1
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Canarutto D, Asperti C, Vavassori V, Porcellini S, Rovelli E, Paulis M, Ferrari S, Varesi A, Fiumara M, Jacob A, Sergi Sergi L, Visigalli I, Ferrua F, González‐Granado LI, Lougaris V, Finocchi A, Villa A, Radrizzani M, Naldini L. Unbiased assessment of genome integrity and purging of adverse outcomes at the target locus upon editing of CD4 + T-cells for the treatment of Hyper IgM1. EMBO J 2023; 42:e114188. [PMID: 37916874 PMCID: PMC10690452 DOI: 10.15252/embj.2023114188] [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: 04/04/2023] [Revised: 09/15/2023] [Accepted: 09/25/2023] [Indexed: 11/03/2023] Open
Abstract
Hyper IgM1 is an X-linked combined immunodeficiency caused by CD40LG mutations, potentially treatable with CD4+ T-cell gene editing with Cas9 and a "one-size-fits-most" corrective template. Contrary to established gene therapies, there is limited data on the genomic alterations following long-range gene editing, and no consensus on the relevant assays. We developed drop-off digital PCR assays for unbiased detection of large on-target deletions and found them at high frequency upon editing. Large deletions were also common upon editing different loci and cell types and using alternative Cas9 and template delivery methods. In CD40LG edited T cells, on-target deletions were counter-selected in culture and further purged by enrichment for edited cells using a selector coupled to gene correction. We then validated the sensitivity of optical genome mapping for unbiased detection of genome wide rearrangements and uncovered on-target trapping of one or more vector copies, which do not compromise functionality, upon editing using an integrase defective lentiviral donor template. No other recurring events were detected. Edited patient cells showed faithful reconstitution of CD40LG regulated expression and function with a satisfactory safety profile. Large deletions and donor template integrations should be anticipated and accounted for when designing and testing similar gene editing strategies.
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Affiliation(s)
- Daniele Canarutto
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
- Università Vita‐Salute San RaffaeleMilanItaly
- Pediatric Immunohematology Unit and BMT ProgramIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Claudia Asperti
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Valentina Vavassori
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Simona Porcellini
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Elisabetta Rovelli
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Marianna Paulis
- Humanitas Clinical and Research Center IRCCSMilanItaly
- UOS Milan UnitIstituto di Ricerca Genetica e Biomedica (IRGB), CNRMilanItaly
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Angelica Varesi
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Martina Fiumara
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Aurelien Jacob
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Lucia Sergi Sergi
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Ilaria Visigalli
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Francesca Ferrua
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
- Pediatric Immunohematology Unit and BMT ProgramIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Luis Ignacio González‐Granado
- Unidad de Immunodeficiencias Primarias y la Unidad de Hematología y Oncología PediátricaInstituto de Investigacíon Hospital 12 de OctubreMadridSpain
| | | | - Andrea Finocchi
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesú Children's HospitalIstituto di Ricovero e Cura a Carattere ScientificoRomeItaly
| | - Anna Villa
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
- UOS Milan UnitIstituto di Ricerca Genetica e Biomedica (IRGB), CNRMilanItaly
| | - Marina Radrizzani
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene TherapyIRCCS San Raffaele Scientific InstituteMilanItaly
- Università Vita‐Salute San RaffaeleMilanItaly
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2
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Gómez-Moreno A, San Sebastian E, Moya J, Gomollón-Zueco P, Isola S, Vales Á, González-Aseguinolaza G, Unzu C, Garaigorta U. Topoisomerase Inhibitors Increase Episomal DNA Expression by Inducing the Integration of Episomal DNA in Hepatic Cells. Pharmaceutics 2023; 15:2459. [PMID: 37896219 PMCID: PMC10610421 DOI: 10.3390/pharmaceutics15102459] [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: 09/14/2023] [Revised: 10/08/2023] [Accepted: 10/12/2023] [Indexed: 10/29/2023] Open
Abstract
Gene therapy is a promising strategy to treat and cure most inherited metabolic liver disorders. Viral vectors such as those based on adeno-associated viruses (AAVs) and lentiviruses (LVs) are used as vehicles to deliver functional genes to affected hepatocytes. Adverse events associated with the use of high vector doses have motivated the use of small molecules as adjuvants to reduce the dose. In this study, we showed that a one-hour treatment with topoisomerase inhibitors (camptothecin and etoposide) prior to viral transduction is enough to increase AAV and LV reporter expression in non-dividing hepatic cells in culture. Topoisomerase inhibitors increased both integration-competent (ICLV) and integration-deficient (IDLV) LV-derived expression, with a much stronger increase in the IDLV transduction system. In agreement with that, topoisomerase inhibitors increased viral genome integration in both strains, with a greater impact on the IDLV strain, supporting the idea that topoisomerase inhibitors increased episomal DNA integration, especially when viral integrase activity is abolished. These effects correlated with an increase in the DNA damage response produced by the treatments. Our study highlights the need to monitor DNA damage and undesired integration of viral episomal DNAs into the host genome when studying chemical compounds that increase viral transduction.
