported that organic extracts derived from soft corals belonging to the genus Sarcophyton have exhibited a wide range of therapeutic characteristics. Based on biochemical and histological techniques, we aimed to assess the hepatoprotective role of the organic extract and its principal steroidal contents derived from the Red Sea soft coral Sarcophyton glaucum on acetaminophen-induced liver fibrosis in rats. Serum liver function parameters (ALT, AST, ALP and total bilirubin) were quantified using a spectrophotometer, and both alpha-fetoprotein (AFP) and carcinoembryonic antigen (CEA) levels were determined by using enzyme-linked immunosorbent assay (ELISA) kits while transformed growth factor beta (TGF-β) and tumor necrosis factor α (TNF-α) in liver tissue homogenate were determined using ELISA, and TGF-β and TNF-α gene expression in liver tissue was determined using real-time PCR following extraction and purification. Histopathological alterations in hepatic tissue were also examined under a microscope. In order to prioritize the isolation and characterization of the most promising marine steroids from the organic extract of the Red Sea soft coral Sarcophyton glaucum as hepatoprotective agents, a computational approach was employed. This approach involved molecular docking (MDock) and analysis of the structure-activity relationship (SAR) against glutathione-S-transferase (GST) and Cu-Zn human superoxide dismutase (Cu-ZnSOD) enzymes. Although the major role in the detoxification of foreign chemicals and toxic metabolites of GST and SOD enzymes is known, there is a lack of knowledge about the mode of action of the hepatoprotective process and those of the targets involved. The present study investigated the multiple interactions of a series of marine steroids with the GST and SOD enzymes, in order to reveal insights into the process of hepatoprotection.
Collapse
Affiliation(s)
- Mohamed A Tammam
- Department of Biochemistry, Faculty of Agriculture, Fayoum University Fayoum 63514 Egypt
| | - Florbela Pereira
- LAQV REQUIMTE, Department of Chemistry, NOVA School of Science and Technology, Universidade Nova de Lisboa 2829516 Caparica Portugal
| | - Omnia Aly
- Department of Medical Biochemistry, National Research Centre Cairo 12622 Egypt
| | - Mohamed Sebak
- Microbiology and Immunology Department, Faculty of Pharmacy, Beni-Suef University Egypt
| | - Yasser M Diab
- Department of Biochemistry, Faculty of Agriculture, Fayoum University Fayoum 63514 Egypt
| | - Aldoushy Mahdy
- Department of Zoology, Faculty of Science, Al-Azhar University (Assiut Branch) Assiut 71524 Egypt
| | - Amr El-Demerdash
- Division of Organic Chemistry, Department of Chemistry, Faculty of Sciences, Mansoura University Mansoura 35516 Egypt
- Department of Biochemistry and Metabolism, the John Innes Centre Norwich Research Park Norwich NR4 7UH UK
| |
Collapse
|
10
|
Arnson B, Kang HR, Brooks ED, Gheorghiu D, Ilich E, Courtney D, Everitt JI, Cullen BR, Koeberl DD. Genome editing using Staphylococcus aureus Cas9 in a canine model of glycogen storage disease Ia. Mol Ther Methods Clin Dev 2023; 29:108-119. [PMID: 37021039 PMCID: PMC10068017 DOI: 10.1016/j.omtm.2023.03.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2022] [Accepted: 03/03/2023] [Indexed: 03/11/2023]
Abstract
Glycogen storage disease type Ia (GSD Ia) is the inherited deficiency of glucose-6-phosphatase (G6Pase), associated with life-threatening hypoglycemia and long-term complications, including hepatocellular carcinoma formation. Gene replacement therapy fails to stably reverse G6Pase deficiency. We attempted genome editing using two adeno-associated virus vectors, one that expressed Staphylococcus aureus Cas9 protein and a second containing a donor transgene encoding G6Pase, in a dog model for GSD Ia. We demonstrated donor transgene integration in the liver of three adult-treated dogs accompanied by stable G6Pase expression and correction of hypoglycemia during fasting. Two puppies with GSD Ia were treated by genome editing that achieved donor transgene integration in the liver. Integration frequency ranged from 0.5% to 1% for all dogs. In adult-treated dogs, anti-SaCas9 antibodies were detected before genome editing, reflecting prior exposure to S. aureus. Nuclease activity was low, as reflected by a low percentage of indel formation at the predicted site of SaCas9 cutting that indicated double-stranded breaks followed by non-homologous end-joining. Thus, genome editing can integrate a therapeutic transgene in the liver of a large animal model, either early or later in life, and further development is warranted to provide a more stable treatment for GSD Ia.
Collapse
Affiliation(s)
- Benjamin Arnson
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical School, Durham, NC, USA
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Hye Ri Kang
- Department of Pediatrics, UT Southwestern Medical Center, Dallas, TX, USA
| | - Elizabeth D. Brooks
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical School, Durham, NC, USA
| | - Dorothy Gheorghiu
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical School, Durham, NC, USA
| | - Ekaterina Ilich
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical School, Durham, NC, USA
| | - David Courtney
- Wellcome-Wolfson Institute for Experimental Medicine, Queen’s University Belfast, Belfast, UK
| | - Jeffrey I. Everitt
- Department of Pathology, Duke University School of Medicine, Durham, NC, USA
| | - Bryan R. Cullen
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| | - Dwight D. Koeberl
- Division of Medical Genetics, Department of Pediatrics, Duke University Medical School, Durham, NC, USA
- Department of Molecular Genetics & Microbiology, Duke University Medical Center, Durham, NC, USA
| |
Collapse
|
11
|
Peña LDM, Burrage LC, Enns GM, Esplin ED, Harding C, Mendell JR, Niu ZN, Scharfe C, Yu T, Koeberl DD. Contributions from medical geneticists in clinical trials of genetic therapies: A points to consider statement of the American College of Medical Genetics and Genomics (ACMG). Genet Med 2023; 25:100831. [PMID: 37031408 PMCID: PMC11040261 DOI: 10.1016/j.gim.2023.100831] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Accepted: 03/13/2023] [Indexed: 04/10/2023] Open
Affiliation(s)
- Loren D M Peña
- Division of Human Genetics, Cincinnati Children's Hospital Medical Center, Cincinnati, OH; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, OH
| | - Lindsay C Burrage
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX; Texas Children's Hospital, Houston, TX
| | - Gregory M Enns
- Department of Pediatrics, Stanford University, Stanford, CA
| | | | - Cary Harding
- School of Medicine, Oregon Health & Science University, Portland, OR
| | - Jerry R Mendell
- Department of Pediatrics, College of Medicine, The Ohio State University, Columbus, OH; Abigail Wexner Research Institute, Nationwide Children's Hospital, Columbus, OH
| | - Zhiyv Neal Niu
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Curt Scharfe
- Department of Genetics, Yale School of Medicine, New Haven, CT
| | - Timothy Yu
- Division of Genetics and Genomics, Boston Children's Hospital, Boston, MA; Harvard Medical School, Boston, MA
| | - Dwight D Koeberl
- Division of Medical Genetics, Department of Pediatrics, Duke University, Durham, NC
| |
Collapse
|
12
|
Calabria A, Cipriani C, Spinozzi G, Rudilosso L, Esposito S, Benedicenti F, Albertini A, Pouzolles M, Luoni M, Giannelli S, Broccoli V, Guilbaud M, Adjali O, Taylor N, Zimmermann VS, Montini E, Cesana D. Intrathymic AAV delivery results in therapeutic site-specific integration at TCR loci in mice. Blood 2023; 141:2316-2329. [PMID: 36790505 PMCID: PMC10356579 DOI: 10.1182/blood.2022017378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2022] [Revised: 12/22/2022] [Accepted: 01/21/2023] [Indexed: 02/16/2023] Open
Abstract
Adeno-associated virus (AAV) vectors have been successfully exploited in gene therapy applications for the treatment of several genetic disorders. AAV is considered an episomal vector, but it has been shown to integrate within the host cell genome after the generation of double-strand DNA breaks or nicks. Although AAV integration raises some safety concerns, it can also provide therapeutic benefit; the direct intrathymic injection of an AAV harboring a therapeutic transgene results in integration in T-cell progenitors and long-term T-cell immunity. To assess the mechanisms of AAV integration, we retrieved and analyzed hundreds of AAV integration sites from lymph node-derived mature T cells and compared these with liver and brain tissue from treated mice. Notably, we found that although AAV integrations in the liver and brain were distributed across the entire mouse genome, >90% of the integrations in T cells were clustered within the T-cell receptor α, β, and γ genes. More precisely, the insertion mapped to DNA breaks created by the enzymatic activity of recombination activating genes (RAGs) during variable, diversity, and joining recombination. Our data indicate that RAG activity during T-cell receptor maturation induces a site-specific integration of AAV genomes and opens new therapeutic avenues for achieving long-term AAV-mediated gene transfer in dividing cells.
