1
|
Luo AC, Wang J, Wang K, Zhu Y, Gong L, Lee U, Li X, Tremmel DM, Lin RZ, Ingber DE, Gorman J, Melero-Martin JM. A streamlined method to generate endothelial cells from human pluripotent stem cells via transient doxycycline-inducible ETV2 activation. Angiogenesis 2024:10.1007/s10456-024-09937-5. [PMID: 38969874 DOI: 10.1007/s10456-024-09937-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2024] [Accepted: 06/28/2024] [Indexed: 07/07/2024]
Abstract
The development of reliable methods for producing functional endothelial cells (ECs) is crucial for progress in vascular biology and regenerative medicine. In this study, we present a streamlined and efficient methodology for the differentiation of human induced pluripotent stem cells (iPSCs) into induced ECs (iECs) that maintain the ability to undergo vasculogenesis in vitro and in vivo using a doxycycline-inducible system for the transient expression of the ETV2 transcription factor. This approach mitigates the limitations of direct transfection methods, such as mRNA-mediated differentiation, by simplifying the protocol and enhancing reproducibility across different stem cell lines. We detail the generation of iPSCs engineered for doxycycline-induced ETV2 expression and their subsequent differentiation into iECs, achieving over 90% efficiency within four days. Through both in vitro and in vivo assays, the functionality and phenotypic stability of the derived iECs were rigorously validated. Notably, these cells exhibit key endothelial markers and capabilities, including the formation of vascular networks in a microphysiological platform in vitro and in a subcutaneous mouse model. Furthermore, our results reveal a close transcriptional and proteomic alignment between the iECs generated via our method and primary ECs, confirming the biological relevance of the differentiated cells. The high efficiency and effectiveness of our induction methodology pave the way for broader application and accessibility of iPSC-derived ECs in scientific research, offering a valuable tool for investigating endothelial biology and for the development of EC-based therapies.
Collapse
Affiliation(s)
- Allen Chilun Luo
- Department of Cardiac Surgery, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
| | - Jiuhai Wang
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Kai Wang
- Department of Cardiac Surgery, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Yonglin Zhu
- Department of Cardiac Surgery, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Liyan Gong
- Department of Cardiac Surgery, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Umji Lee
- Department of Cardiac Surgery, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Xiang Li
- Department of Cardiac Surgery, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Daniel M Tremmel
- Department of Cardiac Surgery, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Ruei-Zeng Lin
- Department of Cardiac Surgery, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA
- Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA
| | - Donald E Ingber
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
- Vascular Biology Program, Boston Children's Hospital, Boston, MA, 02115, USA
- Harvard John A. Paulson School of Engineering and Applied Sciences, Cambridge, MA, 02138, USA
| | - James Gorman
- Wyss Institute for Biologically Inspired Engineering, Harvard University, Boston, MA, 02215, USA
| | - Juan M Melero-Martin
- Department of Cardiac Surgery, Boston Children's Hospital, 300 Longwood Ave, Boston, MA, 02115, USA.
- Department of Surgery, Harvard Medical School, Boston, MA, 02115, USA.
- Harvard Stem Cell Institute, Cambridge, MA, 02138, USA.
| |
Collapse
|
2
|
Li S, Ling S, Wang D, Wang X, Hao F, Yin L, Yuan Z, Liu L, Zhang L, Li Y, Chen Y, Luo L, Dai Y, Zhang L, Chen L, Deng D, Tang W, Zhang S, Wang S, Cai Y. Modified lentiviral globin gene therapy for pediatric β 0/β 0 transfusion-dependent β-thalassemia: A single-center, single-arm pilot trial. Cell Stem Cell 2024; 31:961-973.e8. [PMID: 38759653 DOI: 10.1016/j.stem.2024.04.021] [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: 07/28/2023] [Revised: 01/24/2024] [Accepted: 04/24/2024] [Indexed: 05/19/2024]
Abstract
β0/β0 thalassemia is the most severe type of transfusion-dependent β-thalassemia (TDT) and is still a challenge facing lentiviral gene therapy. Here, we report the interim analysis of a single-center, single-arm pilot trial (NCT05015920) evaluating the safety and efficacy of a β-globin expression-optimized and insulator-engineered lentivirus-modified cell product (BD211) in β0/β0 TDT. Two female children were enrolled, infused with BD211, and followed up for an average of 25.5 months. Engraftment of genetically modified hematopoietic stem and progenitor cells was successful and sustained in both patients. No unexpected safety issues occurred during conditioning or after infusion. Both patients achieved transfusion independence for over 22 months. The treatment extended the lifespan of red blood cells by over 42 days. Single-cell DNA/RNA-sequencing analysis of the dynamic changes of gene-modified cells, transgene expression, and oncogene activation showed no notable adverse effects. Optimized lentiviral gene therapy may safely and effectively treat all β-thalassemia.
