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Tao J, Wang Q, Mendez-Dorantes C, Burns KH, Chiarle R. Frequency and mechanisms of LINE-1 retrotransposon insertions at CRISPR/Cas9 sites. Nat Commun 2022; 13:3685. [PMID: 35760782 PMCID: PMC9237045 DOI: 10.1038/s41467-022-31322-3] [Citation(s) in RCA: 36] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 06/14/2022] [Indexed: 12/11/2022] Open
Abstract
CRISPR/Cas9-based genome editing has revolutionized experimental molecular biology and entered the clinical world for targeted gene therapy. Identifying DNA modifications occurring at CRISPR/Cas9 target sites is critical to determine efficiency and safety of editing tools. Here we show that insertions of LINE-1 (L1) retrotransposons can occur frequently at CRISPR/Cas9 editing sites. Together with PolyA-seq and an improved amplicon sequencing, we characterize more than 2500 de novo L1 insertions at multiple CRISPR/Cas9 editing sites in HEK293T, HeLa and U2OS cells. These L1 retrotransposition events exploit CRISPR/Cas9-induced DSB formation and require L1 RT activity. Importantly, de novo L1 insertions are rare during genome editing by prime editors (PE), cytidine or adenine base editors (CBE or ABE), consistent with their reduced DSB formation. These data demonstrate that insertions of retrotransposons might be a potential outcome of CRISPR/Cas9 genome editing and provide further evidence on the safety of different CRISPR-based editing tools.
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Affiliation(s)
- Jianli Tao
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
| | - Qi Wang
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA
| | | | - Kathleen H Burns
- Department of Oncologic Pathology, Dana-Farber Cancer Institute, Boston, MA, 02115, USA
| | - Roberto Chiarle
- Department of Pathology, Boston Children's Hospital and Harvard Medical School, Boston, MA, 02115, USA.
- Department of Molecular Biotechnology and Health Sciences, University of Torino, Torino, 10126, Italy.
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2
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Xun J, Zhang X, Guo S, Lu H, Chen J. Editing out HIV: application of gene editing technology to achieve functional cure. Retrovirology 2021; 18:39. [PMID: 34922576 PMCID: PMC8684261 DOI: 10.1186/s12977-021-00581-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2021] [Accepted: 11/05/2021] [Indexed: 03/01/2023] Open
Abstract
Highly active antiretroviral therapy (HAART) successfully suppresses human immunodeficiency virus (HIV) replication and improves the quality of life of patients living with HIV. However, current HAART does not eradicate HIV infection because an HIV reservoir is established in latently infected cells and is not recognized by the immune system. The successful curative treatment of the Berlin and London patients following bone marrow transplantation inspired researchers to identify an approach for the functional cure of HIV. As a promising technology, gene editing-based strategies have attracted considerable attention and sparked much debate. Herein, we discuss the development of different gene editing strategies in the functional cure of HIV and highlight the potential for clinical applications prospects. ![]()
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Affiliation(s)
- Jingna Xun
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China.,State Key Laboratory of Genetic Engineering, School of Life Sciences, Fudan University, Shanghai, China
| | - Xinyu Zhang
- Scientific Research Center, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China
| | - Shuyan Guo
- Shanghai Foreign Language School, Shanghai International Studies University, Shanghai, China
| | - Hongzhou Lu
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China
| | - Jun Chen
- Department of Infectious Diseases and Immunology, Shanghai Public Health Clinical Center, Fudan University, 2901 Caolang Road, Shanghai, 201508, China.
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3
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Depreter B, Weening KE, Vandepoele K, Essand M, De Moerloose B, Themeli M, Cloos J, Hanekamp D, Moors I, D'hont I, Denys B, Uyttebroeck A, Van Damme A, Dedeken L, Snauwaert S, Goetgeluk G, De Munter S, Kerre T, Vandekerckhove B, Lammens T, Philippé J. TARP is an immunotherapeutic target in acute myeloid leukemia expressed in the leukemic stem cell compartment. Haematologica 2019; 105:1306-1316. [PMID: 31371409 PMCID: PMC7193481 DOI: 10.3324/haematol.2019.222612] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2019] [Accepted: 07/12/2019] [Indexed: 12/26/2022] Open
Abstract
Immunotherapeutic strategies targeting the rare leukemic stem cell compartment might provide salvage to the high relapse rates currently observed in acute myeloid leukemia (AML). We applied gene expression profiling for comparison of leukemic blasts and leukemic stem cells with their normal counterparts. Here, we show that the T-cell receptor γ chain alternate reading frame protein (TARP) is over-expressed in de novo pediatric (n=13) and adult (n=17) AML sorted leukemic stem cells and blasts compared to hematopoietic stem cells and normal myeloblasts (15 healthy controls). Moreover, TARP expression was significantly associated with a fms-like tyrosine kinase receptor-3 internal tandem duplication in pediatric AML. TARP overexpression was confirmed in AML cell lines (n=9), and was found to be absent in B-cell acute lymphocytic leukemia (n=5) and chronic myeloid leukemia (n=1). Sequencing revealed that both a classical TARP transcript, as described in breast and prostate adenocarcinoma, and an AML-specific alternative TARP transcript, were present. Protein expression levels mostly matched transcript levels. TARP was shown to reside in the cytoplasmic compartment and showed sporadic endoplasmic reticulum co-localization. TARP-T-cell receptor engineered cytotoxic T-cells in vitro killed AML cell lines and patient leukemic cells co-expressing TARP and HLA-A*0201. In conclusion, TARP qualifies as a relevant target for immunotherapeutic T-cell therapy in AML.