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Affiliation(s)
- Andoni Gómez-Moreno
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Calle Darwin 3, 28049 Madrid, Spain; (E.S.S.); (J.M.); (P.G.-Z.)
| | - Enara San Sebastian
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Calle Darwin 3, 28049 Madrid, Spain; (E.S.S.); (J.M.); (P.G.-Z.)
| | - Jennifer Moya
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Calle Darwin 3, 28049 Madrid, Spain; (E.S.S.); (J.M.); (P.G.-Z.)
| | - Pilar Gomollón-Zueco
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Calle Darwin 3, 28049 Madrid, Spain; (E.S.S.); (J.M.); (P.G.-Z.)
| | - Sergio Isola
- DNA & RNA Medicine Division, CIMA, Universidad de Navarra, Avda Pio XII, 55, 31008 Pamplona, Spain; (S.I.); (Á.V.); (G.G.-A.); (C.U.)
| | - África Vales
- DNA & RNA Medicine Division, CIMA, Universidad de Navarra, Avda Pio XII, 55, 31008 Pamplona, Spain; (S.I.); (Á.V.); (G.G.-A.); (C.U.)
| | - Gloria González-Aseguinolaza
- DNA & RNA Medicine Division, CIMA, Universidad de Navarra, Avda Pio XII, 55, 31008 Pamplona, Spain; (S.I.); (Á.V.); (G.G.-A.); (C.U.)
| | - Carmen Unzu
- DNA & RNA Medicine Division, CIMA, Universidad de Navarra, Avda Pio XII, 55, 31008 Pamplona, Spain; (S.I.); (Á.V.); (G.G.-A.); (C.U.)
| | - Urtzi Garaigorta
- Departamento de Biología Molecular y Celular, Centro Nacional de Biotecnología-Consejo Superior de Investigaciones Científicas (CNB-CSIC), Calle Darwin 3, 28049 Madrid, Spain; (E.S.S.); (J.M.); (P.G.-Z.)
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3
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Asperti C, Canarutto D, Porcellini S, Sanvito F, Cecere F, Vavassori V, Ferrari S, Rovelli E, Albano L, Jacob A, Sergi Sergi L, Montaldo E, Ferrua F, González-Granado LI, Lougaris V, Badolato R, Finocchi A, Villa A, Radrizzani M, Naldini L. Scalable GMP-compliant gene correction of CD4+ T cells with IDLV template functionally validated in vitro and in vivo. Mol Ther Methods Clin Dev 2023; 30:546-557. [PMID: 37693944 PMCID: PMC10482894 DOI: 10.1016/j.omtm.2023.08.020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023]
Abstract
Hyper-IgM1 is a rare X-linked combined immunodeficiency caused by mutations in the CD40 ligand (CD40LG) gene with a median survival of 25 years, potentially treatable with in situ CD4+ T cell gene editing with Cas9 and a one-size-fits-most corrective donor template. Here, starting from our research-grade editing protocol, we pursued the development of a good manufacturing practice (GMP)-compliant, scalable process that allows for correction, selection and expansion of edited cells, using an integrase defective lentiviral vector as donor template. After systematic optimization of reagents and conditions we proved maintenance of stem and central memory phenotypes and expression and function of CD40LG in edited healthy donor and patient cells recapitulating the physiological CD40LG regulation. We then documented the preserved fitness of edited cells by xenotransplantation into immunodeficient mice. Finally, we transitioned to large-scale manufacturing, and developed a panel of quality control assays. Overall, our GMP-compliant process takes long-range gene editing one step closer to clinical application with a reassuring safety profile.