Collapse
Affiliation(s)
- Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Carlo Cipriani
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Giulio Spinozzi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Laura Rudilosso
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Simona Esposito
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alessandra Albertini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Marie Pouzolles
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Mirko Luoni
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Serena Giannelli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Vania Broccoli
- Stem Cell and Neurogenesis Unit, Division of Neuroscience, IRCCS San Raffaele Scientific Institute, Milan, Italy
- Neuroscience Institute, National Research Council of Italy, Milan, Italy
| | - Mickael Guilbaud
- Translational Gene Therapy Laboratory, INSERM and Nantes University, Nantes, France
| | - Oumeya Adjali
- Translational Gene Therapy Laboratory, INSERM and Nantes University, Nantes, France
| | - Naomi Taylor
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique (CNRS), Paris, France
- Pediatric Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Valérie S. Zimmermann
- Institut de Génétique Moléculaire de Montpellier, Centre National de la Recherche Scientifique (CNRS), Paris, France
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Daniela Cesana
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Scientific Institute, Milan, Italy
| |
Collapse
|
13
|
Abstract
Gene therapy is poised to revolutionize modern medicine, with seemingly unlimited potential for treating and curing genetic disorders. For otherwise incurable indications, including most inherited metabolic liver disorders, gene therapy provides a realistic therapeutic option. In this Review, we discuss gene supplementation and gene editing involving the use of recombinant adeno-associated virus (rAAV) vectors for the treatment of inherited liver diseases, including updates on several ongoing clinical trials that are producing promising results. Clinical testing has been essential in highlighting many key translational challenges associated with this transformative therapy. In particular, the interaction of a patient's immune system with the vector raises issues of safety and the duration of treatment efficacy. Furthermore, several serious adverse events after the administration of high doses of rAAVs suggest greater involvement of innate immune responses and pre-existing hepatic conditions than initially anticipated. Finally, permanent modification of the host genome associated with rAAV genome integration and gene editing raises concerns about the risk of oncogenicity that require careful evaluation. We summarize the main progress, challenges and pathways forward for gene therapy for liver diseases.
Collapse
|
14
|
Hubbard BT, LaMoia TE, Goedeke L, Gaspar RC, Galsgaard KD, Kahn M, Mason GF, Shulman GI. Q-Flux: A method to assess hepatic mitochondrial succinate dehydrogenase, methylmalonyl-CoA mutase, and glutaminase fluxes in vivo. Cell Metab 2023; 35:212-226.e4. [PMID: 36516861 PMCID: PMC9887731 DOI: 10.1016/j.cmet.2022.11.011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Revised: 09/14/2022] [Accepted: 11/21/2022] [Indexed: 12/15/2022]
Abstract
The mammalian succinate dehydrogenase (SDH) complex has recently been shown as capable of operating bidirectionally. Here, we develop a method (Q-Flux) capable of measuring absolute rates of both forward (VSDH(F)) and reverse (VSDH(R)) flux through SDH in vivo while also deconvoluting the amount of glucose derived from four discreet carbon sources in the liver. In validation studies, a mitochondrial uncoupler increased net SDH flux by >100% in awake rodents but also increased SDH cycling. During hyperglucagonemia, attenuated pyruvate cycling enhances phosphoenolpyruvate carboxykinase efficiency to drive increased gluconeogenesis, which is complemented by increased glutaminase (GLS) flux, methylmalonyl-CoA mutase (MUT) flux, and glycerol conversion to glucose. During hyperinsulinemic-euglycemic clamp, both pyruvate carboxylase and GLS are suppressed, while VSDH(R) is increased. Unstimulated MUT is a minor anaplerotic reaction but is readily induced by small amounts of propionate, which elicits glucagon-like metabolic rewiring. Taken together, Q-Flux yields a comprehensive picture of hepatic mitochondrial metabolism and should be broadly useful to researchers.
Collapse
Affiliation(s)
- Brandon T Hubbard
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Traci E LaMoia
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA
| | - Leigh Goedeke
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Rafael C Gaspar
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Katrine D Galsgaard
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Mario Kahn
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA
| | - Graeme F Mason
- Department of Radiology & Biomedical Imaging, Yale School of Medicine, New Haven, CT 06510, USA; Departments of Psychiatry & Biomedical Engineering, Yale School of Medicine, New Haven, CT 06510, USA
| | - Gerald I Shulman
- Department of Internal Medicine, Yale School of Medicine, New Haven, CT 06510, USA; Department of Cellular & Molecular Physiology, Yale School of Medicine, New Haven, CT 06510, USA.
