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Bexte T, Botezatu L, Miskey C, Gierschek F, Moter A, Wendel P, Reindl LM, Campe J, Villena-Ossa JF, Gebel V, Stein K, Cathomen T, Cremer A, Wels WS, Hudecek M, Ivics Z, Ullrich E. Engineering of potent CAR NK cells using non-viral Sleeping Beauty transposition from minimalistic DNA vectors. Mol Ther 2024; 32:2357-2372. [PMID: 38751112 PMCID: PMC11287004 DOI: 10.1016/j.ymthe.2024.05.022] [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] [Received: 01/23/2024] [Revised: 03/25/2024] [Accepted: 05/09/2024] [Indexed: 06/06/2024] Open
Abstract
Natural killer (NK) cells have high intrinsic cytotoxic capacity, and clinical trials have demonstrated their safety and efficacy for adoptive cancer therapy. Expression of chimeric antigen receptors (CARs) enhances NK cell target specificity, with these cells applicable as off-the-shelf products generated from allogeneic donors. Here, we present for the first time an innovative approach for CAR NK cell engineering employing a non-viral Sleeping Beauty (SB) transposon/transposase-based system and minimized DNA vectors termed minicircles. SB-modified peripheral blood-derived primary NK cells displayed high and stable CAR expression and more frequent vector integration into genomic safe harbors than lentiviral vectors. Importantly, SB-generated CAR NK cells demonstrated enhanced cytotoxicity compared with non-transfected NK cells. A strong antileukemic potential was confirmed using established acute lymphocytic leukemia cells and patient-derived primary acute B cell leukemia and lymphoma samples as targets in vitro and in vivo in a xenograft leukemia mouse model. Our data suggest that the SB-transposon system is an efficient, safe, and cost-effective approach to non-viral engineering of highly functional CAR NK cells, which may be suitable for cancer immunotherapy of leukemia as well as many other malignancies.
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Affiliation(s)
- Tobias Bexte
- Goethe University, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany; Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany; University Cancer Center (UCT) Frankfurt, Frankfurt, Germany; Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Frankfurt, Germany; Institute for Transfusion Medicine and Immunohematology, German Red Cross Blood Service Baden-Württemberg - Hesse, Frankfurt, Germany
| | - Lacramioara Botezatu
- Research Centre, Division of Hematology, Gene and Cell Therapy, Paul-Ehrlich-Institut, Langen, Germany; German Cancer Consortium (DKTK), partner site Heidelberg, Heidelberg, Germany
| | - Csaba Miskey
- Research Centre, Division of Hematology, Gene and Cell Therapy, Paul-Ehrlich-Institut, Langen, Germany
| | - Fenja Gierschek
- Goethe University, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany; Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany
| | - Alina Moter
- Goethe University, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany; Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany
| | - Philipp Wendel
- Goethe University, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany; Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany; German Cancer Consortium (DKTK), partner site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany; Institute for Organic Chemistry and Biochemistry, Technical University of Darmstadt, Darmstadt, Germany
| | - Lisa Marie Reindl
- Goethe University, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany; Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany
| | - Julia Campe
- Goethe University, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany; Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany
| | - Jose Francisco Villena-Ossa
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Freiburg, Germany
| | - Veronika Gebel
- Goethe University, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany; Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany; University Cancer Center (UCT) Frankfurt, Frankfurt, Germany; Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Frankfurt, Germany
| | - Katja Stein
- Goethe University, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany; Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany; University Cancer Center (UCT) Frankfurt, Frankfurt, Germany
| | - Toni Cathomen
- Institute for Transfusion Medicine and Gene Therapy, Medical Center - University of Freiburg, Freiburg, Germany; Center for Chronic Immunodeficiency, Medical Center - University of Freiburg, Freiburg, Germany; Faculty of Medicine, University of Freiburg, Freiburg, Germany; German Cancer Consortium (DKTK), partner site Freiburg, Freiburg, Germany
| | - Anjali Cremer
- Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany; University Cancer Center (UCT) Frankfurt, Frankfurt, Germany; Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Frankfurt, Germany; German Cancer Consortium (DKTK), partner site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany; Department of Hematology/Oncology, University Hospital Frankfurt, Frankfurt am Main, Germany
| | - Winfried S Wels
- Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany; German Cancer Consortium (DKTK), partner site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany; Georg-Speyer-Haus, Institute for Tumor Biology and Experimental Therapy, Frankfurt am Main, Germany
| | - Michael Hudecek
- Department of Medicine II, Chaire in Cellular Immunotherapy, University Hospital Würzburg, Würzburg, Germany; Fraunhofer Institute for Cell Therapy and Immunology, Cellular Immunotherapy Branch Site Würzburg, Würzburg, Germany
| | - Zoltán Ivics
- Research Centre, Division of Hematology, Gene and Cell Therapy, Paul-Ehrlich-Institut, Langen, Germany; German Cancer Consortium (DKTK), partner site Heidelberg, Heidelberg, Germany
| | - Evelyn Ullrich
- Goethe University, Department of Pediatrics, Experimental Immunology and Cell Therapy, Frankfurt am Main, Germany; Frankfurt Cancer Institute (FCI), Goethe University, Frankfurt am Main, Germany; University Cancer Center (UCT) Frankfurt, Frankfurt, Germany; Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Frankfurt, Germany; German Cancer Consortium (DKTK), partner site Frankfurt/Mainz and German Cancer Research Center (DKFZ), Heidelberg, Germany.
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2
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Metanat Y, Viktor P, Amajd A, Kaur I, Hamed AM, Abed Al-Abadi NK, Alwan NH, Chaitanya MVNL, Lakshmaiya N, Ghildiyal P, Khalaf OM, Ciongradi CI, Sârbu I. The paths toward non-viral CAR-T cell manufacturing: A comprehensive review of state-of-the-art methods. Life Sci 2024; 348:122683. [PMID: 38702027 DOI: 10.1016/j.lfs.2024.122683] [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] [Received: 01/24/2024] [Revised: 04/11/2024] [Accepted: 04/28/2024] [Indexed: 05/06/2024]
Abstract
Although CAR-T cell therapy has emerged as a game-changer in cancer immunotherapy several bottlenecks limit its widespread use as a front-line therapy. Current protocols for the production of CAR-T cells rely mainly on the use of lentiviral/retroviral vectors. Nevertheless, according to the safety concerns around the use of viral vectors, there are several regulatory hurdles to their clinical use. Large-scale production of viral vectors under "Current Good Manufacturing Practice" (cGMP) involves rigorous quality control assessments and regulatory requirements that impose exorbitant costs on suppliers and as a result, lead to a significant increase in the cost of treatment. Pursuing an efficient non-viral method for genetic modification of immune cells is a hot topic in cell-based gene therapy. This study aims to investigate the current state-of-the-art in non-viral methods of CAR-T cell manufacturing. In the first part of this study, after reviewing the advantages and disadvantages of the clinical use of viral vectors, different non-viral vectors and the path of their clinical translation are discussed. These vectors include transposons (sleeping beauty, piggyBac, Tol2, and Tc Buster), programmable nucleases (ZFNs, TALENs, and CRISPR/Cas9), mRNA, plasmids, minicircles, and nanoplasmids. Afterward, various methods for efficient delivery of non-viral vectors into the cells are reviewed.
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Affiliation(s)
- Yekta Metanat
- Faculty of Medicine, Zahedan University of Medical Sciences, Sistan and Baluchestan Province, Iran
| | - Patrik Viktor
- Óbuda University, Karoly Keleti faculty, Tavaszmező u. 15-17, H-1084 Budapest, Hungary
| | - Ayesha Amajd
- Faculty of Transport and Aviation Engineering, Silesian University of Technology, Krasińskiego 8 Street, 40-019 Katowice, Poland
| | - Irwanjot Kaur
- Department of Biotechnology and Genetics, Jain (Deemed-to-be) University, Bangalore, Karnataka, India; Department of Allied Healthcare and Sciences, Vivekananda Global University, Jaipur, Rajasthan-303012, India
| | | | | | | | - M V N L Chaitanya
- School of pharmaceutical sciences, Lovely Professional University, Jalandhar-Delhi G.T. Road, Phagwara, Punjab - 144411, India
| | | | - Pallavi Ghildiyal
- Uttaranchal Institute of Pharmaceutical Sciences, Uttaranchal University, Dehradun, India
| | | | - Carmen Iulia Ciongradi
- 2nd Department of Surgery-Pediatric Surgery and Orthopedics, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iași, Romania.
| | - Ioan Sârbu
- 2nd Department of Surgery-Pediatric Surgery and Orthopedics, "Grigore T. Popa" University of Medicine and Pharmacy, 700115 Iași, Romania.
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3
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Rossi M, Breman E. Engineering strategies to safely drive CAR T-cells into the future. Front Immunol 2024; 15:1411393. [PMID: 38962002 PMCID: PMC11219585 DOI: 10.3389/fimmu.2024.1411393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024] Open
Abstract
Chimeric antigen receptor (CAR) T-cell therapy has proven a breakthrough in cancer treatment in the last decade, giving unprecedented results against hematological malignancies. All approved CAR T-cell products, as well as many being assessed in clinical trials, are generated using viral vectors to deploy the exogenous genetic material into T-cells. Viral vectors have a long-standing clinical history in gene delivery, and thus underwent iterations of optimization to improve their efficiency and safety. Nonetheless, their capacity to integrate semi-randomly into the host genome makes them potentially oncogenic via insertional mutagenesis and dysregulation of key cellular genes. Secondary cancers following CAR T-cell administration appear to be a rare adverse event. However several cases documented in the last few years put the spotlight on this issue, which might have been underestimated so far, given the relatively recent deployment of CAR T-cell therapies. Furthermore, the initial successes obtained in hematological malignancies have not yet been replicated in solid tumors. It is now clear that further enhancements are needed to allow CAR T-cells to increase long-term persistence, overcome exhaustion and cope with the immunosuppressive tumor microenvironment. To this aim, a variety of genomic engineering strategies are under evaluation, most relying on CRISPR/Cas9 or other gene editing technologies. These approaches are liable to introduce unintended, irreversible genomic alterations in the product cells. In the first part of this review, we will discuss the viral and non-viral approaches used for the generation of CAR T-cells, whereas in the second part we will focus on gene editing and non-gene editing T-cell engineering, with particular regard to advantages, limitations, and safety. Finally, we will critically analyze the different gene deployment and genomic engineering combinations, delineating strategies with a superior safety profile for the production of next-generation CAR T-cell.
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Merelli I, Beretta S, Cesana D, Gennari A, Benedicenti F, Spinozzi G, Cesini D, Montini E, D’Agostino D, Calabria A. InCliniGene enables high-throughput and comprehensive in vivo clonal tracking toward clinical genomics data integration. Database (Oxford) 2023; 2023:baad069. [PMID: 37935583 PMCID: PMC10630073 DOI: 10.1093/database/baad069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 08/15/2023] [Accepted: 10/04/2023] [Indexed: 11/09/2023]
Abstract
High-throughput clonal tracking in patients under hematopoietic stem cell gene therapy with integrating vector is instrumental in assessing bio-safety and efficacy. Monitoring the fate of millions of transplanted clones and their progeny across differentiation and proliferation over time leverages the identification of the vector integration sites, used as surrogates of clonal identity. Although γ-tracking retroviral insertion sites (γ-TRIS) is the state-of-the-art algorithm for clonal identification, the computational drawbacks in the tracking algorithm, based on a combinatorial all-versus-all strategy, limit its use in clinical studies with several thousands of samples per patient. We developed the first clonal tracking graph database, InCliniGene (https://github.com/calabrialab/InCliniGene), that imports the output files of γ-TRIS and generates the graph of clones (nodes) connected by arches if two nodes share common genomic features as defined by the γ-TRIS rules. Embedding both clonal data and their connections in the graph, InCliniGene can track all clones longitudinally over samples through data queries that fully explore the graph. This approach resulted in being highly accurate and scalable. We validated InCliniGene using an in vitro dataset, specifically designed to mimic clinical cases, and tested the accuracy and precision. InCliniGene allows extensive use of γ-TRIS in large gene therapy clinical applications and naturally realizes the full data integration of molecular and genomics data, clinical and treatment measurements and genomic annotations. Further extensions of InCliniGene with data federation and with application programming interface will support data mining toward precision, personalized and predictive medicine in gene therapy. Database URL: https://github.com/calabrialab/InCliniGene.
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Affiliation(s)
| | - Stefano Beretta
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Daniela Cesana
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Alessandro Gennari
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Giulio Spinozzi
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Daniele Cesini
- Centro Nazionale Analisi Fotogrammi (CNAF), Istituto Nazionale di Fisica Nucleare, Viale Carlo Berti Pichat 6/2, Bologna 40127, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Daniele D’Agostino
- Dipartimento di Informatica, Bioingegneria, Robotica e Ingegneria dei Sistemi (DIBRIS), Università degli Studi di Genova, Viale Causa 13, Genoa 16145, Italy
- Institute of Biomedical Technologies, Italian National Research Council, Via Fratelli Cervi 93, Segrate (MI) 20054, Italy
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy, IRCCS Ospedale San Raffaele, Via Olgettina 60, Milano 20132, Italy
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5
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Bexte T, Reindl LM, Ullrich E. Nonviral technologies can pave the way for CAR-NK cell therapy. J Leukoc Biol 2023; 114:475-486. [PMID: 37403203 DOI: 10.1093/jleuko/qiad074] [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] [Received: 12/03/2022] [Revised: 05/25/2023] [Accepted: 06/22/2023] [Indexed: 07/06/2023] Open
Abstract
Natural killer cells are a promising platform for cancer immunotherapy. Natural killer cells have high intrinsic killing capability, and the insertion of a chimeric antigen receptor can further enhance their antitumor potential. In first-in-human trials, chimeric antigen receptor-natural killer cells demonstrated strong clinical activity without therapy-induced side effects. The applicability of natural killer cells as an "off-the-shelf" product makes them highly attractive for gene-engineered cell therapies. Traditionally, viral transduction has been used for gene editing; however, the use of viral vectors remains a safety concern and is associated with high costs and regulatory requirements. Here, we review the current landscape of nonviral approaches for chimeric antigen receptor-natural killer cell generation. This includes transfection of vector particles and electroporation of mRNA and DNA vectors, resulting in transient modification and chimeric antigen receptor expression. In addition, using nonviral transposon technologies, natural killer cells can be stably modified ensuring long-lasting chimeric antigen receptor expression. Finally, we discuss CRISPR/Cas9 tools to edit key genes for natural killer cell functionality.