Collapse
Affiliation(s)
- Shiqi Li
- 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China, Kunming, Yunnan 650100, China
| | - Sikai Ling
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China; BDgene Therapeutics, Shanghai 200240, China
| | - Dawei Wang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | | | | | - Liufan Yin
- Sequanta Technologies, Shanghai 200131, China
| | - Zhongtao Yuan
- 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China, Kunming, Yunnan 650100, China
| | - Lin Liu
- 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China, Kunming, Yunnan 650100, China
| | - Lin Zhang
- BDgene Therapeutics, Shanghai 200240, China
| | - Yu Li
- 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China, Kunming, Yunnan 650100, China
| | - Yingnian Chen
- 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China, Kunming, Yunnan 650100, China
| | - Le Luo
- 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China, Kunming, Yunnan 650100, China
| | - Ying Dai
- 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China, Kunming, Yunnan 650100, China
| | - Lihua Zhang
- 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China, Kunming, Yunnan 650100, China
| | - Lvzhe Chen
- 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China, Kunming, Yunnan 650100, China
| | | | - Wei Tang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Sujiang Zhang
- Shanghai Institute of Hematology, State Key Laboratory of Medical Genomics, National Research Center for Translational Medicine at Shanghai, Ruijin Hospital Affiliated to Shanghai Jiao Tong University School of Medicine, Shanghai 200025, China
| | - Sanbin Wang
- 920th Hospital of Joint Logistics Support Force of People's Liberation Army of China, Kunming, Yunnan 650100, China.
| | - Yujia Cai
- Key Laboratory of Systems Biomedicine (Ministry of Education), Shanghai Center for Systems Biomedicine, Shanghai Jiao Tong University, Shanghai 200240, China.
| |
Collapse
|
3
|
Meenakshi Sundaram DN, Bahadur K C R, Fu W, Uludağ H. An optimized polymeric delivery system for piggyBac transposition. Biotechnol Bioeng 2024; 121:1503-1517. [PMID: 38372658 DOI: 10.1002/bit.28665] [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: 09/30/2023] [Revised: 12/14/2023] [Accepted: 01/17/2024] [Indexed: 02/20/2024]
Abstract
The piggyBac transposon/transposase system has been explored for long-term, stable gene expression to execute genomic integration of therapeutic genes, thus emerging as a strong alternative to viral transduction. Most studies with piggyBac transposition have employed physical methods for successful delivery of the necessary components of the piggyBac system into the cells. Very few studies have explored polymeric gene delivery systems. In this short communication, we report an effective delivery system based on low molecular polyethylenimine polymer with lipid substitution (PEI-L) capable of delivering three components, (i) a piggyBac transposon plasmid DNA carrying a gene encoding green fluorescence protein (PB-GFP), (ii) a piggyBac transposase plasmid DNA or mRNA, and (iii) a 2 kDa polyacrylic acid as additive for transfection enhancement, all in a single complex. We demonstrate an optimized formulation for stable GFP expression in two model cell lines, MDA-MB-231 and SUM149 recorded till day 108 (3.5 months) and day 43 (1.4 months), respectively, following a single treatment with very low cell number as starting material. Moreover, the stability of the transgene (GFP) expression mediated by piggyBac/PEI-L transposition was retained following three consecutive cryopreservation cycles. The success of this study highlights the feasibility and potential of employing a polymeric delivery system to obtain piggyBac-based stable expression of therapeutic genes.