| |
Collapse
|
15
|
Chandler RJ, Di Pasquale G, Sloan JL, McCoy S, Hubbard BT, Kilts TM, Manoli I, Chiorini JA, Venditti CP. Systemic gene therapy for methylmalonic acidemia using the novel adeno-associated viral vector 44.9. Mol Ther Methods Clin Dev 2022; 27:61-72. [PMID: 36186952 PMCID: PMC9490190 DOI: 10.1016/j.omtm.2022.09.001] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 09/01/2022] [Indexed: 12/03/2022]
Abstract
Methylmalonic acidemia (MMA) is a severe and potentially lethal autosomal recessive inborn error of metabolism most frequently caused by mutations in the methylmalonyl-CoA mutase (MMUT) gene. Proof-of-concept adeno-associated virus (AAV) gene therapy studies using mouse models of MMA have demonstrated promise for this therapeutic approach but translation to the clinic could be limited by preexisting capsid immunity and vector potency. Here we explore the efficacy of a novel clade E capsid, 44.9, as a serotype for systemic AAV gene therapy for MMA. An anti-AAV44.9 neutralizing antibody (NAb) survey in adult volunteers (n = 19) and a large cohort of MMA patients (n = 48) revealed a seroprevalence rate of ∼26% and 13%, respectively. The efficacy of AAV44.9 gene delivery was examined in two murine models of MMA, representing neonatal lethal and juvenile phenotypes of MMA. Systemic delivery of the AAV44.9-Mmut vector prevented lethality and lowered disease-related metabolites in MMA mice. Tissue biodistribution and transgene expression studies in treated MMA mice showed that AAV44.9 was efficient at transducing the liver and heart. In summary, we establish that AAV44.9 exhibits a low prevalence of preexisting NAb in humans, is highly efficacious in the treatment of clinically severe MMA mouse models and is therefore a promising vector for clinical translation.
Collapse
Affiliation(s)
- Randy J. Chandler
- Organic Acid Research Section, Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bldg 10, Room 7N248A, Bethesda, MD 20892, USA
| | - Giovanni Di Pasquale
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Jennifer L. Sloan
- Organic Acid Research Section, Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bldg 10, Room 7N248A, Bethesda, MD 20892, USA
| | - Samantha McCoy
- Organic Acid Research Section, Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bldg 10, Room 7N248A, Bethesda, MD 20892, USA
| | - Brandon T. Hubbard
- Organic Acid Research Section, Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bldg 10, Room 7N248A, Bethesda, MD 20892, USA
| | - Tina M. Kilts
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Irini Manoli
- Organic Acid Research Section, Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bldg 10, Room 7N248A, Bethesda, MD 20892, USA
| | - John A. Chiorini
- National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD 20892, USA
| | - Charles P. Venditti
- Organic Acid Research Section, Metabolic Medicine Branch, National Human Genome Research Institute, National Institutes of Health, Bldg 10, Room 7N248A, Bethesda, MD 20892, USA
| |
Collapse
|
16
|
Nahmad A, Reuveni E, Goldschmidt E, Tenne T, Liberman M, Horovitz-Fried M, Khosravi R, Kobo H, Reinstein E, Madi A, Ben-David U, Barzel A. Frequent aneuploidy in primary human T cells after CRISPR-Cas9 cleavage. Nat Biotechnol 2022; 40:1807-1813. [PMID: 35773341 PMCID: PMC7613940 DOI: 10.1038/s41587-022-01377-0] [Citation(s) in RCA: 56] [Impact Index Per Article: 28.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2021] [Accepted: 05/31/2022] [Indexed: 01/14/2023]
Abstract
Multiple clinical trials of allogeneic T cell therapy use site-specific nucleases to disrupt T cell receptor (TCR) and other genes1-6. In this study, using single-cell RNA sequencing, we investigated genome editing outcomes in primary human T cells transfected with CRISPR-Cas9 and guide RNAs targeting genes for TCR chains and programmed cell death protein 1. Four days after transfection, we found a loss of chromosome 14, harboring the TCRα locus, in up to 9% of the cells and a chromosome 14 gain in up to 1.4% of the cells. Chromosome 7, harboring the TCRβ locus, was truncated in 9.9% of the cells. Aberrations were validated using fluorescence in situ hybridization and digital droplet PCR. Aneuploidy was associated with reduced proliferation, induced p53 activation and cell death. However, at 11 days after transfection, 0.9% of T cells still had a chromosome 14 loss. Aneuploidy and chromosomal truncations are, thus, frequent outcomes of CRISPR-Cas9 cleavage that should be monitored and minimized in clinical protocols.
Collapse
Affiliation(s)
- A.D. Nahmad
- The School of Neurobiology, Biochemistry and Biophysics, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel,The Varda and Boaz Dotan Center for Advanced Therapies, Tel Aviv Sourasky Medical Center and Tel Aviv University, Tel Aviv
| | - E. Reuveni
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - E. Goldschmidt
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Israel
| | - T. Tenne
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba, Israel
| | - M. Liberman
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba, Israel
| | - M. Horovitz-Fried
- The School of Neurobiology, Biochemistry and Biophysics, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel,The Varda and Boaz Dotan Center for Advanced Therapies, Tel Aviv Sourasky Medical Center and Tel Aviv University, Tel Aviv
| | - R. Khosravi
- Single-Cell Genomics Core, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - H. Kobo
- Genomics Research Unit, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel
| | - E. Reinstein
- Medical Genetics Institute, Meir Medical Center, Kfar-Saba, Israel,Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A. Madi
- Department of Pathology, Faculty of Medicine, Tel Aviv University, Israel
| | - U. Ben-David
- Department of Human Molecular Genetics & Biochemistry, Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - A. Barzel
- The School of Neurobiology, Biochemistry and Biophysics, Faculty of Life Sciences, Tel Aviv University, Tel Aviv, Israel,The Varda and Boaz Dotan Center for Advanced Therapies, Tel Aviv Sourasky Medical Center and Tel Aviv University, Tel Aviv
| |
Collapse
|
17
|
Chen S, Guan L, Zhao X, Yang J, Chen L, Guo M, Zhao J, Chen C, Zhou Y, Han Y, Xu L. Optimized thyroid transcription factor-1 core promoter-driven microRNA-7 expression effectively inhibits the growth of human non-small-cell lung cancer cells. J Zhejiang Univ Sci B 2022; 23:915-930. [PMID: 36379611 PMCID: PMC9676096 DOI: 10.1631/jzus.b2200116] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2022] [Accepted: 07/22/2022] [Indexed: 07/22/2023]
Abstract
Targeted gene therapy has become a promising approach for lung cancer treatment. In our previous work, we reported that the targeted expression of microRNA-7 (miR-7) operated by thyroid transcription factor-1 (TTF-1) promoter inhibited the growth of human lung cancer cells in vitro and in vivo; however, the intervention efficiency needed to be further improved. In this study, we identified the core promoter of TTF-1 (from -1299 bp to -871 bp) by 5' deletion assay and screened out the putative transcription factors nuclear factor-1 (NF-1) and activator protein-1 (AP-1). Further analysis revealed that the expression level of NF-1, but not AP-1, was positively connected with the activation of TTF-1 core promoter in human non-small-cell lung cancer (NSCLC) cells. Moreover, the silencing of NF-1 could reduce the expression level of miR-7 operated by TTF-1 core promoter. Of note, we optimized four distinct sequences to form additional NF-1-binding sites (TGGCA) in the sequence of TTF-1 core promoter (termed as optTTF-1 promoter), and verified the binding efficiency of NF-1 on the optTTF-1 promoter by electrophoretic mobility shift assay (EMSA). As expected, the optTTF-1 promoter could more effectively drive miR-7 expression and inhibit the growth of human NSCLC cells in vitro, accompanied by a reduced transduction of NADH dehydrogenase (ubiquinone) 1α subcomplex 4 (NDUFA4)/protein kinase B (Akt) pathway. Consistently, optTTF-1 promoter-driven miR-7 expression could also effectively abrogate the growth and metastasis of tumor cells in a murine xenograft model of human NSCLC. Finally, no significant changes were detected in the biological indicators or the histology of some important tissues and organs, including heart, liver, and spleen. On the whole, our study revealed that the optimized TTF-1 promoter could more effectively operate miR-7 to influence the growth of human NSCLC cells, providing a new basis for the development of microRNA-based targeting gene therapy against clinical lung cancer.