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Affiliation(s)
- Tobias Bexte
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
- University Cancer Center (UCT), Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
| | - Lisa Marie Reindl
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
| | - Evelyn Ullrich
- Goethe University Frankfurt, Department of Pediatrics, Experimental Immunology & Cell Therapy, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Frankfurt Cancer Institute, Goethe University, Paul-Ehrlich-Straße 42-44, 60596 Frankfurt am Main, Germany
- University Cancer Center (UCT), Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- Mildred Scheel Career Center (MSNZ), Hospital of the Goethe University Frankfurt, Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
- German Cancer Consortium (DKTK) and German Cancer Research Center (DKFZ) partner site Frankfurt/Mainz; Theodor-Stern-Kai 7, 60590 Frankfurt am Main, Germany
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6
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Kovač A, Miskey C, Ivics Z. Sleeping Beauty Transposon Insertions into Nucleolar DNA by an Engineered Transposase Localized in the Nucleolus. Int J Mol Sci 2023; 24:14978. [PMID: 37834425 PMCID: PMC10573994 DOI: 10.3390/ijms241914978] [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] [Received: 06/06/2023] [Revised: 09/22/2023] [Accepted: 09/28/2023] [Indexed: 10/15/2023] Open
Abstract
Transposons are nature's gene delivery vehicles that can be harnessed for experimental and therapeutic purposes. The Sleeping Beauty (SB) transposon shows efficient transposition and long-term transgene expression in human cells, and is currently under clinical development for gene therapy. SB transposition occurs into the human genome in a random manner, which carries a risk of potential genotoxic effects associated with transposon integration. Here, we evaluated an experimental strategy to manipulate SB's target site distribution by preferentially compartmentalizing the SB transposase to the nucleolus, which contains repetitive ribosomal RNA (rRNA) genes. We generated a fusion protein composed of the nucleolar protein nucleophosmin (B23) and the SB100X transposase, which was found to retain almost full transposition activity as compared to unfused transposase and to be predominantly localized to nucleoli in transfected human cells. Analysis of transposon integration sites generated by B23-SB100X revealed a significant enrichment into the p-arms of chromosomes containing nucleolus organizing regions (NORs), with preferential integration into the p13 and p11.2 cytobands directly neighboring the NORs. This bias in the integration pattern was accompanied by an enrichment of insertions into nucleolus-associated chromatin domains (NADs) at the periphery of nucleolar DNA and into lamina-associated domains (LADs). Finally, sub-nuclear targeting of the transposase resulted in preferential integration into chromosomal domains associated with the Upstream Binding Transcription Factor (UBTF) that plays a critical role in the transcription of 47S rDNA gene repeats of the NORs by RNA Pol I. Future modifications of this technology may allow the development of methods for specific gene insertion for precision genetic engineering.
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Affiliation(s)
| | | | - Zoltán Ivics
- Transposition and Genome Engineering, Research Centre of the Division of Hematology, Gene and Cell Therapy, Paul Ehrlich Institute, Paul Ehrlich Str. 51–59, D-63225 Langen, Germany; (A.K.); (C.M.)
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7
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Zhao D, Qin J, An J, Zhang H, Li J, Wang H, Du R, He Y. Optimization of piggyBac Transposon System Electrotransfection in Sheep Fibroblasts. Mol Biotechnol 2023; 65:1585-1597. [PMID: 36705779 DOI: 10.1007/s12033-023-00659-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2022] [Accepted: 01/08/2023] [Indexed: 01/28/2023]
Abstract
Electroporation is a non-viral mediated transfection technique, which has the advantages of being harmless, easy to operate, and less expensive. This transfection method can be used for almost all cell types and has gradually become the preferred transfection method for mammalian gene editing. However, further improvements are needed in electroporation efficiency. There is no universal standard electrotransfection step for different types of cells, and the inappropriate electroporation parameters will result in a low transfection efficiency and high cell mortality. Here, we systematically optimized the electrotransfection parameters of piggyBac transposon system into sheep fetal fibroblasts for the first time. We found that the cell transfection efficiency and cell viability could be improved by using traditional cell culture medium DMEM/F12 as an electroporation buffer, and simultaneously using the square-wave pulsing program of 200 V, 2 pulses, 20 ms length, and 20 μg DNA (3 μg/μL) in 4 mm cuvette, and the transfection efficiency and cell viability could eventually reach 78.0% and 40.9%, respectively. The purpose of this study is to provide a method reference and theoretical basis for the plasmid electrotransfection in mammal cells.
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Affiliation(s)
- Dipeng Zhao
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- School of Life Science and Engineering, Foshan University, Foshan, 528000, Guangdong, China
| | - Jian Qin
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- College of Life Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
- Center of Experiment Teaching, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Jie An
- College of Life Science, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Hao Zhang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Junling Li
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Hejie Wang
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China
| | - Rong Du
- College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, China.
| | - Yongming He
- School of Life Science and Engineering, Foshan University, Foshan, 528000, Guangdong, China.
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8
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Tang YJ, Shuldiner EG, Karmakar S, Winslow MM. High-Throughput Identification, Modeling, and Analysis of Cancer Driver Genes In Vivo. Cold Spring Harb Perspect Med 2023; 13:a041382. [PMID: 37277208 PMCID: PMC10317066 DOI: 10.1101/cshperspect.a041382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
The vast number of genomic and molecular alterations in cancer pose a substantial challenge to uncovering the mechanisms of tumorigenesis and identifying therapeutic targets. High-throughput functional genomic methods in genetically engineered mouse models allow for rapid and systematic investigation of cancer driver genes. In this review, we discuss the basic concepts and tools for multiplexed investigation of functionally important cancer genes in vivo using autochthonous cancer models. Furthermore, we highlight emerging technical advances in the field, potential opportunities for future investigation, and outline a vision for integrating multiplexed genetic perturbations with detailed molecular analyses to advance our understanding of the genetic and molecular basis of cancer.
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Affiliation(s)
- Yuning J Tang
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Emily G Shuldiner
- Department of Biology, Stanford University, Stanford, California 94305, USA
| | - Saswati Karmakar
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Monte M Winslow
- Department of Genetics, Stanford University School of Medicine, Stanford, California 94305, USA
- Department of Pathology, Stanford University School of Medicine, Stanford, California 94305, USA
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9
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Fischer A, Lersch R, de Andrade Krätzig N, Strong A, Friedrich MJ, Weber J, Engleitner T, Öllinger R, Yen HY, Kohlhofer U, Gonzalez-Menendez I, Sailer D, Kogan L, Lahnalampi M, Laukkanen S, Kaltenbacher T, Klement C, Rezaei M, Ammon T, Montero JJ, Schneider G, Mayerle J, Heikenwälder M, Schmidt-Supprian M, Quintanilla-Martinez L, Steiger K, Liu P, Cadiñanos J, Vassiliou GS, Saur D, Lohi O, Heinäniemi M, Conte N, Bradley A, Rad L, Rad R. In vivo interrogation of regulatory genomes reveals extensive quasi-insufficiency in cancer evolution. CELL GENOMICS 2023; 3:100276. [PMID: 36950387 PMCID: PMC10025556 DOI: 10.1016/j.xgen.2023.100276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Revised: 09/05/2022] [Accepted: 02/08/2023] [Indexed: 03/10/2023]
Abstract
In contrast to mono- or biallelic loss of tumor-suppressor function, effects of discrete gene dysregulations, as caused by non-coding (epi)genome alterations, are poorly understood. Here, by perturbing the regulatory genome in mice, we uncover pervasive roles of subtle gene expression variation in cancer evolution. Genome-wide screens characterizing 1,450 tumors revealed that such quasi-insufficiency is extensive across entities and displays diverse context dependencies, such as distinct cell-of-origin associations in T-ALL subtypes. We compile catalogs of non-coding regions linked to quasi-insufficiency, show their enrichment with human cancer risk variants, and provide functional insights by engineering regulatory alterations in mice. As such, kilo-/megabase deletions in a Bcl11b-linked non-coding region triggered aggressive malignancies, with allele-specific tumor spectra reflecting gradual gene dysregulations through modular and cell-type-specific enhancer activities. Our study constitutes a first survey toward a systems-level understanding of quasi-insufficiency in cancer and gives multifaceted insights into tumor evolution and the tissue-specific effects of non-coding mutations.
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Affiliation(s)
- Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
| | - Robert Lersch
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Niklas de Andrade Krätzig
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Alexander Strong
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Mathias J. Friedrich
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Thomas Engleitner
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Hsi-Yu Yen
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Comparative Experimental Pathology, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Ursula Kohlhofer
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Irene Gonzalez-Menendez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - David Sailer
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Liz Kogan
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Mari Lahnalampi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Saara Laukkanen
- Faculty of Medicine and Health Technology, Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University, Tampere, Finland
| | - Thorsten Kaltenbacher
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Christine Klement
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Majdaddin Rezaei
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Tim Ammon
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute of Experimental Hematology, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Juan J. Montero
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Günter Schneider
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of General, Visceral and Pediatric Surgery, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Julia Mayerle
- Medical Department II, University Hospital, LMU Munich, Munich, Germany
| | - Mathias Heikenwälder
- German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
- Division of Chronic Inflammation and Cancer, German Cancer Research Center (DKFZ), 69120 Heidelberg, Germany
| | - Marc Schmidt-Supprian
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Institute of Experimental Hematology, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Comprehensive Cancer Center, Eberhard Karls Universität Tübingen, 72076 Tübingen, Germany
| | - Katja Steiger
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Comparative Experimental Pathology, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Pentao Liu
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Li Ka Shing Faculty of Medicine, Stem Cell and Regenerative Medicine Consortium, School of Biomedical Sciences, University of Hong Kong, Hong Kong, China
| | - Juan Cadiñanos
- Instituto de Medicina Oncológica y Molecular de Asturias (IMOMA), 33193 Oviedo, Spain
| | - George S. Vassiliou
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Wellcome Trust-MRC Stem Cell Institute, Cambridge Biomedical Campus, University of Cambridge, Cambridge CB2 0XY, UK
- Department of Haematology, Cambridge University Hospitals NHS Trust, Cambridge CB2 0PT, UK
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Olli Lohi
- Faculty of Medicine and Health Technology, Tampere Center for Child, Adolescent and Maternal Health Research and Tays Cancer Center, Tampere University, Tampere, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, Kuopio, Finland
| | - Nathalie Conte
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
| | - Allan Bradley
- The Wellcome Trust Sanger Institute, Genome Campus, Hinxton, Cambridge, UK
- Cambridge Institute of Therapeutic Immunology & Infectious Disease (CITIID), University of Cambridge, Puddicombe Way, Cambridge CB2 0AW, UK
| | - Lena Rad
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- Institute for Experimental Cancer Therapy, School of Medicine, Technische Universität München, 81675 Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, School of Medicine, Technische Universität München, 81675 Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), School of Medicine, Technische Universität München, 81675 Munich, Germany
- German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Medicine II, Klinikum rechts der Isar, School of Medicine, Technische Universität München, 81675 Munich, Germany
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10
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Bredthauer C, Fischer A, Ahari AJ, Cao X, Weber J, Rad L, Rad R, Wachutka L, Gagneur J. Transmicron: accurate prediction of insertion probabilities improves detection of cancer driver genes from transposon mutagenesis screens. Nucleic Acids Res 2023; 51:e21. [PMID: 36617985 PMCID: PMC9976929 DOI: 10.1093/nar/gkac1215] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2022] [Revised: 11/06/2022] [Accepted: 12/17/2022] [Indexed: 01/10/2023] Open
Abstract
Transposon screens are powerful in vivo assays used to identify loci driving carcinogenesis. These loci are identified as Common Insertion Sites (CISs), i.e. regions with more transposon insertions than expected by chance. However, the identification of CISs is affected by biases in the insertion behaviour of transposon systems. Here, we introduce Transmicron, a novel method that differs from previous methods by (i) modelling neutral insertion rates based on chromatin accessibility, transcriptional activity and sequence context and (ii) estimating oncogenic selection for each genomic region using Poisson regression to model insertion counts while controlling for neutral insertion rates. To assess the benefits of our approach, we generated a dataset applying two different transposon systems under comparable conditions. Benchmarking for enrichment of known cancer genes showed improved performance of Transmicron against state-of-the-art methods. Modelling neutral insertion rates allowed for better control of false positives and stronger agreement of the results between transposon systems. Moreover, using Poisson regression to consider intra-sample and inter-sample information proved beneficial in small and moderately-sized datasets. Transmicron is open-source and freely available. Overall, this study contributes to the understanding of transposon biology and introduces a novel approach to use this knowledge for discovering cancer driver genes.