Collapse
Affiliation(s)
| | - Remant Bahadur K C
- Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, Alberta, Canada
| | - Wei Fu
- Institute of Pediatric Translational Medicine, Shanghai Children's Medical Center, Shanghai Jiao Tong University, Shanghai, China
| | - Hasan Uludağ
- Department of Chemical and Materials Engineering, Faculty of Engineering, University of Alberta, Edmonton, Alberta, Canada
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, Alberta, Canada
| |
Collapse
|
4
|
Tian J, Tong D, Li Z, Wang E, Yu Y, Lv H, Hu Z, Sun F, Wang G, He M, Xia T. Mage transposon: a novel gene delivery system for mammalian cells. Nucleic Acids Res 2024; 52:2724-2739. [PMID: 38300794 PMCID: PMC10954464 DOI: 10.1093/nar/gkae048] [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: 09/14/2023] [Revised: 01/10/2024] [Accepted: 01/22/2024] [Indexed: 02/03/2024] Open
Abstract
Transposons, as non-viral integration vectors, provide a secure and efficient method for stable gene delivery. In this study, we have discovered Mage (MG), a novel member of the piggyBac(PB) family, which exhibits strong transposability in a variety of mammalian cells and primary T cells. The wild-type MG showed a weaker insertion preference for near genes, transcription start sites (TSS), CpG islands, and DNaseI hypersensitive sites in comparison to PB, approaching the random insertion pattern. Utilizing in silico virtual screening and feasible combinatorial mutagenesis in vitro, we effectively produced the hyperactive MG transposase (hyMagease). This variant boasts a transposition rate 60% greater than its native counterpart without significantly altering its insertion pattern. Furthermore, we applied the hyMagease to efficiently deliver chimeric antigen receptor (CAR) into T cells, leading to stable high-level expression and inducing significant anti-tumor effects both in vitro and in xenograft mice models. These findings provide a compelling tool for gene transfer research, emphasizing its potential and prospects in the domains of genetic engineering and gene therapy.
Collapse
Affiliation(s)
- Jinghan Tian
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Doudou Tong
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | | | - Erqiang Wang
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Yifei Yu
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Hangya Lv
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Zhendan Hu
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Fang Sun
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Guoping Wang
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
| | - Min He
- Elongevity Inc, Wuhan, Hubei 430000, China
| | - Tian Xia
- Institute of Pathology, Department of Pathology, School of Basic Medicine, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei 430030, China
- School of Artificial Intelligence and Automation, Huazhong University of Science and Technology, Wuhan, Hubei 430074, China
| |
Collapse
|
5
|
Levstek L, Janžič L, Ihan A, Kopitar AN. Biomarkers for prediction of CAR T therapy outcomes: current and future perspectives. Front Immunol 2024; 15:1378944. [PMID: 38558801 PMCID: PMC10979304 DOI: 10.3389/fimmu.2024.1378944] [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: 01/30/2024] [Accepted: 03/04/2024] [Indexed: 04/04/2024] Open
Abstract
Chimeric antigen receptor (CAR) T cell therapy holds enormous potential for the treatment of hematologic malignancies. Despite its benefits, it is still used as a second line of therapy, mainly because of its severe side effects and patient unresponsiveness. Numerous researchers worldwide have attempted to identify effective predictive biomarkers for early prediction of treatment outcomes and adverse effects in CAR T cell therapy, albeit so far only with limited success. This review provides a comprehensive overview of the current state of predictive biomarkers. Although existing predictive metrics correlate to some extent with treatment outcomes, they fail to encapsulate the complexity of the immune system dynamics. The aim of this review is to identify six major groups of predictive biomarkers and propose their use in developing improved and efficient prediction models. These groups include changes in mitochondrial dynamics, endothelial activation, central nervous system impairment, immune system markers, extracellular vesicles, and the inhibitory tumor microenvironment. A comprehensive understanding of the multiple factors that influence therapeutic efficacy has the potential to significantly improve the course of CAR T cell therapy and patient care, thereby making this advanced immunotherapy more appealing and the course of therapy more convenient and favorable for patients.