Collapse
Affiliation(s)
- Shipeng Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Lian Guan
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Xu Zhao
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Jing Yang
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Longqing Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Mengmeng Guo
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Juanjuan Zhao
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Chao Chen
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China
| | - Ya Zhou
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China. ,
- Department of Medical Physics, Zunyi Medical University, Zunyi 563000, China. ,
| | - Yong Han
- Department of Physiology, Zunyi Medical University, Zunyi 563000, China. ,
| | - Lin Xu
- Special Key Laboratory of Gene Detection and Therapy & Base for Talents in Biotherapy of Guizhou Province, Zunyi 563000, China.
- Department of Immunology, Zunyi Medical University, Zunyi 563000, China.
| |
Collapse
|
18
|
Erratum. Hepatology 2022; 76:1551. [PMID: 36109864 PMCID: PMC10117586 DOI: 10.1002/hep.32763] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/08/2022]
|
19
|
Novel AAV-mediated genome editing therapy improves health and survival in a mouse model of methylmalonic acidemia. PLoS One 2022; 17:e0274774. [PMID: 36126056 PMCID: PMC9488783 DOI: 10.1371/journal.pone.0274774] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2022] [Accepted: 09/04/2022] [Indexed: 11/19/2022] Open
Abstract
Methylmalonic acidemia (MMA) is an inborn error of metabolism mostly caused by mutations in the mitochondrial methylmalonyl-CoA mutase gene (MMUT). MMA patients suffer from frequent episodes of metabolic decompensation, which can be life threatening. To mimic both the dietary restrictions and metabolic decompensation seen in MMA patients, we developed a novel protein-controlled diet regimen in a Mmut deficient mouse model of MMA and demonstrated the therapeutic benefit of mLB-001, a nuclease-free, promoterless recombinant AAV GeneRideTM vector designed to insert the mouse Mmut into the endogenous albumin locus via homologous recombination. A single intravenous administration of mLB-001 to neonatal or adult MMA mice prevented body weight loss and mortality when challenged with a high protein diet. The edited hepatocytes expressed functional MMUT protein and expanded over time in the Mmut deficient mice, suggesting a selective growth advantage over the diseased cells. In mice with a humanized liver, treatment with a human homolog of mLB-001 resulted in site-specific genome editing and transgene expression in the transplanted human hepatocytes. Taken together, these findings support the development of hLB-001 that is currently in clinical trials in pediatric patients with severe forms of MMA.
Collapse
|
20
|
Venturoni LE, Chandler RJ, Liao J, Hoffmann V, Ramesh N, Gordo S, Chau N, Venditti CP. Growth advantage of corrected hepatocytes in a juvenile model of methylmalonic acidemia following liver directed adeno-associated viral mediated nuclease-free genome editing. Mol Genet Metab 2022; 137:1-8. [PMID: 35868241 PMCID: PMC9872049 DOI: 10.1016/j.ymgme.2022.06.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/30/2022] [Accepted: 06/30/2022] [Indexed: 01/26/2023]
Abstract
Methylmalonic acidemia (MMA) is a rare and severe inherited metabolic disease typically caused by mutations of the methylmalonyl-CoA mutase (MMUT) gene. Despite medical management, patients with MMA experience frequent episodes of metabolic instability, severe morbidity, and early mortality. In several preclinical studies, systemic gene therapy has demonstrated impressive improvement in biochemical and clinical phenotypes of MMA murine models. One approach uses a promoterless adeno-associated viral (AAV) vector that relies upon homologous recombination to achieve site-specific in vivo gene addition of MMUT into the last coding exon of albumin (Alb), generating a fused Alb-MMUT transcript after successful editing. We have previously demonstrated that nuclease-free AAV mediated Alb editing could effectively treat MMA mice in the neonatal period and noted that hepatocytes had a growth advantage after correction. Here, we use a transgenic knock-out mouse model of MMA that recapitulates severe clinical and biochemical symptoms to assess the benefits of Alb editing in juvenile animals. As was first noted in the neonatal gene therapy studies, we observe that gene edited hepatocytes in the MMA mice treated as juveniles exhibit a growth advantage, which allows them to repopulate the liver slowly but dramatically by 8-10 months post treatment, and subsequently manifest a biochemical and enzymatic response. In conclusion, our results suggest that the benefit of AAV mediated nuclease-free gene editing of the Alb locus to treat MMA could potentially be therapeutic for older patients.
Collapse
Affiliation(s)
- Leah E Venturoni
- National Human Genome Research Institute, NIH, Bethesda, MD, United States of America
| | - Randy J Chandler
- National Human Genome Research Institute, NIH, Bethesda, MD, United States of America
| | - Jing Liao
- LogicBio Therapeutics, Lexington, MA, United States of America
| | - Victoria Hoffmann
- Office of Research Services, NIH, Bethesda, MD, United States of America
| | - Nikhil Ramesh
- LogicBio Therapeutics, Lexington, MA, United States of America
| | - Susana Gordo
- LogicBio Therapeutics, Lexington, MA, United States of America
| | - Nelson Chau
- LogicBio Therapeutics, Lexington, MA, United States of America
| | - Charles P Venditti
- National Human Genome Research Institute, NIH, Bethesda, MD, United States of America.
| |
Collapse
|
21
|
Venturoni LE, Venditti CP. Treatment of metabolic disorders using genomic technologies: Lessons from methylmalonic acidemia. J Inherit Metab Dis 2022; 45:872-888. [PMID: 35766386 DOI: 10.1002/jimd.12534] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Revised: 06/23/2022] [Accepted: 06/27/2022] [Indexed: 11/12/2022]
Abstract
Hereditary methylmalonic acidemia (MMA) caused by deficiency of the enzyme methylmalonyl-CoA mutase (MMUT) is a relatively common and severe organic acidemia. The recalcitrant nature of the condition to conventional dietary and medical management has led to the use of elective liver and combined liver-kidney transplantation in some patients. However, liver transplantation is intrinsically limited by organ availability, the risks of surgery, procedural and life-long management costs, transplant comorbidities, and a remaining underlying risk of complications related to MMA despite transplantation. Here, we review pre-clinical studies that present alternative approaches to solid organ transplantation as a treatment for MMUT MMA, including adeno-associated viral gene addition therapy, mRNA therapy, and genome editing, with and without nuclease enhancement.