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Affiliation(s)
- Carl Bredthauer
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Computational Health Center, Helmholtz Zentrum Munich, Neuherberg, Germany
| | - Anja Fischer
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Ata Jadid Ahari
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany
| | - Xueqi Cao
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Graduate School of Quantitative Biosciences (QBM), Ludwig-Maximilians-Universität München, 81377 Munich, Germany
| | - Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Lena Rad
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Institute for Experimental Cancer Therapy, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany.,German Cancer Consortium (DKTK), 69120 Heidelberg, Germany.,Department of Medicine II, Klinikum rechts der Isar, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
| | - Leonhard Wachutka
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany
| | - Julien Gagneur
- TUM School of Computation, Information and Technology, Technical University of Munich, 81675 Munich, Germany.,Computational Health Center, Helmholtz Zentrum Munich, Neuherberg, Germany.,Institute of Human Genetics, TUM School of Medicine, Technical University of Munich, 81675 Munich, Germany
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11
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Pellaers E, Bhat A, Christ F, Debyser Z. Determinants of Retroviral Integration and Implications for Gene Therapeutic MLV-Based Vectors and for a Cure for HIV-1 Infection. Viruses 2022; 15:32. [PMID: 36680071 PMCID: PMC9861059 DOI: 10.3390/v15010032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Revised: 12/14/2022] [Accepted: 12/16/2022] [Indexed: 12/24/2022] Open
Abstract
To complete their replication cycle, retroviruses need to integrate a DNA copy of their RNA genome into a host chromosome. Integration site selection is not random and is driven by multiple viral and cellular host factors specific to different classes of retroviruses. Today, overwhelming evidence from cell culture, animal experiments and clinical data suggests that integration sites are important for retroviral replication, oncogenesis and/or latency. In this review, we will summarize the increasing knowledge of the mechanisms underlying the integration site selection of the gammaretrovirus MLV and the lentivirus HIV-1. We will discuss how host factors of the integration site selection of retroviruses may steer the development of safer viral vectors for gene therapy. Next, we will discuss how altering the integration site preference of HIV-1 using small molecules could lead to a cure for HIV-1 infection.
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Affiliation(s)
| | | | | | - Zeger Debyser
- Molecular Virology and Gene Therapy, KU Leuven, Herestraat 49, 3000 Leuven, Belgium
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12
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Jóźwik IK, Li W, Zhang DW, Wong D, Grawenhoff J, Ballandras-Colas A, Aiyer S, Cherepanov P, Engelman A, Lyumkis D. B-to-A transition in target DNA during retroviral integration. Nucleic Acids Res 2022; 50:8898-8918. [PMID: 35947647 PMCID: PMC9410886 DOI: 10.1093/nar/gkac644] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Revised: 07/06/2022] [Accepted: 07/19/2022] [Indexed: 01/21/2023] Open
Abstract
Integration into host target DNA (tDNA), a hallmark of retroviral replication, is mediated by the intasome, a multimer of integrase (IN) assembled on viral DNA (vDNA) ends. To ascertain aspects of tDNA recognition during integration, we have solved the 3.5 Å resolution cryo-EM structure of the mouse mammary tumor virus (MMTV) strand transfer complex (STC) intasome. The tDNA adopts an A-like conformation in the region encompassing the sites of vDNA joining, which exposes the sugar-phosphate backbone for IN-mediated strand transfer. Examination of existing retroviral STC structures revealed conservation of A-form tDNA in the analogous regions of these complexes. Furthermore, analyses of sequence preferences in genomic integration sites selectively targeted by six different retroviruses highlighted consistent propensity for A-philic sequences at the sites of vDNA joining. Our structure additionally revealed several novel MMTV IN-DNA interactions, as well as contacts seen in prior STC structures, including conserved Pro125 and Tyr149 residues interacting with tDNA. In infected cells, Pro125 substitutions impacted the global pattern of MMTV integration without significantly altering local base sequence preferences at vDNA insertion sites. Collectively, these data advance our understanding of retroviral intasome structure and function, as well as factors that influence patterns of vDNA integration in genomic DNA.
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Affiliation(s)
- Ilona K Jóźwik
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Wen Li
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA
| | - Da-Wei Zhang
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA,Department of Medicine, Harvard Medical School, Boston, MA 02115, USA,Institute of Bioinformatics and Medical Engineering, School of Electrical and Information Engineering, Jiangsu University of Technology, Changzhou 213001, China
| | - Doris Wong
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA
| | - Julia Grawenhoff
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Center, Boston, MA 02215, USA
| | | | - Sriram Aiyer
- The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London NW1 1AT, UK,Department of Infectious Disease, St-Mary's Campus, Imperial College London, London W2 1PG, UK
| | - Alan N Engelman
- Correspondence may also be addressed to Alan N. Engelman. Tel: +1 617 632 4361; Fax: +1 617 632 4338;
| | - Dmitry Lyumkis
- To whom correspondence should be addressed. Tel: +1 858 453 4100 (Ext 1155);
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13
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Grau-Bové X, Navarrete C, Chiva C, Pribasnig T, Antó M, Torruella G, Galindo LJ, Lang BF, Moreira D, López-Garcia P, Ruiz-Trillo I, Schleper C, Sabidó E, Sebé-Pedrós A. A phylogenetic and proteomic reconstruction of eukaryotic chromatin evolution. Nat Ecol Evol 2022; 6:1007-1023. [PMID: 35680998 PMCID: PMC7613034 DOI: 10.1038/s41559-022-01771-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2021] [Accepted: 04/21/2022] [Indexed: 02/06/2023]
Abstract
Histones and associated chromatin proteins have essential functions in eukaryotic genome organization and regulation. Despite this fundamental role in eukaryotic cell biology, we lack a phylogenetically-comprehensive understanding of chromatin evolution. Here, we combine comparative proteomics and genomics analysis of chromatin in eukaryotes and archaea. Proteomics uncovers the existence of histone post-translational modifications in Archaea. However, archaeal histone modifications are scarce, in contrast with the highly conserved and abundant marks we identify across eukaryotes. Phylogenetic analysis reveals that chromatin-associated catalytic functions (e.g., methyltransferases) have pre-eukaryotic origins, whereas histone mark readers and chaperones are eukaryotic innovations. We show that further chromatin evolution is characterized by expansion of readers, including capture by transposable elements and viruses. Overall, our study infers detailed evolutionary history of eukaryotic chromatin: from its archaeal roots, through the emergence of nucleosome-based regulation in the eukaryotic ancestor, to the diversification of chromatin regulators and their hijacking by genomic parasites.
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Affiliation(s)
- Xavier Grau-Bové
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Cristina Navarrete
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | | | - Thomas Pribasnig
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Meritxell Antó
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain
| | - Guifré Torruella
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Luis Javier Galindo
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Bernd Franz Lang
- Robert Cedergren Centre in Bioinformatics and Genomics, Department of Biochemistry, Université de Montréal, Montréal, Quebec, Canada
| | - David Moreira
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Purificación López-Garcia
- Unité d'Ecologie Systématique et Evolution, CNRS, Université Paris-Saclay, AgroParisTech, Orsay, France
| | - Iñaki Ruiz-Trillo
- Institut de Biologia Evolutiva (CSIC-Universitat Pompeu Fabra), Barcelona, Spain.,Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Christa Schleper
- Department of Functional and Evolutionary Ecology, Archaea Biology Unit, University of Vienna, Vienna, Austria
| | - Eduard Sabidó
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain.,Universitat Pompeu Fabra (UPF), Barcelona, Spain
| | - Arnau Sebé-Pedrós
- Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology (BIST), Barcelona, Spain. .,Universitat Pompeu Fabra (UPF), Barcelona, Spain.
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14
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Moretti A, Ponzo M, Nicolette CA, Tcherepanova IY, Biondi A, Magnani CF. The Past, Present, and Future of Non-Viral CAR T Cells. Front Immunol 2022; 13:867013. [PMID: 35757746 PMCID: PMC9218214 DOI: 10.3389/fimmu.2022.867013] [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: 01/31/2022] [Accepted: 04/28/2022] [Indexed: 12/14/2022] Open
Abstract
Adoptive transfer of chimeric antigen receptor (CAR) T lymphocytes is a powerful technology that has revolutionized the way we conceive immunotherapy. The impressive clinical results of complete and prolonged response in refractory and relapsed diseases have shifted the landscape of treatment for hematological malignancies, particularly those of lymphoid origin, and opens up new possibilities for the treatment of solid neoplasms. However, the widening use of cell therapy is hampered by the accessibility to viral vectors that are commonly used for T cell transfection. In the era of messenger RNA (mRNA) vaccines and CRISPR/Cas (clustered regularly interspaced short palindromic repeat-CRISPR-associated) precise genome editing, novel and virus-free methods for T cell engineering are emerging as a more versatile, flexible, and sustainable alternative for next-generation CAR T cell manufacturing. Here, we discuss how the use of non-viral vectors can address some of the limitations of the viral methods of gene transfer and allow us to deliver genetic information in a stable, effective and straightforward manner. In particular, we address the main transposon systems such as Sleeping Beauty (SB) and piggyBac (PB), the utilization of mRNA, and innovative approaches of nanotechnology like Lipid-based and Polymer-based DNA nanocarriers and nanovectors. We also describe the most relevant preclinical data that have recently led to the use of non-viral gene therapy in emerging clinical trials, and the related safety and efficacy aspects. We will also provide practical considerations for future trials to enable successful and safe cell therapy with non-viral methods for CAR T cell generation.
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Affiliation(s)
- Alex Moretti
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), Monza, Italy
| | - Marianna Ponzo
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), Monza, Italy
| | | | | | - Andrea Biondi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), Monza, Italy
- Department of Pediatrics, University of Milano - Bicocca, Milan, Italy
- Clinica Pediatrica, University of Milano - Bicocca/Fondazione MBBM, Monza, Italy
| | - Chiara F. Magnani
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione Monza e Brianza per il Bambino e la sua Mamma (MBBM), Monza, Italy
- Department of Medical Oncology and Hematology, University Hospital Zurich and University of Zurich, Zurich, Switzerland
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15
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Ribeiro-Dos-Santos AM, Hogan MS, Luther RD, Brosh R, Maurano MT. Genomic context sensitivity of insulator function. Genome Res 2022; 32:425-436. [PMID: 35082140 PMCID: PMC8896466 DOI: 10.1101/gr.276449.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2021] [Accepted: 01/25/2022] [Indexed: 11/24/2022]
Abstract
The specificity of interactions between genomic regulatory elements and potential target genes is influenced by the binding of insulator proteins such as CTCF, which can act as potent enhancer blockers when interposed between an enhancer and a promoter in a reporter assay. But not all CTCF sites genome-wide function as insulator elements, depending on cellular and genomic context. To dissect the influence of genomic context on enhancer blocker activity, we integrated reporter constructs with promoter-only, promoter and enhancer, and enhancer blocker configurations at hundreds of thousands of genomic sites using the Sleeping Beauty transposase. Deconvolution of reporter activity by genomic position reveals distinct expression patterns subject to genomic context, including a compartment of enhancer blocker reporter integrations with robust expression. The high density of integration sites permits quantitative delineation of characteristic genomic context sensitivity profiles and their decomposition into sensitivity to both local and distant DNase I hypersensitive sites. Furthermore, using a single-cell expression approach to test the effect of integrated reporters for differential expression of nearby endogenous genes reveals that CTCF insulator elements do not completely abrogate reporter effects on endogenous gene expression. Collectively, our results lend new insight into genomic regulatory compartmentalization and its influence on the determinants of promoter–enhancer specificity.
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Affiliation(s)
| | - Megan S Hogan
- Institute for Systems Genetics, NYU Grossman School of Medicine
| | - Raven D Luther
- Institute for Systems Genetics, NYU Grossman School of Medicine
| | - Ran Brosh
- Institute for Systems Genetics, NYU Grossman School of Medicine
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16
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Miskey C, Kesselring L, Querques I, Abrusán G, Barabas O, Ivics Z. OUP accepted manuscript. Nucleic Acids Res 2022; 50:2807-2825. [PMID: 35188569 PMCID: PMC8934666 DOI: 10.1093/nar/gkac092] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2021] [Revised: 01/24/2022] [Accepted: 02/08/2022] [Indexed: 11/14/2022] Open
Abstract
The Sleeping Beauty (SB) transposon system is a popular tool for genome engineering, but random integration into the genome carries a certain genotoxic risk in therapeutic applications. Here we investigate the role of amino acids H187, P247 and K248 in target site selection of the SB transposase. Structural modeling implicates these three amino acids located in positions analogous to amino acids with established functions in target site selection in retroviral integrases and transposases. Saturation mutagenesis of these residues in the SB transposase yielded variants with altered target site selection properties. Transposon integration profiling of several mutants reveals increased specificity of integrations into palindromic AT repeat target sequences in genomic regions characterized by high DNA bendability. The H187V and K248R mutants redirect integrations away from exons, transcriptional regulatory elements and nucleosomal DNA in the human genome, suggesting enhanced safety and thus utility of these SB variants in gene therapy applications.
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Affiliation(s)
| | | | - Irma Querques
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Biochemistry, University of Zurich, Zurich 8057, Switzerland
| | - György Abrusán
- Institute of Biochemistry, Biological Research Center of the Hungarian Academy of Sciences, Szeged 6726, Hungary
| | - Orsolya Barabas
- Structural and Computational Biology Unit, European Molecular Biology Laboratory, Heidelberg 69117, Germany
- Department of Molecular Biology, University of Geneva, Geneva 1211, Switzerland
| | - Zoltán Ivics
- To whom correspondence should be addressed. Tel: +49 6103 77 6000; Fax: +49 6103 77 1280;
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17
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Dawes JC, Uren AG. Forward and Reverse Genetics of B Cell Malignancies: From Insertional Mutagenesis to CRISPR-Cas. Front Immunol 2021; 12:670280. [PMID: 34484175 PMCID: PMC8414522 DOI: 10.3389/fimmu.2021.670280] [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: 02/20/2021] [Accepted: 07/09/2021] [Indexed: 12/21/2022] Open
Abstract
Cancer genome sequencing has identified dozens of mutations with a putative role in lymphomagenesis and leukemogenesis. Validation of driver mutations responsible for B cell neoplasms is complicated by the volume of mutations worthy of investigation and by the complex ways that multiple mutations arising from different stages of B cell development can cooperate. Forward and reverse genetic strategies in mice can provide complementary validation of human driver genes and in some cases comparative genomics of these models with human tumors has directed the identification of new drivers in human malignancies. We review a collection of forward genetic screens performed using insertional mutagenesis, chemical mutagenesis and exome sequencing and discuss how the high coverage of subclonal mutations in insertional mutagenesis screens can identify cooperating mutations at rates not possible using human tumor genomes. We also compare a set of independently conducted screens from Pax5 mutant mice that converge upon a common set of mutations observed in human acute lymphoblastic leukemia (ALL). We also discuss reverse genetic models and screens that use CRISPR-Cas, ORFs and shRNAs to provide high throughput in vivo proof of oncogenic function, with an emphasis on models using adoptive transfer of ex vivo cultured cells. Finally, we summarize mouse models that offer temporal regulation of candidate genes in an in vivo setting to demonstrate the potential of their encoded proteins as therapeutic targets.