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Affiliation(s)
- Claudia Asperti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Daniele Canarutto
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
- Pediatric Immunohematology Unit and BMT Program, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Simona Porcellini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Francesca Sanvito
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
- Pathology Unit, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Francesca Cecere
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Valentina Vavassori
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Samuele Ferrari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Elisabetta Rovelli
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Luisa Albano
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Aurelien Jacob
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Lucia Sergi Sergi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Elisa Montaldo
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Francesca Ferrua
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
- Pediatric Immunohematology Unit and BMT Program, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Luis Ignacio González-Granado
- Primary Immunodeficiencies Unit, Department of Pediatrics, Research Institute Imas12 (i+12), Hospital 12 de Octubre, 28041 Madrid, Spain
- School of Medicine, Complutense University, 28015 Madrid, Spain
| | - Vassilios Lougaris
- Pediatrics Clinic and Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia and ASST-Spedali Civili of Brescia, 25123 Brescia, Italy
| | - Raffaele Badolato
- Pediatrics Clinic and Institute for Molecular Medicine A. Nocivelli, Department of Clinical and Experimental Sciences, University of Brescia and ASST-Spedali Civili of Brescia, 25123 Brescia, Italy
| | - Andrea Finocchi
- Academic Department of Pediatrics (DPUO), Research Unit of Clinical Immunology and Vaccinology, Bambino Gesú Children’s Hospital, Istituto di Ricovero e Cura a Carattere Scientifico, 00165 Rome, Italy
| | - Anna Villa
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
- Istituto di Ricerca Genetica e Biomedica, Consiglio Nazionale Delle Ricerche (IRGB-CNR), 20138 Unit of Milan, Italy
| | - Marina Radrizzani
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
| | - Luigi Naldini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS San Raffaele Hospital, 20132 Milan, Italy
- Vita-Salute San Raffaele University, 20132 Milan, Italy
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4
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Wolff JH, Mikkelsen JG. Delivering genes with human immunodeficiency virus-derived vehicles: still state-of-the-art after 25 years. J Biomed Sci 2022; 29:79. [PMID: 36209077 PMCID: PMC9548131 DOI: 10.1186/s12929-022-00865-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 09/29/2022] [Indexed: 11/10/2022] Open
Abstract
Viruses are naturally endowed with the capacity to transfer genetic material between cells. Following early skepticism, engineered viruses have been used to transfer genetic information into thousands of patients, and genetic therapies are currently attracting large investments. Despite challenges and severe adverse effects along the way, optimized technologies and improved manufacturing processes are driving gene therapy toward clinical translation. Fueled by the outbreak of AIDS in the 1980s and the accompanying focus on human immunodeficiency virus (HIV), lentiviral vectors derived from HIV have grown to become one of the most successful and widely used vector technologies. In 2022, this vector technology has been around for more than 25 years. Here, we celebrate the anniversary by portraying the vector system and its intriguing properties. We dive into the technology itself and recapitulate the use of lentiviral vectors for ex vivo gene transfer to hematopoietic stem cells and for production of CAR T-cells. Furthermore, we describe the adaptation of lentiviral vectors for in vivo gene delivery and cover the important contribution of lentiviral vectors to basic molecular research including their role as carriers of CRISPR genome editing technologies. Last, we dwell on the emerging capacity of lentiviral particles to package and transfer foreign proteins.
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Affiliation(s)
- Jonas Holst Wolff
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus C, Denmark
| | - Jacob Giehm Mikkelsen
- Department of Biomedicine, Aarhus University, Høegh-Guldbergs Gade 10, 8000, Aarhus C, Denmark.