Collapse
Affiliation(s)
- Leah E Venturoni
- Metabolic Medicine Branch, Organic Acid Research Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| | - Charles P Venditti
- Metabolic Medicine Branch, Organic Acid Research Section, National Human Genome Research Institute, National Institutes of Health, Bethesda, Maryland, USA
| |
Collapse
|
22
|
Zabaleta N, Torella L, Weber ND, Gonzalez‐Aseguinolaza G. mRNA and gene editing: Late breaking therapies in liver diseases. Hepatology 2022; 76:869-887. [PMID: 35243655 PMCID: PMC9546265 DOI: 10.1002/hep.32441] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Revised: 02/22/2022] [Accepted: 02/24/2022] [Indexed: 12/13/2022]
Abstract
The efficient delivery of RNA molecules to restore the expression of a missing or inadequately functioning protein in a target cell and the intentional specific modification of the host genome using engineered nucleases represent therapeutic concepts that are revolutionizing modern medicine. The initiation of several clinical trials using these approaches to treat metabolic liver disorders as well as the recently reported remarkable results obtained by patients with transthyretin amyloidosis highlight the advances in this field and show the potential of these therapies to treat these diseases safely and efficaciously. These advances have been possible due, firstly, to significant improvements made in RNA chemistry that increase its stability and prevent activation of the innate immune response and, secondly, to the development of very efficient liver-targeted RNA delivery systems. In parallel, the breakout of CRISPR/CRISPR-associated 9-based technology in the gene editing field has marked a turning point in in vivo modification of the cellular genome with therapeutic purposes, which can be based on gene supplementation, correction, or silencing. In the coming years we are likely to witness the therapeutic potential of these two strategies both separately and in combination. In this review we summarize the preclinical data obtained in animal models treated with mRNA as a therapeutic agent and discuss the different gene editing strategies applied to the treatment of liver diseases, highlighting both their therapeutic efficacy as well as safety concerns.
Collapse
Affiliation(s)
- Nerea Zabaleta
- Grousbeck Gene Therapy CenterSchepens Eye Research InstituteMass Eye and EarBostonMassachusettsUSA
| | - Laura Torella
- Gene Therapy and Regulation of Gene expression Program, Foundation for Applied Medical ResearchUniversity of NavarraIdisNAPamplonaSpain
| | | | - Gloria Gonzalez‐Aseguinolaza
- Gene Therapy and Regulation of Gene expression Program, Foundation for Applied Medical ResearchUniversity of NavarraIdisNAPamplonaSpain,Vivet TherapeuticsPamplonaSpain
| |
Collapse
|
23
|
Modern therapeutic approaches to liver-related disorders. J Hepatol 2022; 76:1392-1409. [PMID: 35589258 DOI: 10.1016/j.jhep.2021.12.015] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/01/2021] [Revised: 11/30/2021] [Accepted: 12/17/2021] [Indexed: 12/19/2022]
Abstract
The liver is a key production and processing site that is essential for health. Liver dysfunction can result in both systemic and liver-specific diseases. To combat these diseases, genetic approaches have been developed that have high liver tropism and are based on gene addition/editing or gene silencing. The gene addition/editing approach has yielded encouraging clinical data on the use of viral vectors in patients with haemophilia, as well as neuromuscular diseases, and has led to trials for liver-related disorders. However, the immune response and the long-term stability of exogenous expression remain important challenges. Gene editing and mRNA therapy have yielded first in-human proof-of-concept therapeutics and vaccines, but the road to the treatment of liver-related disorders remains long. Gene silencing is accomplished primarily via antisense oligonucleotides and small-interfering RNAs (siRNAs). siRNA modification with N-acetyl galactosamine results in hepatocellular-specific targeting and catapulted the liver to the centre of siRNA research. Several siRNA drugs for liver-related disorders have recently been approved, and the pipeline of drugs under investigation is crowded. Loss-of-function mutations might also be treated with enzyme substitution therapy. This review summarises current genetic approaches as well as key enzyme substitution therapies, focusing on recently approved compounds, potential adverse effects, and future challenges. Collectively, these recent advances place the liver at the forefront of precision medicine for metabolic and genetic diseases and are expected to transform the care and treatment of patients with both liver-specific and systemic diseases.
Collapse
|
24
|
Fludarabine increases nuclease-free AAV- and CRISPR/Cas9-mediated homologous recombination in mice. Nat Biotechnol 2022; 40:1285-1294. [PMID: 35393561 DOI: 10.1038/s41587-022-01240-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Accepted: 01/28/2022] [Indexed: 12/12/2022]
Abstract
Homologous recombination (HR)-based gene therapy using adeno-associated viruses (AAV-HR) without nucleases has several advantages over classic gene therapy, especially the potential for permanent transgene expression. However, the low efficiency of AAV-HR remains a major limitation. Here, we tested a series of small-molecule compounds and found that ribonucleotide reductase (RNR) inhibitors substantially enhance AAV-HR efficiency in mouse and human liver cell lines approximately threefold. Short-term administration of the RNR inhibitor fludarabine increased the in vivo efficiency of both non-nuclease- and CRISPR/Cas9-mediated AAV-HR two- to sevenfold in the murine liver, without causing overt toxicity. Fludarabine administration induced transient DNA damage signaling in both proliferating and quiescent hepatocytes. Notably, the majority of AAV-HR events occurred in non-proliferating hepatocytes in both fludarabine-treated and control mice, suggesting that the induction of transient DNA repair signaling in non-dividing hepatocytes was responsible for enhancing AAV-HR efficiency in mice. These results suggest that use of a clinically approved RNR inhibitor can potentiate AAV-HR-based genome-editing therapeutics.
Collapse
|
25
|
Bijlani S, Pang KM, Sivanandam V, Singh A, Chatterjee S. The Role of Recombinant AAV in Precise Genome Editing. Front Genome Ed 2022; 3:799722. [PMID: 35098210 PMCID: PMC8793687 DOI: 10.3389/fgeed.2021.799722] [Citation(s) in RCA: 21] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2021] [Accepted: 12/14/2021] [Indexed: 12/14/2022] Open
Abstract
The replication-defective, non-pathogenic, nearly ubiquitous single-stranded adeno-associated viruses (AAVs) have gained importance since their discovery about 50 years ago. Their unique life cycle and virus-cell interactions have led to the development of recombinant AAVs as ideal genetic medicine tools that have evolved into effective commercialized gene therapies. A distinctive property of AAVs is their ability to edit the genome precisely. In contrast to all current genome editing platforms, AAV exclusively utilizes the high-fidelity homologous recombination (HR) pathway and does not require exogenous nucleases for prior cleavage of genomic DNA. Together, this leads to a highly precise editing outcome that preserves genomic integrity without incorporation of indel mutations or viral sequences at the target site while also obviating the possibility of off-target genotoxicity. The stem cell-derived AAV (AAVHSCs) were found to mediate precise and efficient HR with high on-target accuracy and at high efficiencies. AAVHSC editing occurs efficiently in post-mitotic cells and tissues in vivo. Additionally, AAV also has the advantage of an intrinsic delivery mechanism. Thus, this distinctive genome editing platform holds tremendous promise for the correction of disease-associated mutations without adding to the mutational burden. This review will focus on the unique properties of direct AAV-mediated genome editing and their potential mechanisms of action.