Collapse
Affiliation(s)
| | | | | | - Andreja Nataša Kopitar
- Institute of Microbiology and Immunology, Faculty of Medicine, University of Ljubljana, Ljubljana, Slovenia
| |
Collapse
|
6
|
Kagoya Y. Cytokine signaling in chimeric antigen receptor T-cell therapy. Int Immunol 2024; 36:49-56. [PMID: 37591521 PMCID: PMC10872714 DOI: 10.1093/intimm/dxad033] [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: 05/12/2023] [Accepted: 08/15/2023] [Indexed: 08/19/2023] Open
Abstract
Adoptive immunotherapy using chimeric antigen-receptor (CAR)-engineered T cells can induce robust antitumor responses against hematologic malignancies. However, its efficacy is not durable in the majority of the patients, warranting further improvement of T-cell functions. Cytokine signaling is one of the key cascades regulating T-cell survival and effector functions. In addition to cytokines that use the common γ chain as a receptor subunit, multiple cytokines regulate T-cell functions directly or indirectly. Modulating cytokine signaling in CAR-T cells by genetic engineering is one promising strategy to augment their therapeutic efficacy. These strategies include ectopic expression of cytokines, cytokine receptors, and synthetic molecules that mimic endogenous cytokine signaling. Alternatively, autocrine IL-2 signaling can be augmented through reprogramming of CAR-T cell properties through transcriptional and epigenetic modification. On the other hand, cytokine production by CAR-T cells triggers systemic inflammatory responses, which mainly manifest as adverse events such as cytokine-release syndrome (CRS) and neurotoxicity. In addition to inhibiting direct inflammatory mediators such as IL-6 and IL-1 released from activated macrophages, suppression of T-cell-derived cytokines associated with the priming of macrophages can be accomplished through genetic modification of CAR-T cells. In this review, I will outline recently developed synthetic biology approaches to exploit cytokine signaling to enhance CAR-T cell functions. I will also discuss therapeutic target molecules to prevent or alleviate CAR-T cell-related toxicities.
Collapse
Affiliation(s)
- Yuki Kagoya
- Division of Tumor Immunology, Institute for Advanced Medical Research, Keio University School of Medicine, 35 Shinanomachi, Shinjuku, Tokyo 160-8582, Japan
| |
Collapse
|
7
|
Kim J, Park M, Baek G, Kim JI, Kwon E, Kang BC, Kim JI, Kang HJ. Tagmentation-based analysis reveals the clonal behavior of CAR-T cells in association with lentivector integration sites. Mol Ther Oncolytics 2023; 30:1-13. [PMID: 37360944 PMCID: PMC10285042 DOI: 10.1016/j.omto.2023.05.004] [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: 08/24/2022] [Accepted: 05/12/2023] [Indexed: 06/28/2023] Open
Abstract
Integration site (IS) analysis is essential in ensuring safety and efficacy of gene therapies when integrating vectors are used. Although clinical trials of gene therapy are rapidly increasing, current methods have limited use in clinical settings because of their lengthy protocols. Here, we describe a novel genome-wide IS analysis method, "detection of the integration sites in a time-efficient manner, quantifying clonal size using tagmentation sequencing" (DIStinct-seq). In DIStinct-seq, a bead-linked Tn5 transposome is used, allowing the sequencing library to be prepared within a single day. We validated the quantification performance of DIStinct-seq for measuring clonal size with clones of known IS. Using ex vivo chimeric antigen receptor (CAR)-T cells, we revealed the characteristics of lentiviral IS. We then applied it to CAR-T cells collected at various times from tumor-engrafted mice, detecting 1,034-6,233 IS. Notably, we observed that the highly expanded clones had a higher integration frequency in the transcription units and vice versa in genomic safe harbors (GSH). Also, in GSH, persistent clones had more frequent IS. Together with these findings, the new IS analysis method will help to improve the safety and efficacy of gene therapies.