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Affiliation(s)
- Barbara Depreter
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Karin E Weening
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Karl Vandepoele
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Magnus Essand
- Science for Life Laboratory, Department of Immunology, Genetics and Pathology, Uppsala University, Uppsala, Sweden
| | - Barbara De Moerloose
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium.,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Maria Themeli
- Department of Hematology, VU University Medical Center, Amsterdam, the Netherlands
| | - Jacqueline Cloos
- Department of Hematology, VU University Medical Center, Amsterdam, the Netherlands
| | - Diana Hanekamp
- Department of Hematology, VU University Medical Center, Amsterdam, the Netherlands
| | - Ine Moors
- Department of Hematology, Ghent University Hospital, Ghent, Belgium
| | - Inge D'hont
- Department of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Barbara Denys
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
| | - Anne Uyttebroeck
- Department of Pediatrics, University Hospital Gasthuisberg, Louvain, Belgium
| | - An Van Damme
- Department of Pediatric Hematology Oncology, University Hospital Saint-Luc, Brussels, Belgium
| | - Laurence Dedeken
- Department of Pediatric Hematology Oncology, Queen Fabiola Children's University Hospital, Brussels, Belgium
| | - Sylvia Snauwaert
- Department of Hematology, AZ Sint-Jan Hospital Bruges, Bruges, Belgium
| | - Glenn Goetgeluk
- Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Stijn De Munter
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Tessa Kerre
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Hematology, Ghent University Hospital, Ghent, Belgium
| | - Bart Vandekerckhove
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium
| | - Tim Lammens
- Department of Internal Medicine and Pediatrics, Ghent University, Ghent, Belgium .,Cancer Research Institute Ghent, Ghent University, Ghent, Belgium
| | - Jan Philippé
- Cancer Research Institute Ghent, Ghent University, Ghent, Belgium.,Department of Diagnostic Sciences, Ghent University, Ghent, Belgium.,Department of Laboratory Medicine, Ghent University Hospital, Ghent, Belgium
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4
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Li X, Bai Y, Cheng X, Kalds PGT, Sun B, Wu Y, Lv H, Xu K, Zhang Z. Efficient SSA-mediated precise genome editing using CRISPR/Cas9. FEBS J 2018; 285:3362-3375. [PMID: 30085411 DOI: 10.1111/febs.14626] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2018] [Revised: 06/11/2018] [Accepted: 08/03/2018] [Indexed: 12/23/2022]
Abstract
CRISPR/Cas9 has been emerging as a main player in genome editing field since its advent. However, CRISPR/Cas9-induced precise gene editing remains challenging since it requires no scar left after editing. Among the few reports regarding two-step 'pop in & out' technologies for precise gene editing, the combination of CRISPR/Cas9 with Cre/LoxP demonstrates a higher efficiency, but leaves behind a 34-base pair of tag sequence due to its inherent property. Another method utilizes piggyBac transposon for removing the selection cassette, and its disadvantage is the difficulty in controlling its random reintegration after releasing. Here, we report a novel two-step precise gene-editing method by leveraging the SSA-mediated repair mechanism into the CRISPR/Cas9-mediated gene-editing system. An integrating cassette was developed with positive and negative selection markers, which was flanked by direct repeat sequences with desired mutations as SSA arms. After the targeted integration of the cassette mediated by CRISPR/Cas9-induced homologous-directed repair, cell clones were first selected through the positive selection. In the second round targeting, the selection cassette was removed by the SSA-mediated DNA double-strand break (DSB) repair without any scar left behind. The novel seamless genome editing technique was tested on CCR5 and APP loci, and finally demonstrated, respectively, up to 45.83% and 68% of precise genome editing efficiency. This study provides a new efficient approach for precise genome editing and gene correction.
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Affiliation(s)
- Xinyi Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yichun Bai
- Institute of Lung and Molecular Therapy, Xinxiang Medical University, China
| | - Xinzhen Cheng
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Peter Girgis Tawfek Kalds
- College of Animal Science and Technology, Northwest A&F University, Yangling, China.,Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, Egypt
| | - Bing Sun
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yun Wu
- College of Biology and Agriculture Science, Zunyi Normal University, China
| | - Huijiao Lv
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kun Xu
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Zhiying Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
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