Collapse
|
26
|
Schneller JL, Lee CM, Venturoni LE, Chandler RJ, Li A, Myung S, Cradick TJ, Hurley AE, Lagor WR, Bao G, Venditti CP. In vivo genome editing at the albumin locus to treat methylmalonic acidemia. Mol Ther Methods Clin Dev 2021; 23:619-632. [PMID: 34901307 PMCID: PMC8634044 DOI: 10.1016/j.omtm.2021.11.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2021] [Accepted: 11/08/2021] [Indexed: 12/13/2022]
Abstract
Methylmalonic acidemia (MMA) is a metabolic disorder most commonly caused by mutations in the methylmalonyl-CoA mutase (MMUT) gene. Although adeno-associated viral (AAV) gene therapy has been effective at correcting the disease phenotype in MMA mouse models, clinical translation may be impaired by loss of episomal transgene expression and magnified by the need to treat patients early in life. To achieve permanent correction, we developed a dual AAV strategy to express a codon-optimized MMUT transgene from Alb and tested various CRISPR-Cas9 genome-editing vectors in newly developed knockin mouse models of MMA. For one target site in intron 1 of Alb, we designed rescue cassettes expressing MMUT behind a 2A-peptide or an internal ribosomal entry site sequence. A second guide RNA targeted the initiator codon, and the donor cassette encompassed the proximal albumin promoter in the 5' homology arm. Although all editing approaches were therapeutic, targeting the start codon of albumin allowed the use of a donor cassette that also functioned as an episome and after homologous recombination, even without the expression of Cas9, as an integrant. Targeting the albumin locus using these strategies would be effective for other metabolic disorders where early treatment and permanent long-term correction are needed.
Collapse
Affiliation(s)
| | - Ciaran M. Lee
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Leah E. Venturoni
- National Human Genome Research Institute, NIH, Bethesda, 20892 MD, USA
| | - Randy J. Chandler
- National Human Genome Research Institute, NIH, Bethesda, 20892 MD, USA
| | - Ang Li
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | - Sangho Myung
- National Human Genome Research Institute, NIH, Bethesda, 20892 MD, USA
| | | | - Ayrea E. Hurley
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - William R. Lagor
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77005, USA
| | | |
Collapse
|
27
|
Luciani A, Denley MCS, Govers LP, Sorrentino V, Froese DS. Mitochondrial disease, mitophagy, and cellular distress in methylmalonic acidemia. Cell Mol Life Sci 2021; 78:6851-6867. [PMID: 34524466 PMCID: PMC8558192 DOI: 10.1007/s00018-021-03934-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 08/18/2021] [Accepted: 08/30/2021] [Indexed: 01/09/2023]
Abstract
Mitochondria—the intracellular powerhouse in which nutrients are converted into energy in the form of ATP or heat—are highly dynamic, double-membraned organelles that harness a plethora of cellular functions that sustain energy metabolism and homeostasis. Exciting new discoveries now indicate that the maintenance of this ever changing and functionally pleiotropic organelle is particularly relevant in terminally differentiated cells that are highly dependent on aerobic metabolism. Given the central role in maintaining metabolic and physiological homeostasis, dysregulation of the mitochondrial network might therefore confer a potentially devastating vulnerability to high-energy requiring cell types, contributing to a broad variety of hereditary and acquired diseases. In this Review, we highlight the biological functions of mitochondria-localized enzymes from the perspective of understanding—and potentially reversing—the pathophysiology of inherited disorders affecting the homeostasis of the mitochondrial network and cellular metabolism. Using methylmalonic acidemia as a paradigm of complex mitochondrial dysfunction, we discuss how mitochondrial directed-signaling circuitries govern the homeostasis and physiology of specialized cell types and how these may be disturbed in disease. This Review also provides a critical analysis of affected tissues, potential molecular mechanisms, and novel cellular and animal models of methylmalonic acidemia which are being used to develop new therapeutic options for this disease. These insights might ultimately lead to new therapeutics, not only for methylmalonic acidemia, but also for other currently intractable mitochondrial diseases, potentially transforming our ability to regulate homeostasis and health.
Collapse
Affiliation(s)
- Alessandro Luciani
- Mechanisms of Inherited Kidney Diseases Group, Institute of Physiology, University of Zurich, 8032, Zurich, Switzerland.
| | - Matthew C S Denley
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland
| | - Larissa P Govers
- Mechanisms of Inherited Kidney Diseases Group, Institute of Physiology, University of Zurich, 8032, Zurich, Switzerland
| | - Vincenzo Sorrentino
- Department of Musculo-Skeletal Health, Nestlé Institute of Health Sciences, Nestlé Research, 1015, Lausanne, Switzerland.
| | - D Sean Froese
- Division of Metabolism and Children's Research Center, University Children's Hospital Zurich, University of Zurich, 8032, Zurich, Switzerland.
| |
Collapse
|
28
|
Parés M, Fornaguera C, Vila-Julià F, Oh S, Fan SHY, Tam YK, Comes N, Vidal F, Martí R, Borrós S, Barquinero J. Preclinical Assessment of a Gene-Editing Approach in a Mouse Model of Mitochondrial Neurogastrointestinal Encephalomyopathy. Hum Gene Ther 2021; 32:1210-1223. [PMID: 34498979 DOI: 10.1089/hum.2021.152] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
Mitochondrial neurogastrointestinal encephalomyopathy (MNGIE) is a rare disease caused by recessive mutations in the TYMP gene, which encodes the enzyme thymidine phosphorylase (TP). In this study, the efficient integration of a TYMP transgene into introns of the Tymp and Alb loci of hepatocytes in a murine model of MNGIE was achieved by the coordinated delivery and activity of CRISPR/Cas9 and a TYMP cDNA. CRISPR/Cas9 was delivered either as mRNA using lipid nanoparticle (LNP) or polymeric nanoparticle, respectively, or in an AAV2/8 viral vector; the latter was also used to package the TYMP cDNA. Insertion of the cDNA template downstream of the Tymp and Alb promoters ensured transgene expression. The best in vivo results were obtained using LNP carrying the CRISPR/Cas9 mRNAs. Treated mice showed a consistent long-term (1 year) reduction in plasma nucleoside (thymidine and deoxyuridine) levels that correlated with the presence of TYMP mRNA and functional enzyme in liver cells. In mice with an edited Alb locus, the transgene produced a hybrid Alb-hTP protein that was secreted, with supraphysiological levels of TP activity detected in the plasma. Equivalent results were obtained in mice edited at the Tymp locus. Finally, some degree of gene editing was found in animals treated only with AAV vectors containing the DNA templates, in the absence of nucleases, although there was no impact on plasma nucleoside levels. Overall, these results demonstrate the feasibility of liver-directed genome editing in the long-term correction of MNGIE, with several advantages over other methods.