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Affiliation(s)
- Joanna C Dawes
- Medical Research Council, London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
| | - Anthony G Uren
- Medical Research Council, London Institute of Medical Sciences, London, United Kingdom.,Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, London, United Kingdom
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18
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Shahryari A, Burtscher I, Nazari Z, Lickert H. Engineering Gene Therapy: Advances and Barriers. ADVANCED THERAPEUTICS 2021. [DOI: 10.1002/adtp.202100040] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Alireza Shahryari
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- School of Medicine Department of Human Genetics Technical University of Munich Klinikum Rechts der Isar 81675 München Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
- Stem Cell Research Center Golestan University of Medical Sciences Gorgan 49341‐74515 Iran
| | - Ingo Burtscher
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
| | - Zahra Nazari
- Department of Biology School of Basic Sciences Golestan University Gorgan 49361‐79142 Iran
| | - Heiko Lickert
- Institute of Diabetes and Regeneration Research Helmholtz Zentrum München 85764 Neuherberg Germany
- School of Medicine Department of Human Genetics Technical University of Munich Klinikum Rechts der Isar 81675 München Germany
- Institute of Stem Cell Research Helmholtz Zentrum München 85764 Neuherberg Germany
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19
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Zhou Y, Ma G, Yang J, Gao Z, Guo Y. The Integration Preference of Sleeping Beauty at Non-TA Site Is Related to the Transposon End Sequences. Front Genet 2021; 12:639125. [PMID: 33777107 PMCID: PMC7987939 DOI: 10.3389/fgene.2021.639125] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Accepted: 02/17/2021] [Indexed: 11/13/2022] Open
Abstract
Recently, we proved that Sleeping Beauty (SB) transposon integrates into non-TA sites at a lower frequency. Here, we performed a further study on the non-TA integration of SB and showed that (1) SB can integrate into non-TA sites in HEK293T cells as well as in mouse cell lines; (2) Both the hyperactive transposase SB100X and the traditional SB11 catalyze integrations at non-TA sites; (3) The consensus sequence of the non-TA target sites only occurs at the opposite side of the sequenced junction between the transposon end and the genomic sequences, indicating that the integrations at non-TA sites are mainly aberrant integrations; and (4) The consensus sequence of the non-TA target sites is corresponding to the transposon end sequence. The consensus sequences changed following the changes of the transposon ends. This result indicated that the interaction between the SB transposon end and genomic DNA (gDNA) may be involved in the target site selection of the SB integrations at non-TA sites.
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Affiliation(s)
- Yiting Zhou
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Guangwei Ma
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jiawen Yang
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Zenghong Gao
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
| | - Yabin Guo
- Guangdong Provincial Key Laboratory of Malignant Tumor Epigenetics and Gene Regulation, Medical Research Center, Sun Yat-sen Memorial Hospital, Sun Yat-sen University, Guangzhou, China
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20
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Ochmann MT, Ivics Z. Jumping Ahead with Sleeping Beauty: Mechanistic Insights into Cut-and-Paste Transposition. Viruses 2021; 13:76. [PMID: 33429848 PMCID: PMC7827188 DOI: 10.3390/v13010076] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/16/2020] [Accepted: 12/28/2020] [Indexed: 12/13/2022] Open
Abstract
Sleeping Beauty (SB) is a transposon system that has been widely used as a genetic engineering tool. Central to the development of any transposon as a research tool is the ability to integrate a foreign piece of DNA into the cellular genome. Driven by the need for efficient transposon-based gene vector systems, extensive studies have largely elucidated the molecular actors and actions taking place during SB transposition. Close transposon relatives and other recombination enzymes, including retroviral integrases, have served as useful models to infer functional information relevant to SB. Recently obtained structural data on the SB transposase enable a direct insight into the workings of this enzyme. These efforts cumulatively allowed the development of novel variants of SB that offer advanced possibilities for genetic engineering due to their hyperactivity, integration deficiency, or targeting capacity. However, many aspects of the process of transposition remain poorly understood and require further investigation. We anticipate that continued investigations into the structure-function relationships of SB transposition will enable the development of new generations of transposition-based vector systems, thereby facilitating the use of SB in preclinical studies and clinical trials.
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Affiliation(s)
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, 63225 Langen, Germany;
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21
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Magnani CF, Gaipa G, Lussana F, Belotti D, Gritti G, Napolitano S, Matera G, Cabiati B, Buracchi C, Borleri G, Fazio G, Zaninelli S, Tettamanti S, Cesana S, Colombo V, Quaroni M, Cazzaniga G, Rovelli A, Biagi E, Galimberti S, Calabria A, Benedicenti F, Montini E, Ferrari S, Introna M, Balduzzi A, Valsecchi MG, Dastoli G, Rambaldi A, Biondi A. Sleeping Beauty-engineered CAR T cells achieve antileukemic activity without severe toxicities. J Clin Invest 2020; 130:6021-6033. [PMID: 32780725 PMCID: PMC7598053 DOI: 10.1172/jci138473] [Citation(s) in RCA: 88] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/29/2020] [Indexed: 12/27/2022] Open
Abstract
BACKGROUNDChimeric antigen receptor (CAR) T cell immunotherapy has resulted in complete remission (CR) and durable response in highly refractory patients. However, logistical complexity and high costs of manufacturing autologous viral products limit CAR T cell availability.METHODSWe report the early results of a phase I/II trial in B cell acute lymphoblastic leukemia (B-ALL) patients relapsed after allogeneic hematopoietic stem cell transplantation (HSCT) using donor-derived CD19 CAR T cells generated with the Sleeping Beauty (SB) transposon and differentiated into cytokine-induced killer (CIK) cells.RESULTSThe cellular product was produced successfully for all patients from the donor peripheral blood (PB) and consisted mostly of CD3+ lymphocytes with 43% CAR expression. Four pediatric and 9 adult patients were infused with a single dose of CAR T cells. Toxicities reported were 2 grade I and 1 grade II cytokine-release syndrome (CRS) cases at the highest dose in the absence of graft-versus-host disease (GVHD), neurotoxicity, or dose-limiting toxicities. Six out of 7 patients receiving the highest doses achieved CR and CR with incomplete blood count recovery (CRi) at day 28. Five out of 6 patients in CR were also minimal residual disease negative (MRD-). Robust expansion was achieved in the majority of the patients. CAR T cells were measurable by transgene copy PCR up to 10 months. Integration site analysis showed a positive safety profile and highly polyclonal repertoire in vitro and at early time points after infusion.CONCLUSIONSB-engineered CAR T cells expand and persist in pediatric and adult B-ALL patients relapsed after HSCT. Antileukemic activity was achieved without severe toxicities.TRIAL REGISTRATIONClinicalTrials.gov NCT03389035.FUNDINGThis study was supported by grants from the Fondazione AIRC per la Ricerca sul Cancro (AIRC); Cancer Research UK (CRUK); the Fundación Científica de la Asociación Española Contra el Cáncer (FC AECC); Ministero Della Salute; Fondazione Regionale per la Ricerca Biomedica (FRRB).
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Affiliation(s)
- Chiara F. Magnani
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Giuseppe Gaipa
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Federico Lussana
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Daniela Belotti
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
- Department of Pediatrics, University of Milano–Bicocca, Milan, Italy
| | - Giuseppe Gritti
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Sara Napolitano
- Clinica Pediatrica, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Giada Matera
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Benedetta Cabiati
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Chiara Buracchi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Gianmaria Borleri
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Grazia Fazio
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | | | - Sarah Tettamanti
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Stefania Cesana
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Valentina Colombo
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Michele Quaroni
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
| | - Giovanni Cazzaniga
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Attilio Rovelli
- Clinica Pediatrica, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Ettore Biagi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Clinica Pediatrica, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Stefania Galimberti
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre, Department of Medicine and Surgery, University of Milano–Bicocca, Milan, Italy
| | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET)/IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Fabrizio Benedicenti
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET)/IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (SR-TIGET)/IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Silvia Ferrari
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
| | - Martino Introna
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
- USS Centro di Terapia Cellulare “G. Lanzani,” Bergamo, Italy
| | - Adriana Balduzzi
- Department of Pediatrics, University of Milano–Bicocca, Milan, Italy
- Clinica Pediatrica, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Maria Grazia Valsecchi
- Bicocca Bioinformatics, Biostatistics and Bioimaging Centre, Department of Medicine and Surgery, University of Milano–Bicocca, Milan, Italy
| | - Giuseppe Dastoli
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
| | - Alessandro Rambaldi
- Hematology and Bone Marrow Transplant Unit, ASST Papa Giovanni XXIII, Bergamo, Italy
- Department of Oncology and Hematology, University of Milan, Milan, Italy
| | - Andrea Biondi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
- Laboratorio di Terapia Cellulare e Genica Stefano Verri, ASST-Monza, Ospedale San Gerardo, Monza, Italy
- Clinica Pediatrica, University of Milano-Bicocca/Fondazione MBBM, Monza, Italy
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22
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Weber J, Braun CJ, Saur D, Rad R. In vivo functional screening for systems-level integrative cancer genomics. Nat Rev Cancer 2020; 20:573-593. [PMID: 32636489 DOI: 10.1038/s41568-020-0275-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 05/19/2020] [Indexed: 02/06/2023]
Abstract
With the genetic portraits of all major human malignancies now available, we next face the challenge of characterizing the function of mutated genes, their downstream targets, interactions and molecular networks. Moreover, poorly understood at the functional level are also non-mutated but dysregulated genomes, epigenomes or transcriptomes. Breakthroughs in manipulative mouse genetics offer new opportunities to probe the interplay of molecules, cells and systemic signals underlying disease pathogenesis in higher organisms. Herein, we review functional screening strategies in mice using genetic perturbation and chemical mutagenesis. We outline the spectrum of genetic tools that exist, such as transposons, CRISPR and RNAi and describe discoveries emerging from their use. Genome-wide or targeted screens are being used to uncover genomic and regulatory landscapes in oncogenesis, metastasis or drug resistance. Versatile screening systems support experimentation in diverse genetic and spatio-temporal settings to integrate molecular, cellular or environmental context-dependencies. We also review the combination of in vivo screening and barcoding strategies to study genetic interactions and quantitative cancer dynamics during tumour evolution. These scalable functional genomics approaches are transforming our ability to interrogate complex biological systems.
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Affiliation(s)
- Julia Weber
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
| | - Christian J Braun
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany
- Department of Pediatrics, Dr. von Hauner Children's Hospital, University Hospital, LMU Munich, Munich, Germany
- Hopp Children's Cancer Center Heidelberg (KiTZ), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dieter Saur
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany
- Institute of Translational Cancer Research and Experimental Cancer Therapy, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, TUM School of Medicine, Technische Universität München, Munich, Germany.
- Center for Translational Cancer Research (TranslaTUM), TUM School of Medicine, Technische Universität München, Munich, Germany.
- Department of Medicine II, Klinikum rechts der Isar, Technische Universität München, Munich, Germany.
- German Cancer Consortium (DKTK), German Cancer Research Center (DKFZ), Heidelberg, Germany.
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23
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Abstract
The mouse is one of the most widely used model organisms for genetic study. The tools available to alter the mouse genome have developed over the preceding decades from forward screens to gene targeting in stem cells to the recent influx of CRISPR approaches. In this review, we first consider the history of mice in genetic study, the development of classic approaches to genome modification, and how such approaches have been used and improved in recent years. We then turn to the recent surge of nuclease-mediated techniques and how they are changing the field of mouse genetics. Finally, we survey common classes of alleles used in mice and discuss how they might be engineered using different methods.
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Affiliation(s)
- James F Clark
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Colin J Dinsmore
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
| | - Philippe Soriano
- Department of Cell, Developmental, and Regenerative Biology, Icahn School of Medicine at Mt. Sinai, New York, New York 10029, USA
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24
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Campos TL, Korhonen PK, Hofmann A, Gasser RB, Young ND. Combined use of feature engineering and machine-learning to predict essential genes in Drosophila melanogaster. NAR Genom Bioinform 2020; 2:lqaa051. [PMID: 33575603 PMCID: PMC7671374 DOI: 10.1093/nargab/lqaa051] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Revised: 06/05/2020] [Accepted: 07/04/2020] [Indexed: 12/17/2022] Open
Abstract
Characterizing genes that are critical for the survival of an organism (i.e. essential) is important to gain a deep understanding of the fundamental cellular and molecular mechanisms that sustain life. Functional genomic investigations of the vinegar fly, Drosophila melanogaster, have unravelled the functions of numerous genes of this model species, but results from phenomic experiments can sometimes be ambiguous. Moreover, the features underlying gene essentiality are poorly understood, posing challenges for computational prediction. Here, we harnessed comprehensive genomic-phenomic datasets publicly available for D. melanogaster and a machine-learning-based workflow to predict essential genes of this fly. We discovered strong predictors of such genes, paving the way for computational predictions of essentiality in less-studied arthropod pests and vectors of infectious diseases.
