3
|
La Bella T, Imbeaud S, Peneau C, Mami I, Datta S, Bayard Q, Caruso S, Hirsch TZ, Calderaro J, Morcrette G, Guettier C, Paradis V, Amaddeo G, Laurent A, Possenti L, Chiche L, Bioulac-Sage P, Blanc JF, Letouze E, Nault JC, Zucman-Rossi J. Adeno-associated virus in the liver: natural history and consequences in tumour development. Gut 2020; 69:737-747. [PMID: 31375600 DOI: 10.1136/gutjnl-2019-318281] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 06/28/2019] [Accepted: 06/29/2019] [Indexed: 02/06/2023]
Abstract
OBJECTIVE Adeno-associated virus (AAV) is a defective mono-stranded DNA virus, endemic in human population (35%-80%). Recurrent clonal AAV2 insertions are associated with the pathogenesis of rare human hepatocellular carcinoma (HCC) developed on normal liver. This study aimed to characterise the natural history of AAV infection in the liver and its consequence in tumour development. DESIGN Viral DNA was quantified in tumour and non-tumour liver tissues of 1461 patients. Presence of episomal form and viral mRNA expression were analysed using a DNAse/TaqMan-based assay and quantitative RT-PCR. In silico analyses using viral capture data explored viral variants and new clonal insertions. RESULTS AAV DNA was detected in 21% of the patients, including 8% of the tumour tissues, equally distributed in two major viral subtypes: one similar to AAV2, the other hybrid between AAV2 and AAV13 sequences. Episomal viral forms were found in 4% of the non-tumour tissues, frequently associated with viral RNA expression and human herpesvirus type 6, the candidate natural AAV helper virus. In 30 HCC, clonal AAV insertions were recurrently identified in CCNA2, CCNE1, TERT, TNFSF10, KMT2B and GLI1/INHBE. AAV insertion triggered oncogenic overexpression through multiple mechanisms that differ according to the localisation of the integration site. CONCLUSION We provided an integrated analysis of the wild-type AAV infection in the liver with the identification of viral genotypes, molecular forms, helper virus relationship and viral integrations. Clonal AAV insertions were positive selected during HCC development on non-cirrhotic liver challenging the notion of AAV as a non-pathogenic virus.
Collapse
Affiliation(s)
- Tiziana La Bella
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Sandrine Imbeaud
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Camille Peneau
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Iadh Mami
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Shalini Datta
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Indian Statistical Institute, University of Kalyani, Kalyani, West Bengal, India
| | - Quentin Bayard
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Stefano Caruso
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Theo Z Hirsch
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Julien Calderaro
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Pathology Department, APHP, CHU Henri Mondor, Créteil, Île-de-France, France
| | - Guillaume Morcrette
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Pathology Department, APHP, Bicetre-Paul Brousse Hospitals, Le Kremlin Bicêtre, Île-de-France, France.,Physiopathogenesis and treatment of liver diseases, INSERM, Paris, Île-de-France, France
| | - Catherine Guettier
- Pathology Department, APHP, Bicetre-Paul Brousse Hospitals, Le Kremlin Bicêtre, Île-de-France, France.,Physiopathogenesis and treatment of liver diseases, INSERM, Paris, Île-de-France, France
| | - Valerie Paradis
- Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Pathology Department, APHP, Beaujon Hospital, Paris, Île-de-France, France.,The Research Center on Inflammation labeled, INSERM, Paris, Île-de-France
| | - Giuliana Amaddeo
- Hepatology Department, APHP, Henri Mondor Hospital, Créteil, Île-de-France, France.,Molecular virology and immunology, INSERM, Institut Mondor de Recherche Biomédicale, Créteil, Île-de-France, France
| | - Alexis Laurent
- Department of Digestive Surgery, APHP, Henri Mondor Hospital, Créteil, Île-de-France, France
| | - Laurent Possenti
- Department of Hepato-Gastroenterology and Digestive Oncology, CHU de Bordeaux, Haut-Lévêque Hospital, Bordeaux, Aquitaine, France
| | - Laurence Chiche
- Department of Digestive Surgery, Centre Médico Chirurgical Magellan, CHU de Bordeaux, Haut-Lévêque Hospital, Bordeaux, Aquitaine, France
| | - Paulette Bioulac-Sage
- Department of Pathology, CHU de Bordeaux, Pellegrin Hospital, Bordeaux, Aquitaine, France.,Bordeaux Research in Translational Oncology, Université Bordeaux, Bordeaux, Aquitaine, France
| | - Jean-Frederic Blanc
- Department of Hepato-Gastroenterology and Digestive Oncology, CHU de Bordeaux, Haut-Lévêque Hospital, Bordeaux, Aquitaine, France.,Department of Pathology, CHU de Bordeaux, Pellegrin Hospital, Bordeaux, Aquitaine, France.,Bordeaux Research in Translational Oncology, Université Bordeaux, Bordeaux, Aquitaine, France
| | - Eric Letouze
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France
| | - Jean-Charles Nault
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Department of Hepatology, Université Paris Nord, APHP, Hospital Jean Verdier, Bondy, Île-de-France, France
| | - Jessica Zucman-Rossi