Collapse
Affiliation(s)
- Marta Parés
- Gene and Cell Therapy, Institut de Recerca Hospital Universitari Vall d'Hebron (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| | - Cristina Fornaguera
- Grup d'Enginyeria de Materials (GEMAT), Institut Químic de Sarrià (IQS), Ramon Llull University (URL), Barcelona, Spain
| | - Ferran Vila-Julià
- Research Group on Neuromuscular and Mitochondrial Diseases, Institut de Recerca Hospital Universitari Vall d'Hebron (VHIR), Universitat Autònoma de Barcelona (UAB), and Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Sejin Oh
- Grup d'Enginyeria de Materials (GEMAT), Institut Químic de Sarrià (IQS), Ramon Llull University (URL), Barcelona, Spain
| | - Steven H Y Fan
- Acuitas Therapeutics, Vancouver, British Columbia, Canada
| | - Ying K Tam
- Acuitas Therapeutics, Vancouver, British Columbia, Canada
| | | | - Francisco Vidal
- Blood and Tissue Bank, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Enfermedades Cardiovasculares (CIBERCV), Madrid, Spain
| | - Ramon Martí
- Research Group on Neuromuscular and Mitochondrial Diseases, Institut de Recerca Hospital Universitari Vall d'Hebron (VHIR), Universitat Autònoma de Barcelona (UAB), and Biomedical Network Research Centre on Rare Diseases (CIBERER), Instituto de Salud Carlos III, Barcelona, Spain
| | - Salvador Borrós
- Grup d'Enginyeria de Materials (GEMAT), Institut Químic de Sarrià (IQS), Ramon Llull University (URL), Barcelona, Spain
| | - Jordi Barquinero
- Gene and Cell Therapy, Institut de Recerca Hospital Universitari Vall d'Hebron (VHIR), Universitat Autònoma de Barcelona (UAB), Barcelona, Spain
| |
Collapse
|
29
|
Maestro S, Weber ND, Zabaleta N, Aldabe R, Gonzalez-Aseguinolaza G. Novel vectors and approaches for gene therapy in liver diseases. JHEP Rep 2021; 3:100300. [PMID: 34159305 PMCID: PMC8203845 DOI: 10.1016/j.jhepr.2021.100300] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Revised: 03/23/2021] [Accepted: 04/18/2021] [Indexed: 12/13/2022] Open
Abstract
Gene therapy is becoming an increasingly valuable tool to treat many genetic diseases with no or limited treatment options. This is the case for hundreds of monogenic metabolic disorders of hepatic origin, for which liver transplantation remains the only cure. Furthermore, the liver contains 10-15% of the body's total blood volume, making it ideal for use as a factory to secrete proteins into the circulation. In recent decades, an expanding toolbox has become available for liver-directed gene delivery. Although viral vectors have long been the preferred approach to target hepatocytes, an increasing number of non-viral vectors are emerging as highly efficient vehicles for the delivery of genetic material. Herein, we review advances in gene delivery vectors targeting the liver and more specifically hepatocytes, covering strategies based on gene addition and gene editing, as well as the exciting results obtained with the use of RNA as a therapeutic molecule. Moreover, we will briefly summarise some of the limitations of current liver-directed gene therapy approaches and potential ways of overcoming them.
Collapse
Key Words
- AAT, α1-antitrypsin
- AAV, adeno-associated virus
- AHP, acute hepatic porphyrias
- AIP, acute intermittent porphyria
- ALAS1, aminolevulic synthase 1
- APCs, antigen-presenting cells
- ASGCT, American Society of Gene and Cell Therapy
- ASGPR, asialoglycoprotein receptor
- ASOs, antisense oligonucleotides
- Ad, adenovirus
- CBS, cystathionine β-synthase
- CN, Crigel-Najjar
- CRISPR, clustered regularly interspaced short palindromic repeats
- CRISPR/Cas9, CRISPR associated protein 9
- DSBs, double-strand breaks
- ERT, enzyme replacement therapy
- FH, familial hypercholesterolemia
- FSP27, fat-specific protein 27
- GO, glycolate oxidase
- GSD1a, glycogen storage disorder 1a
- GT, gene therapy
- GUSB, β-glucuronidase
- GalNAc, N-acetyl-D-galactosamine
- HDAd, helper-dependent adenovirus
- HDR, homology-directed repair
- HT, hereditary tyrosinemia
- HemA/B, haemophilia A/B
- IDS, iduronate 2-sulfatase
- IDUA, α-L-iduronidase
- IMLD, inherited metabolic liver diseases
- ITR, inverted terminal repetition
- LDH, lactate dehydrogenase
- LDLR, low-density lipoprotein receptor
- LNP, Lipid nanoparticles
- LTR, long terminal repeat
- LV, lentivirus
- MMA, methylmalonic acidemia
- MPR, metabolic pathway reprograming
- MPS type I, MPSI
- MPS type VII, MPSVII
- MPS, mucopolysaccharidosis
- NASH, non-alcoholic steatohepatitis
- NHEJ, non-homologous end joining
- NHPs, non-human primates
- Non-viral vectors
- OLT, orthotopic liver transplantation
- OTC, ornithine transcarbamylase
- PA, propionic acidemia
- PB, piggyBac
- PCSK9, proprotein convertase subtilisin/kexin type 9
- PEG, polyethylene glycol
- PEI, polyethyleneimine
- PFIC3, progressive familial cholestasis type 3
- PH1, Primary hyperoxaluria type 1
- PKU, phenylketonuria
- RV, retrovirus
- S/MAR, scaffold matrix attachment regions
- SB, Sleeping Beauty
- SRT, substrate reduction therapy
- STK25, serine/threonine protein kinase 25
- TALEN, transcription activator-like effector nucleases
- TTR, transthyretin
- UCD, urea cycle disorders
- VLDLR, very-low-density lipoprotein receptor
- WD, Wilson’s disease
- ZFN, zinc finger nucleases
- apoB/E, apolipoprotein B/E
- dCas9, dead Cas9
- efficacy
- gene addition
- gene editing
- gene silencing
- hepatocytes
- immune response
- lncRNA, long non-coding RNA
- miRNAs, microRNAs
- siRNA, small-interfering RNA
- toxicity
- viral vectors
Collapse
Affiliation(s)
- Sheila Maestro
- Gene Therapy Area, Foundation for Applied Medical Research, University of Navarra, IdisNA, Pamplona, Spain
| | | | - Nerea Zabaleta
- Grousbeck Gene Therapy Center, Schepens Eye Research Institute, Mass Eye and Ear, Boston, MA, USA
| | - Rafael Aldabe
- Gene Therapy Area, Foundation for Applied Medical Research, University of Navarra, IdisNA, Pamplona, Spain
- Corresponding authors. Address: CIMA, Universidad de Navarra. Av. Pio XII 55 31008 Pamplona. Spain
| | - Gloria Gonzalez-Aseguinolaza
- Gene Therapy Area, Foundation for Applied Medical Research, University of Navarra, IdisNA, Pamplona, Spain
- Vivet Therapeutics, Pamplona, Spain
- Corresponding authors. Address: CIMA, Universidad de Navarra. Av. Pio XII 55 31008 Pamplona. Spain
| |
Collapse
|
30
|
Vernon HJ, Manoli I. Milestones in treatments for inborn errors of metabolism: Reflections on Where chemistry and medicine meet. Am J Med Genet A 2021; 185:3350-3358. [PMID: 34165242 DOI: 10.1002/ajmg.a.62385] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/23/2021] [Accepted: 05/25/2021] [Indexed: 12/16/2022]
Abstract
From Sir Archibald Garrod's initial description of the tetrad of albinism, alkaptonuria, cystinuria, and pentosuria to today, the field of medicine dedicated to inborn errors of metabolism has evolved from disease identification and mechanistic discovery to the development of therapies designed to subvert biochemical defects. In this review, we highlight major milestones in the treatment and diagnosis of inborn errors of metabolism, starting with dietary therapy for phenylketonuria in the 1950s and 1960s, and ending with current approaches in genetic manipulation.