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Affiliation(s)
- Tulio L Campos
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Pasi K Korhonen
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Andreas Hofmann
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Robin B Gasser
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Neil D Young
- Department of Veterinary Biosciences, Melbourne Veterinary School, The University of Melbourne, Parkville, Victoria 3010, Australia
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25
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Zhang X, Zhao M, McCarty DR, Lisch D. Transposable elements employ distinct integration strategies with respect to transcriptional landscapes in eukaryotic genomes. Nucleic Acids Res 2020; 48:6685-6698. [PMID: 32442316 PMCID: PMC7337890 DOI: 10.1093/nar/gkaa370] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2019] [Revised: 04/24/2020] [Accepted: 04/29/2020] [Indexed: 12/27/2022] Open
Abstract
Transposable elements (TEs) are ubiquitous DNA segments capable of moving from one site to another within host genomes. The extant distributions of TEs in eukaryotic genomes have been shaped by both bona fide TE integration preferences in eukaryotic genomes and by selection following integration. Here, we compare TE target site distribution in host genomes using multiple de novo transposon insertion datasets in both plants and animals and compare them in the context of genome-wide transcriptional landscapes. We showcase two distinct types of transcription-associated TE targeting strategies that suggest a process of convergent evolution among eukaryotic TE families. The integration of two precision-targeting elements are specifically associated with initiation of RNA Polymerase II transcription of highly expressed genes, suggesting the existence of novel mechanisms of precision TE targeting in addition to passive targeting of open chromatin. We also highlight two features that can facilitate TE survival and rapid proliferation: tissue-specific transposition and minimization of negative impacts on nearby gene function due to precision targeting.
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Affiliation(s)
- Xinyan Zhang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
| | - Meixia Zhao
- Department of Biology, Miami University, Oxford, OH 45056, USA
| | - Donald R McCarty
- Horticultural Sciences Department, University of Florida, Gainesville, FL 32611, USA
| | - Damon Lisch
- Department of Botany and Plant Pathology, Purdue University, West Lafayette, IN 47907, USA
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26
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Rotiroti MC, Buracchi C, Arcangeli S, Galimberti S, Valsecchi MG, Perriello VM, Rasko T, Alberti G, Magnani CF, Cappuzzello C, Lundberg F, Pande A, Dastoli G, Introna M, Serafini M, Biagi E, Izsvák Z, Biondi A, Tettamanti S. Targeting CD33 in Chemoresistant AML Patient-Derived Xenografts by CAR-CIK Cells Modified with an Improved SB Transposon System. Mol Ther 2020; 28:1974-1986. [PMID: 32526203 DOI: 10.1016/j.ymthe.2020.05.021] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 03/31/2020] [Accepted: 05/26/2020] [Indexed: 12/20/2022] Open
Abstract
The successful implementation of chimeric antigen receptor (CAR)-T cell therapy in the clinical context of B cell malignancies has paved the way for further development in the more critical setting of acute myeloid leukemia (AML). Among the potentially targetable AML antigens, CD33 is insofar one of the main validated molecules. Here, we describe the feasibility of engineering cytokine-induced killer (CIK) cells with a CD33.CAR by using the latest optimized version of the non-viral Sleeping Beauty (SB) transposon system "SB100X-pT4." This offers the advantage of improving CAR expression on CIK cells, while reducing the amount of DNA transposase as compared to the previously employed "SB11-pT" version. SB-modified CD33.CAR-CIK cells exhibited significant antileukemic activity in vitro and in vivo in patient-derived AML xenograft models, reducing AML development when administered as an "early treatment" and delaying AML progression in mice with established disease. Notably, by exploiting an already optimized xenograft chemotherapy model that mimics human induction therapy in mice, we demonstrated for the first time that CD33.CAR-CIK cells are also effective toward chemotherapy resistant/residual AML cells, further supporting its future clinical development and implementation within the current standard regimens.
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Affiliation(s)
- Maria Caterina Rotiroti
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Chiara Buracchi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Silvia Arcangeli
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Stefania Galimberti
- Center of Biostatistics for Clinical Epidemiology, School of Medicine and Surgery, University of Milano - Bicocca, 20900 Monza, Italy
| | - Maria Grazia Valsecchi
- Center of Biostatistics for Clinical Epidemiology, School of Medicine and Surgery, University of Milano - Bicocca, 20900 Monza, Italy
| | - Vincenzo Maria Perriello
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy; Università degli Studi di Perugia, 06123 Perugia, Italy
| | - Tamas Rasko
- Max-Delbrück-Centrum für Molekulare Medizin in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Gaia Alberti
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Chiara Francesca Magnani
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Claudia Cappuzzello
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Felix Lundberg
- Max-Delbrück-Centrum für Molekulare Medizin in the Helmholtz Association (MDC), 13125 Berlin, Germany; The Milner Centre for Evolution, University of Bath, BA2 7AY Bath, UK
| | - Amit Pande
- Max-Delbrück-Centrum für Molekulare Medizin in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Giuseppe Dastoli
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Martino Introna
- Center of Cellular Therapy "G. Lanzani," USC Ematologia ASST Papa Giovanni XXIII, 24124 Bergamo, Italy
| | - Marta Serafini
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Ettore Biagi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
| | - Zsuzsanna Izsvák
- Max-Delbrück-Centrum für Molekulare Medizin in the Helmholtz Association (MDC), 13125 Berlin, Germany
| | - Andrea Biondi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy.
| | - Sarah Tettamanti
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca/Fondazione MBBM, 20900 Monza, Italy
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27
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Tschorn N, Berg K, Stitz J. Transposon vector-mediated stable gene transfer for the accelerated establishment of recombinant mammalian cell pools allowing for high-yield production of biologics. Biotechnol Lett 2020; 42:1103-1112. [PMID: 32323079 PMCID: PMC7275939 DOI: 10.1007/s10529-020-02889-y] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2019] [Accepted: 04/13/2020] [Indexed: 12/11/2022]
Abstract
Stable recombinant mammalian cells are of growing importance in pharmaceutical biotechnology production scenarios for biologics such as monoclonal antibodies, growth and blood factors, cytokines and subunit vaccines. However, the establishment of recombinant producer cells using classical stable transfection of plasmid DNA is hampered by low stable gene transfer efficiencies. Consequently, subsequent selection of transgenic cells and the screening of clonal cell populations are time- and thus cost-intensive. To overcome these limitations, expression cassettes were embedded into transposon-derived donor vectors. Upon the co-transfection with transposase-encoding constructs, elevated vector copy numbers stably integrated into the genomes of the host cells are readily achieved facilitating under stringent selection pressure the establishment of cell pools characterized by sustained and high-yield recombinant protein production. Here, we discuss some aspects of transposon vector technologies, which render these vectors promising candidates for their further utilization in the production of biologics.
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Affiliation(s)
- Natalie Tschorn
- Research Group Pharmaceutical Biotechnology, TH Köln - University of Applied Sciences, Chempark Leverkusen E28, Kaiser-Wilhelm-Allee, 51368, Leverkusen, Germany.,Institute of Technical Chemistry, Leibniz University Hannover, Hannover, Germany
| | - Karen Berg
- Research Group Pharmaceutical Biotechnology, TH Köln - University of Applied Sciences, Chempark Leverkusen E28, Kaiser-Wilhelm-Allee, 51368, Leverkusen, Germany.,Research Group Translational Hepatology and Stem Cell Biology, Cluster of Excellence REBIRTH, Department of Gastroenterology, Hepatology, and Endocrinology, Hannover Medical School, Hannover, Germany
| | - Jörn Stitz
- Research Group Pharmaceutical Biotechnology, TH Köln - University of Applied Sciences, Chempark Leverkusen E28, Kaiser-Wilhelm-Allee, 51368, Leverkusen, Germany.
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28
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de Macedo Abdo L, Barros LRC, Saldanha Viegas M, Vieira Codeço Marques L, de Sousa Ferreira P, Chicaybam L, Bonamino MH. Development of CAR-T cell therapy for B-ALL using a point-of-care approach. Oncoimmunology 2020; 9:1752592. [PMID: 32363126 PMCID: PMC7185214 DOI: 10.1080/2162402x.2020.1752592] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2019] [Revised: 03/31/2020] [Accepted: 03/31/2020] [Indexed: 12/31/2022] Open
Abstract
Recently approved by the FDA and European Medicines Agency, CAR-T cell therapy is a new treatment option for B-cell malignancies. Currently, CAR-T cells are manufactured in centralized facilities and face bottlenecks like complex scaling up, high costs, and logistic operations. These difficulties are mainly related to the use of viral vectors and the requirement to expand CAR-T cells to reach the therapeutic dose. In this paper, by using Sleeping Beauty-mediated genetic modification delivered by electroporation, we show that CAR-T cells can be generated and used without the need for ex vivo activation and expansion, consistent with a point-of-care (POC) approach. Our results show that minimally manipulated CAR-T cells are effective in vivo against RS4;11 leukemia cells engrafted in NSG mice even when inoculated after only 4 h of gene transfer. In an effort to better characterize the infused CAR-T cells, we show that 19BBz T lymphocytes infused after 24 h of electroporation (where CAR expression is already detectable) can improve the overall survival and reduce tumor burden in organs of mice engrafted with RS4;11 or Nalm-6 B cell leukemia. A side-by-side comparison of POC approach with a conventional 8-day expansion protocol using Transact beads demonstrated that both approaches have equivalent antitumor activity in vivo. Our data suggest that POC approach is a viable alternative for the generation and use of CAR-T cells, overcoming the limitations of current manufacturing protocols. Its use has the potential to expand CAR immunotherapy to a higher number of patients, especially in the context of low-income countries.
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Affiliation(s)
- Luiza de Macedo Abdo
- Immunology and Tumor Biology Program - Research Coordination, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | | | - Mariana Saldanha Viegas
- Immunology and Tumor Biology Program - Research Coordination, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Luisa Vieira Codeço Marques
- Immunology and Tumor Biology Program - Research Coordination, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Priscila de Sousa Ferreira
- Immunology and Tumor Biology Program - Research Coordination, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil
| | - Leonardo Chicaybam
- Vice-Presidency of Research and Biological Collections (VPPCB), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
| | - Martín Hernán Bonamino
- Immunology and Tumor Biology Program - Research Coordination, Brazilian National Cancer Institute (INCA), Rio de Janeiro, Brazil.,Vice-Presidency of Research and Biological Collections (VPPCB), Oswaldo Cruz Foundation (FIOCRUZ), Rio de Janeiro, Brazil
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29
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Dawes JC, Webster P, Iadarola B, Garcia-Diaz C, Dore M, Bolt BJ, Dewchand H, Dharmalingam G, McLatchie AP, Kaczor J, Caceres JJ, Paccanaro A, Game L, Parrinello S, Uren AG. LUMI-PCR: an Illumina platform ligation-mediated PCR protocol for integration site cloning, provides molecular quantitation of integration sites. Mob DNA 2020; 11:7. [PMID: 32042315 PMCID: PMC7001329 DOI: 10.1186/s13100-020-0201-4] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2019] [Accepted: 01/08/2020] [Indexed: 12/21/2022] Open
Abstract
BACKGROUND Ligation-mediated PCR protocols have diverse uses including the identification of integration sites of insertional mutagens, integrating vectors and naturally occurring mobile genetic elements. For approaches that employ NGS sequencing, the relative abundance of integrations within a complex mixture is typically determined through the use of read counts or unique fragment lengths from a ligation of sheared DNA; however, these estimates may be skewed by PCR amplification biases and saturation of sequencing coverage. RESULTS Here we describe a modification of our previous splinkerette based ligation-mediated PCR using a novel Illumina-compatible adapter design that prevents amplification of non-target DNA and incorporates unique molecular identifiers. This design reduces the number of PCR cycles required and improves relative quantitation of integration abundance for saturating sequencing coverage. By inverting the forked adapter strands from a standard orientation, the integration-genome junction can be sequenced without affecting the sequence diversity required for cluster generation on the flow cell. Replicate libraries of murine leukemia virus-infected spleen samples yielded highly reproducible quantitation of clonal integrations as well as a deep coverage of subclonal integrations. A dilution series of DNAs bearing integrations of MuLV or piggyBac transposon shows linearity of the quantitation over a range of concentrations. CONCLUSIONS Merging ligation and library generation steps can reduce total PCR amplification cycles without sacrificing coverage or fidelity. The protocol is robust enough for use in a 96 well format using an automated liquid handler and we include programs for use of a Beckman Biomek liquid handling workstation. We also include an informatics pipeline that maps reads, builds integration contigs and quantitates integration abundance using both fragment lengths and unique molecular identifiers. Suggestions for optimizing the protocol to other target DNA sequences are included. The reproducible distinction of clonal and subclonal integration sites from each other allows for analysis of populations of cells undergoing selection, such as those found in insertional mutagenesis screens.