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5
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Cortijo-Gutiérrez M, Sánchez-Hernández S, Tristán-Manzano M, Maldonado-Pérez N, Lopez-Onieva L, Real PJ, Herrera C, Marchal JA, Martin F, Benabdellah K. Improved Functionality of Integration-Deficient Lentiviral Vectors ( IDLVs) by the Inclusion of IS 2 Protein Docks. Pharmaceutics 2021; 13:pharmaceutics13081217. [PMID: 34452178 PMCID: PMC8401568 DOI: 10.3390/pharmaceutics13081217] [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: 07/09/2021] [Revised: 07/30/2021] [Accepted: 08/03/2021] [Indexed: 11/16/2022] Open
Abstract
Integration-deficient lentiviral vectors (IDLVs) have recently generated increasing interest, not only as a tool for transient gene delivery, but also as a technique for detecting off-target cleavage in gene-editing methodologies which rely on customized endonucleases (ENs). Despite their broad potential applications, the efficacy of IDLVs has historically been limited by low transgene expression and by the reduced sensitivity to detect low-frequency off-target events. We have previously reported that the incorporation of the chimeric sequence element IS2 into the long terminal repeat (LTR) of IDLVs increases gene expression levels, while also reducing the episome yield inside transduced cells. Our study demonstrates that the effectiveness of IDLVs relies on the balance between two parameters which can be modulated by the inclusion of IS2 sequences. In the present study, we explore new IDLV configurations harboring several elements based on IS2 modifications engineered to mediate more efficient transgene expression without affecting the targeted cell load. Of all the insulators and configurations analysed, the insertion of the IS2 into the 3′LTR produced the best results. After demonstrating a DAPI-low nuclear gene repositioning of IS2-containing episomes, we determined whether, in addition to a positive effect on transcription, the IS2 could improve the capture of IDLVs on double strand breaks (DSBs). Thus, DSBs were randomly generated, using the etoposide or locus-specific CRISPR-Cas9. Our results show that the IS2 element improved the efficacy of IDLV DSB detection. Altogether, our data indicate that the insertion of IS2 into the LTR of IDLVs improved, not only their transgene expression levels, but also their ability to be inserted into existing DSBs. This could have significant implications for the development of an unbiased detection tool for off-target cleavage sites from different specific nucleases.
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Affiliation(s)
- Marina Cortijo-Gutiérrez
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
| | - Sabina Sánchez-Hernández
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
| | - María Tristán-Manzano
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
| | - Noelia Maldonado-Pérez
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
| | - Lourdes Lopez-Onieva
- GENYO, Centre for Genomics and Oncological Research, Molecular Oncology Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (L.L.-O.); (P.J.R.)
- Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, Avenida Fuentenueva s/n, 18071 Granada, Spain
| | - Pedro J. Real
- GENYO, Centre for Genomics and Oncological Research, Molecular Oncology Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (L.L.-O.); (P.J.R.)
- Department of Biochemistry and Molecular Biology I, Faculty of Science, University of Granada, Avenida Fuentenueva s/n, 18071 Granada, Spain
- Personalized Oncology Group, Bio-Health Research Institute (ibs Granada), 18016 Granada, Spain
| | - Concha Herrera
- Maimonides Institute of Biomedical Research in Cordoba (IMIBIC), 14004 Cordoba, Spain;
- Department of Haematology, Reina Sofía University Hospital, 14004 Cordoba, Spain
| | - Juan Antonio Marchal
- Biomedical Research Institute (ibs. Granada), 18012 Granada, Spain;
- Biopathology and Regenerative Medicine Institute (IBIMER), Centre for Biomedical Research (CIBM), University of Granada, 18016 Granada, Spain
- Department of Human Anatomy and Embryology, Faculty of Medicine, University of Granada, 18016 Granada, Spain
- Excellence Research Unit: Modeling Nature (MNat), University of Granada, 18016 Granada, Spain
| | - Francisco Martin
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
| | - Karim Benabdellah
- GENYO, Centre for Genomics and Oncological Research, Genomic Medicine Department, Pfizer-University of Granada-Andalusian Regional Government, Health Sciences Technology Park, Av. de la Illustration 114, 18016 Granada, Spain; (M.C.-G.); (S.S.-H.); (M.T.-M.); (N.M.-P.); (F.M.)
- Correspondence: ; Tel.: +34-958-715-500
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6
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Abstract
Clustered regularly interspaced short palindromic repeat (CRISPR) and other gene editing technologies such as zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) show great promises for research and therapeutic applications. One major concern is the off-target effects generated by these nucleases at unintended genomic sequences. In silico methods are usually used for off-target site prediction. However, based on currently available algorithms, the predicted cleavage activity at these potential off-target sites does not always reflect the true cleavage in vivo. Here we present an unbiased screening protocol using integration-defective lentiviral vector (IDLV) and deep sequencing to map the off-target sites generated by gene editing tools.
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Affiliation(s)
- Xiaoling Wang
- Guangzhou Medical University, Guangzhou, Guangdong, China
| | - Youjun Wu
- Department of Translational Research & Cellular Therapeutics, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA
| | - Jiing-Kuan Yee
- Department of Translational Research & Cellular Therapeutics, Beckman Research Institute, City of Hope National Medical Center, Duarte, CA, USA.