Collapse
Affiliation(s)
- Hilary J Vernon
- McKusick-Nathans Department of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, Maryland, USA
| | - Irini Manoli
- Medical Genomics and Metabolic Genetics Branch, National Human Genome Research Institute, National Institutes of Health (NIH), Bethesda, Maryland, USA
| |
Collapse
|
31
|
De Giorgi M, Li A, Hurley A, Barzi M, Doerfler AM, Cherayil NA, Smith HE, Brown JD, Lin CY, Bissig KD, Bao G, Lagor WR. Targeting the Apoa1 locus for liver-directed gene therapy. Mol Ther Methods Clin Dev 2021; 21:656-669. [PMID: 34141821 PMCID: PMC8166646 DOI: 10.1016/j.omtm.2021.04.011] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 04/21/2021] [Indexed: 12/25/2022]
Abstract
Clinical application of somatic genome editing requires therapeutics that are generalizable to a broad range of patients. Targeted insertion of promoterless transgenes can ensure that edits are permanent and broadly applicable while minimizing risks of off-target integration. In the liver, the Albumin (Alb) locus is currently the only well-characterized site for promoterless transgene insertion. Here, we target the Apoa1 locus with adeno-associated viral (AAV) delivery of CRISPR-Cas9 and achieve rates of 6% to 16% of targeted hepatocytes, with no evidence of toxicity. We further show that the endogenous Apoa1 promoter can drive robust and sustained expression of therapeutic proteins, such as apolipoprotein E (APOE), dramatically reducing plasma lipids in a model of hypercholesterolemia. Finally, we demonstrate that Apoa1-targeted fumarylacetoacetate hydrolase (FAH) can correct and rescue the severe metabolic liver disease hereditary tyrosinemia type I. In summary, we identify and validate Apoa1 as a novel integration site that supports durable transgene expression in the liver for gene therapy applications.
Collapse
Affiliation(s)
- Marco De Giorgi
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Ang Li
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - Ayrea Hurley
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Mercedes Barzi
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27710, USA
| | - Alexandria M. Doerfler
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Nikitha A. Cherayil
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Harrison E. Smith
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
| | - Jonathan D. Brown
- Division of Cardiovascular Medicine, Vanderbilt University Medical Center, Nashville, TN 37232, USA
| | - Charles Y. Lin
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, TX 77030, USA
- Therapeutic Innovation Center, Department of Biochemistry and Molecular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Karl-Dimiter Bissig
- Department of Pediatrics, Division of Medical Genetics, Duke University, Durham, NC 27710, USA
| | - Gang Bao
- Department of Bioengineering, Rice University, Houston, TX 77030, USA
| | - William R. Lagor
- Department of Molecular Physiology and Biophysics, Baylor College of Medicine, Houston, TX 77030, USA
| |
Collapse
|
32
|
1- 13C-propionate breath testing as a surrogate endpoint to assess efficacy of liver-directed therapies in methylmalonic acidemia (MMA). Genet Med 2021; 23:1522-1533. [PMID: 33820958 PMCID: PMC8354855 DOI: 10.1038/s41436-021-01143-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 02/25/2021] [Accepted: 03/01/2021] [Indexed: 12/15/2022] Open
Abstract
PURPOSE To develop a safe and noninvasive in vivo assay of hepatic propionate oxidative capacity. METHODS A modified 1-13C-propionate breath test was administered to 57 methylmalonic acidemia (MMA) subjects, including 19 transplant recipients, and 16 healthy volunteers. Isotopomer enrichment (13CO2/12CO2) was measured in exhaled breath after an enteral bolus of sodium-1-13C-propionate, and normalized for CO2 production. 1-13C-propionate oxidation was then correlated with clinical, laboratory, and imaging parameters collected via a dedicated natural history protocol. RESULTS Lower propionate oxidation was observed in patients with the severe mut0 and cblB subtypes of MMA, but was near normal in those with the cblA and mut- forms of the disorder. Liver transplant recipients demonstrated complete restoration of 1-13C-propionate oxidation to control levels. 1-13C-propionate oxidation correlated with cognitive test result, growth indices, bone mineral density, renal function, and serum biomarkers. Test repeatability was robust in controls and in MMA subjects (mean coefficient of variation 6.9% and 12.8%, respectively), despite widely variable serum methylmalonic acid concentrations in the patients. CONCLUSION Propionate oxidative capacity, as measured with 1-13C-propionate breath testing, predicts disease severity and clinical outcomes, and could be used to assess the therapeutic effects of liver-targeted genomic therapies for MMA and related disorders of propionate metabolism. TRIAL REGISTRATION This clinical study is registered in www.clinicaltrials.gov with the ID: NCT00078078. Study URL: http://clinicaltrials.gov/ct2/show/NCT00078078.
Collapse
|
33
|
Genome editing in the human liver: Progress and translational considerations. PROGRESS IN MOLECULAR BIOLOGY AND TRANSLATIONAL SCIENCE 2021; 182:257-288. [PMID: 34175044 DOI: 10.1016/bs.pmbts.2021.01.030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
Abstract
Liver-targeted genome editing offers the prospect of life-long therapeutic benefit following a single treatment and is set to rapidly supplant conventional gene addition approaches. Combining progress in liver-targeted gene delivery with genome editing technology, makes this not only feasible but realistically achievable in the near term. However, important challenges remain to be addressed. These include achieving therapeutic levels of editing, particularly in vivo, avoidance of off-target effects on the genome and the potential impact of pre-existing immunity to bacteria-derived nucleases, when used to improve editing rates. In this chapter, we outline the unique features of the liver that make it an attractive target for genome editing, the impact of liver biology on therapeutic efficacy, and disease specific challenges, including whether the approach targets a cell autonomous or non-cell autonomous disease. We also discuss strategies that have been used successfully to achieve genome editing outcomes in the liver and address translational considerations as genome editing technology moves into the clinic.
Collapse
|