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Affiliation(s)
- Joanna C. Dawes
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Philip Webster
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
- Imperial College Healthcare NHS Trust, London, UK
| | - Barbara Iadarola
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Claudia Garcia-Diaz
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, WC1E 6DD, London, UK
| | - Marian Dore
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Bruce J. Bolt
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Hamlata Dewchand
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Gopuraja Dharmalingam
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | | | - Jakub Kaczor
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Juan J. Caceres
- Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, London, UK
| | - Alberto Paccanaro
- Centre for Systems and Synthetic Biology, Department of Computer Science, Royal Holloway, University of London, London, UK
| | - Laurence Game
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
| | - Simona Parrinello
- Samantha Dickson Brain Cancer Unit, UCL Cancer Institute, WC1E 6DD, London, UK
| | - Anthony G. Uren
- MRC London Institute of Medical Sciences (LMS), Du Cane Road, London, W12 0NN UK
- Institute of Clinical Sciences (ICS), Faculty of Medicine, Imperial College London, Du Cane Road, London, UK
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30
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Tellier M, Chalmers R. Human SETMAR is a DNA sequence-specific histone-methylase with a broad effect on the transcriptome. Nucleic Acids Res 2019; 47:122-133. [PMID: 30329085 PMCID: PMC6326780 DOI: 10.1093/nar/gky937] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2018] [Accepted: 10/12/2018] [Indexed: 12/26/2022] Open
Abstract
Transposons impart dynamism to the genomes they inhabit and their movements frequently rewire the control of nearby genes. Occasionally, their proteins are domesticated when they evolve a new function. SETMAR is a protein methylase with a sequence-specific DNA binding domain. It began to evolve about 50 million years ago when an Hsmar1 transposon integrated downstream of a SET-domain methylase gene. Here we show that the DNA-binding domain of the transposase targets the enzyme to transposon-end remnants and that this is capable of regulating gene expression, dependent on the methylase activity. When SETMAR was modestly overexpressed in human cells, almost 1500 genes changed expression by more than 2-fold (65% up- and 35% down-regulated). These genes were enriched for the KEGG Pathways in Cancer and include several transcription factors important for development and differentiation. Expression of a similar level of a methylase-deficient SETMAR changed the expression of many fewer genes, 77% of which were down-regulated with no significant enrichment of KEGG Pathways. Our data is consistent with a model in which SETMAR is part of an anthropoid primate-specific regulatory network centered on the subset of genes containing a transposon end.
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Affiliation(s)
- Michael Tellier
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
| | - Ronald Chalmers
- School of Life Sciences, University of Nottingham, Queen's Medical Centre, Nottingham NG7 2UH, UK
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31
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Huang BJ, Wandler AM, Meyer LK, Dail M, Daemen A, Sampath D, Li Q, Wang X, Wong JC, Nakitandwe J, Downing JR, Zhang J, Taylor BS, Shannon K. Convergent genetic aberrations in murine and human T lineage acute lymphoblastic leukemias. PLoS Genet 2019; 15:e1008168. [PMID: 31199785 PMCID: PMC6594654 DOI: 10.1371/journal.pgen.1008168] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2019] [Revised: 06/26/2019] [Accepted: 04/29/2019] [Indexed: 12/22/2022] Open
Abstract
The lack of predictive preclinical models is a fundamental barrier to translating knowledge about the molecular pathogenesis of cancer into improved therapies. Insertional mutagenesis (IM) in mice is a robust strategy for generating malignancies that recapitulate the extensive inter- and intra-tumoral genetic heterogeneity found in advanced human cancers. While the central role of "driver" viral insertions in IM models that aberrantly increase the expression of proto-oncogenes or disrupt tumor suppressors has been appreciated for many years, the contributions of cooperating somatic mutations and large chromosomal alterations to tumorigenesis are largely unknown. Integrated genomic studies of T lineage acute lymphoblastic leukemias (T-ALLs) generated by IM in wild-type (WT) and Kras mutant mice reveal frequent point mutations and other recurrent non-insertional genetic alterations that also occur in human T-ALL. These somatic mutations are sensitive and specific markers for defining clonal dynamics and identifying candidate resistance mechanisms in leukemias that relapse after an initial therapeutic response. Primary cancers initiated by IM and resistant clones that emerge during in vivo treatment close key gaps in existing preclinical models, and are robust platforms for investigating the efficacy of new therapies and for elucidating how drug exposure shapes tumor evolution and patterns of resistance. A lack of predictive cancer models is a major bottleneck for prioritizing new anti-cancer drugs for clinical trials. We comprehensively profiled a panel of primary mouse T lineage leukemias initiated by insertional mutagenesis and found remarkable similarities with human T-ALL in regard to overall mutational burden, the occurrence of specific somatic mutations and large chromosomal alterations, and concordant gene expression signatures. We observed frequent duplication of the Kras oncogene with loss of the normal allele, which has potential therapeutic implications that merit further investigation in human leukemia and in other preclinical models. Mutations identified in mouse leukemias that relapsed after in vivo treatment with signal transduction inhibitors were also observed in relapsed human T-ALL, indicating that this model system can be utilized to investigate strategies for overcoming intrinsic and acquired drug resistance. Finally, preclinical models similar to the one described here that are characterized by a normal endogenous tumor microenvironment and intact immune system will become increasingly important for testing immunotherapy approaches for human cancer.
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Affiliation(s)
- Benjamin J. Huang
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States of America
| | - Anica M. Wandler
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States of America
| | - Lauren K. Meyer
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States of America
| | - Monique Dail
- Department of Oncology Biomarker Development, Genentech, South San Francisco, CA, United States of America
| | - Anneleen Daemen
- Department of Bioinformatics & Computational Biology, Genentech, South San Francisco, CA, United States of America
| | - Deepak Sampath
- Department of Translational Oncology, Genentech, South San Francisco, CA, United States of America
| | - Qing Li
- Division of Hematology/Oncology, Department of Medicine, University of Michigan, Ann Arbor, MI, United States of America
| | - Xinyue Wang
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States of America
| | - Jasmine C. Wong
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States of America
| | - Joy Nakitandwe
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - James R. Downing
- Department of Pathology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Jinghui Zhang
- Department of Computational Biology, St Jude Children’s Research Hospital, Memphis, Tennessee, United States of America
| | - Barry S. Taylor
- Marie-Josée and Henry R. Kravis Center for Molecular Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Human Oncology and Pathogenesis Program, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY, United States of America
| | - Kevin Shannon
- Department of Pediatrics, University of California San Francisco, San Francisco, CA, United States of America
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, United States of America
- * E-mail:
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32
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Leemans C, van der Zwalm MCH, Brueckner L, Comoglio F, van Schaik T, Pagie L, van Arensbergen J, van Steensel B. Promoter-Intrinsic and Local Chromatin Features Determine Gene Repression in LADs. Cell 2019; 177:852-864.e14. [PMID: 30982597 PMCID: PMC6506275 DOI: 10.1016/j.cell.2019.03.009] [Citation(s) in RCA: 84] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Revised: 01/23/2019] [Accepted: 03/04/2019] [Indexed: 12/28/2022]
Abstract
It is largely unclear whether genes that are naturally embedded in lamina-associated domains (LADs) are inactive due to their chromatin environment or whether LADs are merely secondary to the lack of transcription. We show that hundreds of human promoters become active when moved from their native LAD position to a neutral context in the same cells, indicating that LADs form a repressive environment. Another set of promoters inside LADs is able to "escape" repression, although their transcription elongation is attenuated. By inserting reporters into thousands of genomic locations, we demonstrate that escaper promoters are intrinsically less sensitive to LAD repression. This is not simply explained by promoter strength but by the interplay between promoter sequence and local chromatin features that vary strongly across LADs. Enhancers also differ in their sensitivity to LAD chromatin. This work provides a general framework for the systematic understanding of gene regulation by repressive chromatin.
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Affiliation(s)
- Christ Leemans
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Marloes C H van der Zwalm
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Laura Brueckner
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Federico Comoglio
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Tom van Schaik
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Ludo Pagie
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Joris van Arensbergen
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Bas van Steensel
- Division of Gene Regulation and Oncode Institute, Netherlands Cancer Institute, Amsterdam, the Netherlands.
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33
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Gisler S, Gonçalves JP, Akhtar W, de Jong J, Pindyurin AV, Wessels LFA, van Lohuizen M. Multiplexed Cas9 targeting reveals genomic location effects and gRNA-based staggered breaks influencing mutation efficiency. Nat Commun 2019; 10:1598. [PMID: 30962441 PMCID: PMC6453899 DOI: 10.1038/s41467-019-09551-w] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Accepted: 03/14/2019] [Indexed: 12/16/2022] Open
Abstract
Understanding the impact of guide RNA (gRNA) and genomic locus on CRISPR-Cas9 activity is crucial to design effective gene editing assays. However, it is challenging to profile Cas9 activity in the endogenous cellular environment. Here we leverage our TRIP technology to integrate ~ 1k barcoded reporter genes in the genomes of mouse embryonic stem cells. We target the integrated reporters (IRs) using RNA-guided Cas9 and characterize induced mutations by sequencing. We report that gRNA-sequence and IR locus explain most variation in mutation efficiency. Predominant insertions of a gRNA-specific nucleotide are consistent with template-dependent repair of staggered DNA ends with 1-bp 5' overhangs. We confirm that such staggered ends are induced by Cas9 in mouse pre-B cells. To explain observed insertions, we propose a model generating primarily blunt and occasionally staggered DNA ends. Mutation patterns indicate that gRNA-sequence controls the fraction of staggered ends, which could be used to optimize Cas9-based insertion efficiency.
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Affiliation(s)
- Santiago Gisler
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Joana P Gonçalves
- Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Waseem Akhtar
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Johann de Jong
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
- Data & Translational Sciences Group, UCB Biosciences GmbH, Alfred-Nobel-Straße 10, Monheim am Rhein, 40789, Germany
| | - Alexey V Pindyurin
- Institute of Molecular and Cellular Biology, Siberian Branch of Russian Academy of Sciences, Acad. Lavrentiev Ave. 8, Novosibirsk, 630090, Russia
- Division of Gene Regulation, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands
| | - Lodewyk F A Wessels
- Department of Intelligent Systems, Delft University of Technology, Van Mourik Broekmanweg 6, Delft, 2628 XE, The Netherlands.
- Division of Molecular Carcinogenesis, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
| | - Maarten van Lohuizen
- Division of Molecular Genetics, Oncode and The Netherlands Cancer Institute, Plesmanlaan 121, Amsterdam, 1066 CX, The Netherlands.
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34
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Schumann GG, Fuchs NV, Tristán-Ramos P, Sebe A, Ivics Z, Heras SR. The impact of transposable element activity on therapeutically relevant human stem cells. Mob DNA 2019; 10:9. [PMID: 30899334 PMCID: PMC6408843 DOI: 10.1186/s13100-019-0151-x] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2018] [Accepted: 02/27/2019] [Indexed: 12/11/2022] Open
Abstract
Human stem cells harbor significant potential for basic and clinical translational research as well as regenerative medicine. Currently ~ 3000 adult and ~ 30 pluripotent stem cell-based, interventional clinical trials are ongoing worldwide, and numbers are increasing continuously. Although stem cells are promising cell sources to treat a wide range of human diseases, there are also concerns regarding potential risks associated with their clinical use, including genomic instability and tumorigenesis concerns. Thus, a deeper understanding of the factors and molecular mechanisms contributing to stem cell genome stability are a prerequisite to harnessing their therapeutic potential for degenerative diseases. Chemical and physical factors are known to influence the stability of stem cell genomes, together with random mutations and Copy Number Variants (CNVs) that accumulated in cultured human stem cells. Here we review the activity of endogenous transposable elements (TEs) in human multipotent and pluripotent stem cells, and the consequences of their mobility for genomic integrity and host gene expression. We describe transcriptional and post-transcriptional mechanisms antagonizing the spread of TEs in the human genome, and highlight those that are more prevalent in multipotent and pluripotent stem cells. Notably, TEs do not only represent a source of mutations/CNVs in genomes, but are also often harnessed as tools to engineer the stem cell genome; thus, we also describe and discuss the most widely applied transposon-based tools and highlight the most relevant areas of their biomedical applications in stem cells. Taken together, this review will contribute to the assessment of the risk that endogenous TE activity and the application of genetically engineered TEs constitute for the biosafety of stem cells to be used for substitutive and regenerative cell therapies.
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Affiliation(s)
- Gerald G Schumann
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Nina V Fuchs
- 2Host-Pathogen Interactions, Paul-Ehrlich-Institut, Paul-Ehrlich-Str. 51-59, 63225 Langen, Germany
| | - Pablo Tristán-Ramos
- 3GENYO. Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada-Avenida de la Ilustración, 114, 18016 Granada, Spain.,4Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
| | - Attila Sebe
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Zoltán Ivics
- 1Division of Medical Biotechnology, Paul-Ehrlich-Institut, Paul-Ehrlich-Str.51-59, 63225 Langen, Germany
| | - Sara R Heras
- 3GENYO. Centre for Genomics and Oncological Research, Pfizer/University of Granada/Andalusian Regional Government, PTS Granada-Avenida de la Ilustración, 114, 18016 Granada, Spain.,4Department of Biochemistry and Molecular Biology II, Faculty of Pharmacy, University of Granada, Campus Universitario de Cartuja, 18071 Granada, Spain
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Abstract
Cancer is a complex disease that originates from genetic changes leading to multiple phenotypic manifestations that ultimately result in suffering and death from cancer. Attempts have been made to define the phenotypic and genetic "hallmarks" of cancer, but many of these "hallmarks" remain descriptive, while the underlying mechanisms responsible for these hallmarks remain elusive. For decades, cancer researchers have been methodically identifying the molecular mechanisms that result in tumor initiation, growth, metastases, and resistance to therapy. Great strides forward have been made and we are entering an era of "precision medicine" with the goal of treating each cancer based on its unique etiology. Increasingly, the decision to use targeted therapies and immunotherapies in the clinic is based on the genotype of the cancer being treated. For example, specific tyrosine kinase inhibitors are only prescribed to patients that express the tyrosine kinase protein on their cancer cells. Likewise, a genetically unstable cancer is predictive for successful immunotherapy. Knowledge of the specific genetic changes that result in overproduction of oncogenes and reduced production of tumor suppressors is crucial for advancing therapeutic options for cancer. The first chapter of this book presents a brief history of cancer gene discovery. In the remaining chapters of this book, we present protocols using in silico, in vitro, and in vivo techniques for identifying genetic drivers of cancer, in the hope that these protocols will be used to increase our knowledge of the molecular mechanisms driving cancer.