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7
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Gallinaro A, Borghi M, Pirillo MF, Cecchetti S, Bona R, Canitano A, Michelini Z, Di Virgilio A, Olvera A, Brander C, Negri D, Cara A. Development and Preclinical Evaluation of an Integrase Defective Lentiviral Vector Vaccine Expressing the HIVACAT T Cell Immunogen in Mice. Mol Ther Methods Clin Dev 2020; 17:418-428. [PMID: 32154327 PMCID: PMC7056611 DOI: 10.1016/j.omtm.2020.01.013] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2020] [Accepted: 01/22/2020] [Indexed: 12/25/2022]
Abstract
Cellular immune responses play a fundamental role in controlling viral replication and AIDS progression in human immunodeficiency virus (HIV)-infected subjects and in simian immunodeficiency virus (SIV)-infected macaques. Integrase defective lentiviral vector (IDLV) represents a promising vaccine candidate, inducing functional and durable immune responses in mice and non-human primates. Here, we designed HIV- and SIV-based IDLVs to express the HIVACAT T cell immunogen (HTI), a mosaic antigen designed to cover vulnerable sites in HIV-1 Gag, Pol, Vif, and Nef. We observed that HTI expression during lentiviral vector production interfered profoundly with IDLV particles release because of sequestration of both HIV- and SIV-Gag proteins in the cytoplasm of the vector-producing cells. However, modifications in IDLV design and vector production procedures greatly improved recovery of both HIV- and SIV-based IDLV-HTI. Immunization experiments in BALB/c mice showed that both IDLVs elicited HTI-specific T cell responses. However, immunization with HIV-based IDLV elicited also a T cell response toward exogenous HIV proteins in IDLV particles, suggesting that SIV-based IDLV may be a preferable platform to assess the induction of transgene-specific immune responses against rationally designed HIV structural antigens. These data support the further evaluation of IDLV as an effective platform of T cell immunogens for the development of an effective HIV vaccine.
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Affiliation(s)
| | - Martina Borghi
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | | | - Serena Cecchetti
- Confocal Microscopy Unit NMR, Confocal Microscopy Area Core Facilities, Istituto Superiore di Sanità, Rome, Italy
| | - Roberta Bona
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Andrea Canitano
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Zuleika Michelini
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
| | - Antonio Di Virgilio
- Center for Animal Research and Welfare, Istituto Superiore di Sanità, Rome, Italy
| | - Alex Olvera
- Irsicaixa AIDS Research Institute, 08916 Badalona, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Barcelona, Spain
| | - Christian Brander
- Irsicaixa AIDS Research Institute, 08916 Badalona, Catalonia, Spain
- Universitat de Vic-Universitat Central de Catalunya (UVic-UCC), 08500 Vic, Barcelona, Spain
- ICREA, Pg. Lluís Companys 23, 08010 Barcelona, Spain
- AELIX Therapeutics, Barcelona, Spain
| | - Donatella Negri
- Department of Infectious Diseases, Istituto Superiore di Sanità, Rome, Italy
| | - Andrea Cara
- National Center for Global Health, Istituto Superiore di Sanità, Rome, Italy
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8
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Sánchez-Hernández S, Gutierrez-Guerrero A, Martín-Guerra R, Cortijo-Gutierrez M, Tristán-Manzano M, Rodriguez-Perales S, Sanchez L, Garcia-Perez JL, Chato-Astrain J, Fernandez-Valades R, Carrillo-Galvez AB, Anderson P, Montes R, Real PJ, Martin F, Benabdellah K. The IS2 Element Improves Transcription Efficiency of Integration-Deficient Lentiviral Vector Episomes. Mol Ther Nucleic Acids 2018; 13:16-28. [PMID: 30227274 PMCID: PMC6141704 DOI: 10.1016/j.omtn.2018.08.007] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 01/12/2018] [Revised: 07/02/2018] [Accepted: 08/14/2018] [Indexed: 02/06/2023]
Abstract
Integration-defective lentiviral vectors (IDLVs) have become an important alternative tool for gene therapy applications and basic research. Unfortunately, IDLVs show lower transgene expression as compared to their integrating counterparts. In this study, we aimed to improve the expression levels of IDLVs by inserting the IS2 element, which harbors SARs and HS4 sequences, into their LTRs (SE-IS2-IDLVs). Contrary to our expectations, the presence of the IS2 element did not abrogate epigenetic silencing by histone deacetylases. In addition, the IS2 element reduced episome levels in IDLV-transduced cells. Interestingly, despite these negative effects, SE-IS2-IDLVs outperformed SE-IDLVs in terms of percentage and expression levels of the transgene in several cell lines, including neurons, neuronal progenitor cells, and induced pluripotent stem cells. We estimated that the IS2 element enhances the transcriptional activity of IDLV LTR circles 6- to 7-fold. The final effect the IS2 element in IDLVs will greatly depend on the target cell and the balance between the negative versus the positive effects of the IS2 element in each cell type. The better performance of SE-IS2-IDLVs was not due to improved stability or differences in the proportions of 1-LTR versus 2-LTR circles but probably to a re-positioning of IS2-episomes into transcriptionally active regions.