- Centre de Recherche des Cordeliers, Sorbonne Universités, INSERM, Paris, Île-de-France, France.,Functional Genomics of Solid Tumor, Labex Immuno- Oncology, équipe labellisée Ligue Contre le Cancer, Université de Paris, Université Paris 13, Paris, Île-de-France, France.,Department of Oncology, APHP, Hospital Européen Georges Pompidou, Paris, Île-de-France, France
| |
Collapse
|
6
|
Mizuno N, Mizutani E, Sato H, Kasai M, Ogawa A, Suchy F, Yamaguchi T, Nakauchi H. Intra-embryo Gene Cassette Knockin by CRISPR/Cas9-Mediated Genome Editing with Adeno-Associated Viral Vector. iScience 2018; 9:286-297. [PMID: 30447647 PMCID: PMC6240711 DOI: 10.1016/j.isci.2018.10.030] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2018] [Revised: 09/24/2018] [Accepted: 10/29/2018] [Indexed: 12/20/2022] Open
Abstract
Intra-embryo genome editing by CRISPR/Cas9 enables easy generation of gene-modified animals by non-homologous end joining (NHEJ)-mediated frameshift mutations or homology-directed repair (HDR)-mediated point mutations. However, large modifications, such as gene replacement or gene fusions, are still difficult to introduce in embryos without costly micromanipulators. Moreover, micromanipulation techniques for intra-embryo genome editing have been established in only a small set of animals. To overcome these issues, we developed a method of large-fragment DNA knockin without micromanipulation. In this study, we successfully delivered the knockin donor DNA into zygotes by adeno-associated virus (AAV) without removing the zona pellucida, and we succeeded in both large-DNA fragment knockin and whole exon exchange with electroporation of CRISPR/Cas9 ribonucleoprotein. By this method, we can exchange large DNA fragments conveniently in various animal species without micromanipulation.
Collapse
Affiliation(s)
- Naoaki Mizuno
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Eiji Mizutani
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Hideyuki Sato
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Mariko Kasai
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Aki Ogawa
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan
| | - Fabian Suchy
- Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Tomoyuki Yamaguchi
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan.
| | - Hiromitsu Nakauchi
- Division of Stem Cell Therapy, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo 1088639, Japan; Institute for Stem Cell Biology and Regenerative Medicine, Department of Genetics, Stanford University School of Medicine, Stanford, CA 94305, USA.
| |
Collapse
|
7
|
Smith LJ, Wright J, Clark G, Ul-Hasan T, Jin X, Fong A, Chandra M, St Martin T, Rubin H, Knowlton D, Ellsworth JL, Fong Y, Wong KK, Chatterjee S. Stem cell-derived clade F AAVs mediate high-efficiency homologous recombination-based genome editing. Proc Natl Acad Sci U S A 2018; 115:E7379-E7388. [PMID: 30018062 PMCID: PMC6077703 DOI: 10.1073/pnas.1802343115] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
The precise correction of genetic mutations at the nucleotide level is an attractive permanent therapeutic strategy for human disease. However, despite significant progress, challenges to efficient and accurate genome editing persist. Here, we report a genome editing platform based upon a class of hematopoietic stem cell (HSC)-derived clade F adeno-associated virus (AAV), which does not require prior nuclease-mediated DNA breaks and functions exclusively through BRCA2-dependent homologous recombination. Genome editing is guided by complementary homology arms and is highly accurate and seamless, with no evidence of on-target mutations, including insertion/deletions or inclusion of AAV inverted terminal repeats. Efficient genome editing was demonstrated at different loci within the human genome, including a safe harbor locus, AAVS1, and the therapeutically relevant IL2RG gene, and at the murine Rosa26 locus. HSC-derived AAV vector (AAVHSC)-mediated genome editing was robust in primary human cells, including CD34+ cells, adult liver, hepatic endothelial cells, and myocytes. Importantly, high-efficiency gene editing was achieved in vivo upon a single i.v. injection of AAVHSC editing vectors in mice. Thus, clade F AAV-mediated genome editing represents a promising, highly efficient, precise, single-component approach that enables the development of therapeutic in vivo genome editing for the treatment of a multitude of human gene-based diseases.
Collapse
Affiliation(s)
- Laura J Smith
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | | | - Gabriella Clark
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | - Taihra Ul-Hasan
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | - Xiangyang Jin
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | - Abigail Fong
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | - Manasa Chandra
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | | | | | | | | | - Yuman Fong
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010
| | - Kamehameha K Wong
- Department of Hematology and Stem Cell Transplantation, City of Hope Medical Center, Duarte, CA 91010
| | - Saswati Chatterjee
- Department of Surgery, Beckman Research Institute, City of Hope Medical Center, Duarte, CA 91010;
| |
Collapse
|