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36
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Abstract
While sequencing and array-based studies are creating catalogues of genetic alterations in cancer, discriminating cancer drivers among the large sets of epigenetically, transcriptionally or posttranslationally dysregulated genes remains a challenge. Transposon-based genetic screening in mice has proven to be a powerful approach to address this challenge. Insertional mutagenesis directly flags biologically relevant genes and, combined with the transposon's unique molecular fingerprint, facilitates the recovery of insertion sites. We have generated transgenic mouse lines harboring different versions of PiggyBac-based oncogenic transposons, which in conjunction with PiggyBac transposase mice can be used for whole-body or tissue-specific insertional mutagenesis screens. We have also developed QiSeq, a method for (semi-)quantitative transposon insertion site sequencing, which overcomes biasing limitations of previous library preparation methods. QiSeq can be used in multiplexed high-throughput formats for candidate cancer gene discovery and gives insights into the clonal distribution of insertions for the study of genetic tumor evolution.
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37
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Guimaraes-Young A, Feddersen CR, Dupuy AJ. Sleeping Beauty Mouse Models of Cancer: Microenvironmental Influences on Cancer Genetics. Front Oncol 2019; 9:611. [PMID: 31338332 PMCID: PMC6629774 DOI: 10.3389/fonc.2019.00611] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2019] [Accepted: 06/21/2019] [Indexed: 12/13/2022] Open
Abstract
The Sleeping Beauty (SB) transposon insertional mutagenesis system offers a streamlined approach to identify genetic drivers of cancer. With a relatively random insertion profile, SB is uniquely positioned for conducting unbiased forward genetic screens. Indeed, SB mouse models of cancer have revealed insights into the genetics of tumorigenesis. In this review, we highlight experiments that have exploited the SB system to interrogate the genetics of cancer in distinct biological contexts. We also propose experimental designs that could further our understanding of the relationship between tumor microenvironment and tumor progression.
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Affiliation(s)
- Amy Guimaraes-Young
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Charlotte R Feddersen
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, Roy J. and Lucille A. Carver College of Medicine, University of Iowa, Iowa City, IA, United States
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38
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Reich DP, Bass BL. Inverted repeat structures are associated with essential and highly expressed genes on C. elegans autosome distal arms. RNA (NEW YORK, N.Y.) 2018; 24:1634-1646. [PMID: 30190375 PMCID: PMC6239182 DOI: 10.1261/rna.067405.118] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Accepted: 08/30/2018] [Indexed: 06/08/2023]
Abstract
Complementary sequences in cellular transcripts base-pair to form double-stranded RNA (dsRNA) structures. Because transposon-derived repeats often give rise to self-complementary sequences, dsRNA structures are prevalent in eukaryotic genomes, typically occurring in gene introns and untranslated regions (UTRs). However, the regulatory impact of double-stranded structures within genes is not fully understood. We used three independent methods to define loci in Caenorhabditis elegans predicted to form dsRNA and correlated these structures with patterns of gene expression, gene essentiality, and genome organization. As previously observed, dsRNA loci are enriched on distal arms of C. elegans autosomes, where genes typically show less conservation and lower overall expression. In contrast, we find that dsRNAs are associated with essential genes on autosome arms, and dsRNA-associated genes exhibit higher-than-expected expression and histone modification patterns associated with transcriptional elongation. Genes with significant repetitive sequence content are also highly expressed, and, thus, observed gene expression trends may relate either to dsRNA structures or to repeat content. Our results raise the possibility that as-yet-undescribed mechanisms promote expression of loci that produce dsRNAs, despite their well-characterized roles in gene silencing.
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Affiliation(s)
- Daniel P Reich
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Brenda L Bass
- Department of Biochemistry, University of Utah, Salt Lake City, Utah 84112, USA
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Magnani CF, Turazzi N, Benedicenti F, Calabria A, Tenderini E, Tettamanti S, Giordano Attianese GMP, Cooper LJN, Aiuti A, Montini E, Biondi A, Biagi E. Immunotherapy of acute leukemia by chimeric antigen receptor-modified lymphocytes using an improved Sleeping Beauty transposon platform. Oncotarget 2018; 7:51581-51597. [PMID: 27323395 PMCID: PMC5239498 DOI: 10.18632/oncotarget.9955] [Citation(s) in RCA: 42] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2016] [Accepted: 05/20/2016] [Indexed: 12/20/2022] Open
Abstract
Chimeric antigen receptor (CAR)-modified T-cell adoptive immunotherapy is a remarkable therapeutic option proven effective in the treatment of hematological malignancies. In order to optimize cell manufacturing, we sought to develop a novel clinical-grade protocol to obtain CAR-modified cytokine-induced killer cells (CIKs) using the Sleeping Beauty (SB) transposon system. Administration of irradiated PBMCs overcame cell death of stimulating cells induced by non-viral transfection, enabling robust gene transfer together with efficient T-cell expansion. Upon single stimulation, we reached an average of 60% expression of CD123- and CD19- specific 3rd generation CARs (CD28/OX40/TCRzeta). Furthermore, modified cells displayed persistence of cell subsets with memory phenotype, specific and effective lytic activity against leukemic cell lines and primary blasts, cytokine secretion, and proliferation. Adoptive transfer of CD123.CAR or CD19.CAR lymphocytes led to a significant anti-tumor response against acute myelogenous leukemia (AML) and acute lymphoblastic leukemia (ALL) disseminated diseases in NSG mice. Notably, we found no evidence of integration enrichment near cancer genes and transposase expression at the end of the differentiation. Taken all together, our findings describe a novel donor-derived non-viral CAR approach that may widen the repertoire of available methods for T cell-based immunotherapy.
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Affiliation(s)
- Chiara F Magnani
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca, San Gerardo Hospital/Fondazione MBBM, Monza, Italy
| | - Nice Turazzi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca, San Gerardo Hospital/Fondazione MBBM, Monza, Italy
| | | | - Andrea Calabria
- San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET), Milan, Italy
| | - Erika Tenderini
- San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET), Milan, Italy
| | - Sarah Tettamanti
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca, San Gerardo Hospital/Fondazione MBBM, Monza, Italy
| | - Greta M P Giordano Attianese
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca, San Gerardo Hospital/Fondazione MBBM, Monza, Italy.,University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | | | - Alessandro Aiuti
- San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET), Milan, Italy
| | - Eugenio Montini
- San Raffaele Telethon Institute for Gene Therapy (HSR-TIGET), Milan, Italy
| | - Andrea Biondi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca, San Gerardo Hospital/Fondazione MBBM, Monza, Italy
| | - Ettore Biagi
- Tettamanti Research Center, Department of Pediatrics, University of Milano-Bicocca, San Gerardo Hospital/Fondazione MBBM, Monza, Italy
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40
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Kawakami K, Largaespada DA, Ivics Z. Transposons As Tools for Functional Genomics in Vertebrate Models. Trends Genet 2017; 33:784-801. [PMID: 28888423 DOI: 10.1016/j.tig.2017.07.006] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Revised: 07/14/2017] [Accepted: 07/18/2017] [Indexed: 02/06/2023]
Abstract
Genetic tools and mutagenesis strategies based on transposable elements are currently under development with a vision to link primary DNA sequence information to gene functions in vertebrate models. By virtue of their inherent capacity to insert into DNA, transposons can be developed into powerful tools for chromosomal manipulations. Transposon-based forward mutagenesis screens have numerous advantages including high throughput, easy identification of mutated alleles, and providing insight into genetic networks and pathways based on phenotypes. For example, the Sleeping Beauty transposon has become highly instrumental to induce tumors in experimental animals in a tissue-specific manner with the aim of uncovering the genetic basis of diverse cancers. Here, we describe a battery of mutagenic cassettes that can be applied in conjunction with transposon vectors to mutagenize genes, and highlight versatile experimental strategies for the generation of engineered chromosomes for loss-of-function as well as gain-of-function mutagenesis for functional gene annotation in vertebrate models, including zebrafish, mice, and rats.
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Affiliation(s)
- Koichi Kawakami
- Division of Molecular and Developmental Biology, National Institute of Genetics, Mishima, Japan; These authors contributed equally to this work
| | - David A Largaespada
- Department of Genetics, Cell Biology and Development, University of Minnesota, MN, USA; These authors contributed equally to this work
| | - Zoltán Ivics
- Division of Medical Biotechnology, Paul Ehrlich Institute, Langen, Germany; These authors contributed equally to this work..
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41
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Bryner D, Criscione S, Leith A, Huynh Q, Huffer F, Neretti N. GINOM: A statistical framework for assessing interval overlap of multiple genomic features. PLoS Comput Biol 2017; 13:e1005586. [PMID: 28617797 PMCID: PMC5491313 DOI: 10.1371/journal.pcbi.1005586] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2016] [Revised: 06/29/2017] [Accepted: 05/20/2017] [Indexed: 11/18/2022] Open
Abstract
A common problem in genomics is to test for associations between two or more genomic features, typically represented as intervals interspersed across the genome. Existing methodologies can test for significant pairwise associations between two genomic intervals; however, they cannot test for associations involving multiple sets of intervals. This limits our ability to uncover more complex, yet biologically important associations between multiple sets of genomic features. We introduce GINOM (Genomic INterval Overlap Model), a new method that enables testing of significant associations between multiple genomic features. We demonstrate GINOM’s ability to identify higher-order associations with both simulated and real data. In particular, we used GINOM to explore L1 retrotransposable element insertion bias in lung cancer and found a significant pairwise association between L1 insertions and heterochromatic marks. Unlike other methods, GINOM also detected an association between L1 insertions and gene bodies marked by a facultative heterochromatic mark, which could explain the observed bias for L1 insertions towards cancer-associated genes. The age of genomics has made a large number of datasets available for the wider scientific community. Many of these datasets come in the form of genomics tracks, represented as features associated with a collections of genomic intervals along chromosomes. A common talk in genomics is to identify putative associations between these features that can lead to new insights about genome organization and function. For example, activity of certain classes of genes might be influenced by the presence of specific combinations of chromatin modifications and binding of transcription factors at their promoters or enhancers. Here, we present a novel methodology, named GINOM (Genomic INterval Overlap Model), to test for the significance of these associations. We apply it to the problem of detecting biases of the locations along chromosomes where mobile genetic elements tend to insert themselves, and identify a potential preference for L1 elements towards gene bodies marked by a facultative heterochromatic mark.
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Affiliation(s)
- Darshan Bryner
- Naval Surface Warfare Center Panama City Division, Panama City, Florida, United States of America
| | - Stephen Criscione
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
| | - Andrew Leith
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
| | - Quyen Huynh
- Institute for Brain and Neural Systems, Brown University, Providence, Rhode Island, United States of America
| | - Fred Huffer
- Department of Statistics, Florida State University, Tallahassee, Florida, United States of America
| | - Nicola Neretti
- Department of Molecular Biology, Cell Biology and Biochemistry, Brown University, Providence, Rhode Island, United States of America
- Center for Computational Molecular Biology, Brown University, Providence, Rhode Island, United States of America
- * E-mail:
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42
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Yoshida J, Akagi K, Misawa R, Kokubu C, Takeda J, Horie K. Chromatin states shape insertion profiles of the piggyBac, Tol2 and Sleeping Beauty transposons and murine leukemia virus. Sci Rep 2017; 7:43613. [PMID: 28252665 PMCID: PMC5333637 DOI: 10.1038/srep43613] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2016] [Accepted: 01/26/2017] [Indexed: 12/31/2022] Open
Abstract
DNA transposons and retroviruses are versatile tools in functional genomics and gene therapy. To facilitate their application, we conducted a genome-wide insertion site profiling of the piggyBac (PB), Tol2 and Sleeping Beauty (SB) transposons and the murine leukemia virus (MLV) in mouse embryonic stem cells (ESCs). PB and MLV preferred highly expressed genes, whereas Tol2 and SB preferred weakly expressed genes. However, correlations with DNase I hypersensitive sites were different for all vectors, indicating that chromatin accessibility is not the sole determinant. Therefore, we analysed various chromatin states. PB and MLV highly correlated with Cohesin, Mediator and ESC-specific transcription factors. Notably, CTCF sites were correlated with PB but not with MLV, suggesting MLV prefers smaller promoter-enhancer loops, whereas PB insertion encompasses larger chromatin loops termed topologically associating domains. Tol2 also correlated with Cohesin and CTCF. However, correlations with ESC-specific transcription factors were weaker, suggesting that Tol2 prefers transcriptionally weak chromatin loops. Consistently, Tol2 insertions were associated with bivalent histone modifications characteristic of silent and inducible loci. SB showed minimum preference to all chromatin states, suggesting the least adverse effect on adjacent genes. These results will be useful for vector selection for various applications.
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Affiliation(s)
- Junko Yoshida
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan.,Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Keiko Akagi
- Comprehensive Cancer Center, Ohio State University, Columbus, Ohio 43210, USA
| | - Ryo Misawa
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan
| | - Chikara Kokubu
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Junji Takeda
- Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan
| | - Kyoji Horie
- Department of Physiology II, Nara Medical University, Kashihara, Nara 634-8521, Japan.,Department of Genome Biology, Graduate School of Medicine, Osaka University, Suita, Osaka 565-0871, Japan.,Precursory Research for Embryonic Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama 332-0012, Japan
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43
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Retroviruses integrate into a shared, non-palindromic DNA motif. Nat Microbiol 2016; 2:16212. [PMID: 27841853 DOI: 10.1038/nmicrobiol.2016.212] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Accepted: 09/21/2016] [Indexed: 12/12/2022]
Abstract
Many DNA-binding factors, such as transcription factors, form oligomeric complexes with structural symmetry that bind to palindromic DNA sequences1. Palindromic consensus nucleotide sequences are also found at the genomic integration sites of retroviruses2-6 and other transposable elements7-9, and it has been suggested that this palindromic consensus arises as a consequence of the structural symmetry in the integrase complex2,3. However, we show here that the palindromic consensus sequence is not present in individual integration sites of human T-cell lymphotropic virus type 1 (HTLV-1) and human immunodeficiency virus type 1 (HIV-1), but arises in the population average as a consequence of the existence of a non-palindromic nucleotide motif that occurs in approximately equal proportions on the plus strand and the minus strand of the host genome. We develop a generally applicable algorithm to sort the individual integration site sequences into plus-strand and minus-strand subpopulations, and use this to identify the integration site nucleotide motifs of five retroviruses of different genera: HTLV-1, HIV-1, murine leukaemia virus (MLV), avian sarcoma leucosis virus (ASLV) and prototype foamy virus (PFV). The results reveal a non-palindromic motif that is shared between these retroviruses.