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Affiliation(s)
- Sabina Sánchez-Hernández
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Alejandra Gutierrez-Guerrero
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Rocío Martín-Guerra
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Marina Cortijo-Gutierrez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - María Tristán-Manzano
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Sandra Rodriguez-Perales
- Molecular Cytogenetics and Genome Editing Unit, Human Cancer Genetics Department, CNIO, Melchor Fernandez Almagro 3, 28029 Madrid, Spain
| | - Laura Sanchez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Jose Luis Garcia-Perez
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Jesus Chato-Astrain
- Department of Histology, Tissue Engineering Group, University of Granada, Granada, Spain
| | - Ricardo Fernandez-Valades
- Pediatric Surgery Department, University Hospital "Virgen de las Nieves," Avda. Fuerzas Armadas 2, 18014 Granada, Spain
| | - Ana Belén Carrillo-Galvez
- Oncology Department, GENYO, Centre for Genomics and Oncology, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Per Anderson
- LentiStem Biotech, GENYO, Avda. de la Ilustración 114, 18016 PTS Granada, Spain; Oncology Department, GENYO, Centre for Genomics and Oncology, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Rosa Montes
- Oncology Department, GENYO, Centre for Genomics and Oncology, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain
| | - Pedro J Real
- Oncology Department, GENYO, Centre for Genomics and Oncology, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; Departament of Biochemistry and Molecular Biology I, University of Granada, Granada, Spain
| | - Francisco Martin
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; LentiStem Biotech, GENYO, Avda. de la Ilustración 114, 18016 PTS Granada, Spain.
| | - Karim Benabdellah
- Genomic Medicine Department, GENYO, Centre for Genomics and Oncological Research, Pfizer-University of Granada-Andalusian Regional Government, PTS Granada, 18016 Granada, Spain; LentiStem Biotech, GENYO, Avda. de la Ilustración 114, 18016 PTS Granada, Spain.
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Cai Y, Mikkelsen JG. Driving DNA transposition by lentiviral protein transduction. Mob Genet Elements 2014; 4:e29591. [PMID: 25057443 PMCID: PMC4092313 DOI: 10.4161/mge.29591] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2014] [Revised: 06/11/2014] [Accepted: 06/16/2014] [Indexed: 12/16/2022] Open
Abstract
Gene vectors derived from DNA transposable elements have become powerful molecular tools in biomedical research and are slowly moving into the clinic as carriers of therapeutic genes. Conventional uses of DNA transposon-based gene vehicles rely on the intracellular production of the transposase protein from transfected nucleic acids. The transposase mediates mobilization of the DNA transposon, which is typically provided in the context of plasmid DNA. In recent work, we established lentiviral protein transduction from Gag precursors as a new strategy for direct delivery of the transposase protein. Inspired by the natural properties of infecting viruses to carry their own enzymes, we loaded lentivirus-derived particles not only with vector genomes carrying the DNA transposon vector but also with hundreds of transposase subunits. Such particles were found to drive efficient transposition of the piggyBac transposable element in a range of different cell types, including primary cells, and offer a new transposase delivery approach that guarantees short-term activity and limits potential cytotoxicity. DNA transposon vectors, originally developed and launched as a non-viral alternative to viral integrating vectors, have truly become viral. Here, we briefly review our findings and speculate on the perspectives and potential advantages of transposase delivery by lentiviral protein transduction.
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Affiliation(s)
- Yujia Cai
- Department of Biomedicine; Aarhus University; Aarhus C, Denmark
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