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44
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Brueckner L, van Arensbergen J, Akhtar W, Pagie L, van Steensel B. High-throughput assessment of context-dependent effects of chromatin proteins. Epigenetics Chromatin 2016; 9:43. [PMID: 27777628 PMCID: PMC5069885 DOI: 10.1186/s13072-016-0096-y] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2016] [Accepted: 09/27/2016] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Chromatin proteins control gene activity in a concerted manner. We developed a high-throughput assay to study the effects of the local chromatin environment on the regulatory activity of a protein of interest. The assay combines a previously reported multiplexing strategy based on barcoded randomly integrated reporters with Gal4-mediated tethering. We applied the assay to Drosophila heterochromatin protein 1a (HP1a), which is mostly known as a repressive protein but has also been linked to transcriptional activation. RESULTS Recruitment to over 1000 genomic locations revealed that HP1a is a potent repressor able to silence even highly expressing reporter genes. However, the local chromatin context can modulate HP1a function. In pericentromeric regions, HP1a-induced repression was enhanced by twofold. In regions marked by a H3K36me3-rich chromatin signature, HP1a-dependent silencing was significantly decreased. We found no evidence for an activating function of HP1a in our experimental system. Furthermore, we did not observe stable transmission of repression over mitotic divisions after loss of targeted HP1a. CONCLUSIONS The multiplexed tethered reporter assay should be applicable to a large number of chromatin proteins and will be a useful tool to dissect combinatorial regulatory interactions in chromatin.
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Affiliation(s)
- Laura Brueckner
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Joris van Arensbergen
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Waseem Akhtar
- Division of Molecular Genetics, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Ludo Pagie
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Bas van Steensel
- Division of Gene Regulation, Netherlands Cancer Institute, Amsterdam, The Netherlands
- Department of Cell Biology, Erasmus University Medical Center, Rotterdam, The Netherlands
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45
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Narayanavari SA, Chilkunda SS, Ivics Z, Izsvák Z. Sleeping Beauty transposition: from biology to applications. Crit Rev Biochem Mol Biol 2016; 52:18-44. [PMID: 27696897 DOI: 10.1080/10409238.2016.1237935] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Sleeping Beauty (SB) is the first synthetic DNA transposon that was shown to be active in a wide variety of species. Here, we review studies from the last two decades addressing both basic biology and applications of this transposon. We discuss how host-transposon interaction modulates transposition at different steps of the transposition reaction. We also discuss how the transposon was translated for gene delivery and gene discovery purposes. We critically review the system in clinical, pre-clinical and non-clinical settings as a non-viral gene delivery tool in comparison with viral technologies. We also discuss emerging SB-based hybrid vectors aimed at combining the attractive safety features of the transposon with effective viral delivery. The success of the SB-based technology can be fundamentally attributed to being able to insert fairly randomly into genomic regions that allow stable long-term expression of the delivered transgene cassette. SB has emerged as an efficient and economical toolkit for safe and efficient gene delivery for medical applications.
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Affiliation(s)
- Suneel A Narayanavari
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Shreevathsa S Chilkunda
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
| | - Zoltán Ivics
- b Division of Medical Biotechnology , Paul Ehrlich Institute , Langen , Germany
| | - Zsuzsanna Izsvák
- a Mobile DNA , Max Delbrück Center for Molecular Medicine in the Helmholtz Association (MDC) , Berlin , Germany
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46
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Babu D, Fullwood MJ. 3D genome organization in health and disease: emerging opportunities in cancer translational medicine. Nucleus 2016; 6:382-93. [PMID: 26553406 PMCID: PMC4915485 DOI: 10.1080/19491034.2015.1106676] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Organizing the DNA to fit inside a spatially constrained nucleus is a challenging problem that has attracted the attention of scientists across all disciplines of science. Increasing evidence has demonstrated the importance of genome geometry in several cellular contexts that affect human health. Among several approaches, the application of sequencing technologies has substantially increased our understanding of this intricate organization, also known as chromatin interactions. These structures are involved in transcriptional control of gene expression by connecting distal regulatory elements with their target genes and regulating co-transcriptional splicing. In addition, chromatin interactions play pivotal roles in the organization of the genome, the formation of structural variants, recombination, DNA replication and cell division. Mutations in factors that regulate chromatin interactions lead to the development of pathological conditions, for example, cancer. In this review, we discuss key findings that have shed light on the importance of these structures in the context of cancers, and highlight the applicability of chromatin interactions as potential biomarkers in molecular medicine as well as therapeutic implications of chromatin interactions.
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Affiliation(s)
- Deepak Babu
- a Cancer Science Institute of Singapore: Singapore; National University of Singapore ; Singapore
| | - Melissa J Fullwood
- a Cancer Science Institute of Singapore: Singapore; National University of Singapore ; Singapore.,b School of Biological Sciences; Nanyang Technological University ; Singapore.,c Institute of Molecular and Cell Biology; Agency for Science; Technology and Research (A*STAR) ; Singapore.,d Yale-NUS Liberal Arts College ; Singapore
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47
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Enhanced CAR T-cell engineering using non-viral Sleeping Beauty transposition from minicircle vectors. Leukemia 2016; 31:186-194. [PMID: 27491640 DOI: 10.1038/leu.2016.180] [Citation(s) in RCA: 169] [Impact Index Per Article: 21.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2016] [Revised: 06/08/2016] [Accepted: 06/10/2016] [Indexed: 12/28/2022]
Abstract
Immunotherapy with T cell modified with gamma-retroviral or lentiviral (LV) vectors to express a chimeric antigen receptor (CAR) has shown remarkable efficacy in clinical trials. However, the potential for insertional mutagenesis and genotoxicity of viral vectors is a safety concern, and their cost and regulatory demands a roadblock for rapid and broad clinical translation. Here, we demonstrate that CAR T cells can be engineered through non-viral Sleeping Beauty (SB) transposition of CAR genes from minimalistic DNA vectors called minicircles (MCs). We analyzed genomic distribution of SB and LV integrations and show that a significantly higher proportion of MC-derived CAR transposons compared with LV integrants had occurred outside of highly expressed and cancer-related genes into genomic safe harbor loci that are not expected to cause mutagenesis or genotoxicity. CD19-CAR T cells engineered with our enhanced SB approach conferred potent reactivity in vitro and eradicated lymphoma in a xenograft model in vivo. Intriguingly, electroporation of SB MCs is substantially more effective and less toxic compared with conventional plasmids, and enables cost-effective rapid preparation of therapeutic CAR T-cell doses. This approach sets a new standard in advanced cellular and gene therapy and will accelerate and increase the availability of CAR T-cell therapy to treat hematologic malignancies.
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48
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Campos-Sánchez R, Cremona MA, Pini A, Chiaromonte F, Makova KD. Integration and Fixation Preferences of Human and Mouse Endogenous Retroviruses Uncovered with Functional Data Analysis. PLoS Comput Biol 2016; 12:e1004956. [PMID: 27309962 PMCID: PMC4911145 DOI: 10.1371/journal.pcbi.1004956] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2016] [Accepted: 04/29/2016] [Indexed: 01/24/2023] Open
Abstract
Endogenous retroviruses (ERVs), the remnants of retroviral infections in the germ line, occupy ~8% and ~10% of the human and mouse genomes, respectively, and affect their structure, evolution, and function. Yet we still have a limited understanding of how the genomic landscape influences integration and fixation of ERVs. Here we conducted a genome-wide study of the most recently active ERVs in the human and mouse genome. We investigated 826 fixed and 1,065 in vitro HERV-Ks in human, and 1,624 fixed and 242 polymorphic ETns, as well as 3,964 fixed and 1,986 polymorphic IAPs, in mouse. We quantitated >40 human and mouse genomic features (e.g., non-B DNA structure, recombination rates, and histone modifications) in ±32 kb of these ERVs' integration sites and in control regions, and analyzed them using Functional Data Analysis (FDA) methodology. In one of the first applications of FDA in genomics, we identified genomic scales and locations at which these features display their influence, and how they work in concert, to provide signals essential for integration and fixation of ERVs. The investigation of ERVs of different evolutionary ages (young in vitro and polymorphic ERVs, older fixed ERVs) allowed us to disentangle integration vs. fixation preferences. As a result of these analyses, we built a comprehensive model explaining the uneven distribution of ERVs along the genome. We found that ERVs integrate in late-replicating AT-rich regions with abundant microsatellites, mirror repeats, and repressive histone marks. Regions favoring fixation are depleted of genes and evolutionarily conserved elements, and have low recombination rates, reflecting the effects of purifying selection and ectopic recombination removing ERVs from the genome. In addition to providing these biological insights, our study demonstrates the power of exploiting multiple scales and localization with FDA. These powerful techniques are expected to be applicable to many other genomic investigations.
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Affiliation(s)
- Rebeca Campos-Sánchez
- Genetics Graduate Program, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America
| | - Marzia A. Cremona
- MOX—Modeling and Scientific Computing, Department of Mathematics, Politecnico di Milano, Milano, Italy
- Department of Statistics, Penn State University, University Park, Pennsylvania, United States of America
| | - Alessia Pini
- MOX—Modeling and Scientific Computing, Department of Mathematics, Politecnico di Milano, Milano, Italy
| | - Francesca Chiaromonte
- Department of Statistics, Penn State University, University Park, Pennsylvania, United States of America
- Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America
| | - Kateryna D. Makova
- Center for Medical Genomics, The Huck Institutes of the Life Sciences, Penn State University, University Park, Pennsylvania, United States of America
- Department of Biology, Penn State University, University Park, Pennsylvania, United States of America
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49
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Smith RP, Riordan JD, Feddersen CR, Dupuy AJ. A Hybrid Adenoviral Vector System Achieves Efficient Long-Term Gene Expression in the Liver via piggyBac Transposition. Hum Gene Ther 2016; 26:377-85. [PMID: 25808258 DOI: 10.1089/hum.2014.123] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Abstract
Much research has gone into the development of hybrid gene delivery systems that combine the broad tropism and efficient transduction of adenoviral vectors with the ability to achieve stable expression of cargo genes. In addition to gene therapy applications, such a system has considerable advantages for studies of gene function in vivo, permitting fine-tuned genetic manipulation with higher throughput than can be achieved using standard transgenic and DNA targeting techniques. Existing strategies are limited, however, by low integration efficiencies, small cargo capacity, and/or a dependence on target cell division. The utility of this approach could be enhanced by a system that provides all of the following: (1) efficient delivery, (2) stable expression in a high percentage of target cells (whether mitotic or not), (3) large cargo capacity, (4) flexibility to use with a wide range of additional experimental conditions, and (5) simple experimental technique. Here we report the initial characterization of a hybrid system that meets these criteria by utilizing piggyBac (PB) transposition to achieve genomic integration from adenoviral vectors. We demonstrate stable expression of an adenovirus (Ad)-PB-delivered reporter gene in ∼20-40% of hepatocytes following standard tail vein injection. Its high efficiency and flexibility relative to existing hybrid adenoviral gene delivery approaches indicate a considerable potential utility of the Ad-PB system for therapeutic gene delivery and in vivo studies of gene function.
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Affiliation(s)
- Ryan P Smith
- Department of Anatomy and Cell Biology, Roy J. & Lucille A. Carver College of Medicine, University of Iowa , Iowa City, IA 52242
| | - Jesse D Riordan
- Department of Anatomy and Cell Biology, Roy J. & Lucille A. Carver College of Medicine, University of Iowa , Iowa City, IA 52242
| | - Charlotte R Feddersen
- Department of Anatomy and Cell Biology, Roy J. & Lucille A. Carver College of Medicine, University of Iowa , Iowa City, IA 52242
| | - Adam J Dupuy
- Department of Anatomy and Cell Biology, Roy J. & Lucille A. Carver College of Medicine, University of Iowa , Iowa City, IA 52242
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50
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Genome-Wide Analysis of Transposon and Retroviral Insertions Reveals Preferential Integrations in Regions of DNA Flexibility. G3-GENES GENOMES GENETICS 2016; 6:805-17. [PMID: 26818075 PMCID: PMC4825651 DOI: 10.1534/g3.115.026849] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
DNA transposons and retroviruses are important transgenic tools for genome engineering. An important consideration affecting the choice of transgenic vector is their insertion site preferences. Previous large-scale analyses of Ds transposon integration sites in plants were done on the basis of reporter gene expression or germ-line transmission, making it difficult to discern vertebrate integration preferences. Here, we compare over 1300 Ds transposon integration sites in zebrafish with Tol2 transposon and retroviral integration sites. Genome-wide analysis shows that Ds integration sites in the presence or absence of marker selection are remarkably similar and distributed throughout the genome. No strict motif was found, but a preference for structural features in the target DNA associated with DNA flexibility (Twist, Tilt, Rise, Roll, Shift, and Slide) was observed. Remarkably, this feature is also found in transposon and retroviral integrations in maize and mouse cells. Our findings show that structural features influence the integration of heterologous DNA in genomes, and have implications for targeted genome engineering.
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