Collapse
Affiliation(s)
- Jaeryuk Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
| | - Miyoung Park
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Children’s Hospital, Seoul, Republic of Korea
| | - Gyungwon Baek
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Children’s Hospital, Seoul, Republic of Korea
| | - Joo-Il Kim
- Graduate School of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Experimental Animal Research, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Euna Kwon
- Department of Experimental Animal Research, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
| | - Byeong-Cheol Kang
- Graduate School of Translational Medicine, Seoul National University College of Medicine, Seoul, Republic of Korea
- Department of Experimental Animal Research, Biomedical Research Institute, Seoul National University Hospital, Seoul, Republic of Korea
- Biomedical Center for Animal Resource and Development; Seoul National University College of Medicine, Seoul, Republic of Korea
- Designed Animal Resource Center, Institute of GreenBio Science Technology, Seoul National University, Pyeongchang-gun, Gangwon-do, Republic of Korea
| | - Jong-Il Kim
- Genomic Medicine Institute, Medical Research Center, Seoul National University, Seoul, Republic of Korea
- Department of Biomedical Sciences, Seoul National University Graduate School, Seoul, Republic of Korea
- Department of Biochemistry and Molecular Biology, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
| | - Hyoung Jin Kang
- Seoul National University Cancer Research Institute, Seoul, Republic of Korea
- Department of Pediatrics, Seoul National University College of Medicine, Seoul, Republic of Korea
- Seoul National University Children’s Hospital, Seoul, Republic of Korea
- Wide River Institute of Immunology, Hongcheon, Republic of Korea
| |
Collapse
|
8
|
Hua WK, Hsu JC, Chen YC, Chang PS, Wen KLK, Wang PN, Yang WC, Shen CN, Yu YS, Chen YC, Cheng IC, Wu SCY. Quantum pBac: An effective, high-capacity piggyBac-based gene integration vector system for unlocking gene therapy potential. FASEB J 2023; 37:e23108. [PMID: 37534940 DOI: 10.1096/fj.202201654r] [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: 10/13/2022] [Revised: 06/02/2023] [Accepted: 07/12/2023] [Indexed: 08/04/2023]
Abstract
Recent advances in gene therapy have brought novel treatment options for cancer. However, the full potential of this approach has yet to be unlocked due to the limited payload capacity of commonly utilized viral vectors. Virus-free DNA transposons, including piggyBac, have the potential to obviate these shortcomings. In this study, we improved a previously modified piggyBac system with superior transposition efficiency. We demonstrated that the internal domain sequences (IDS) within the 3' terminal repeat domain of hyperactive piggyBac (hyPB) donor vector contain dominant enhancer elements. Plasmid-free donor vector devoid of IDS was used in conjunction with a helper plasmid expressing Quantum PBase™ v2 to generate an optimal piggyBac system, Quantum pBac™ (qPB), for use in T cells. qPB outperformed hyPB in CD20/CD19 CAR-T production in terms of performance as well as yield of the CAR-T cells produced. Furthermore, qPB also produced CAR-T cells with lower donor-associated variabilities compared to lentiviral vector. Importantly, qPB yielded mainly CD8+ CAR-TSCM cells, and the qPB-produced CAR-T cells effectively eliminated CD20/CD19-expressing tumor cells both in vitro and in vivo. Our findings confirm qPB as a promising virus-free vector system with an enhanced payload capacity to incorporate multiple genes. This highly efficient and potentially safe system will be expected to further advance gene therapy applications.
Collapse
Affiliation(s)
- Wei-Kai Hua
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Jeff C Hsu
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Yi-Chun Chen
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Peter S Chang
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | | | - Po-Nan Wang
- Division of Hematology, Chang Gung Medical Foundation, Taipei City, Taiwan ROC
| | - Wei-Cheng Yang
- Biomedical Translation Research Center, Academia Sinica, Taipei City, Taiwan ROC
| | - Chia-Ning Shen
- Biomedical Translation Research Center, Academia Sinica, Taipei City, Taiwan ROC
- Genomics Research Center, Academia Sinica, Taipei City, Taiwan ROC
| | - Yi-Shan Yu
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - Ying-Chun Chen
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | - I-Cheng Cheng
- GenomeFrontier Therapeutics, Inc, New Taipei City, Taiwan ROC
| | | |
Collapse
|
9
|
Li X, Chen W, Martin BK, Calderon D, Lee C, Choi J, Chardon FM, McDiarmid T, Kim H, Lalanne JB, Nathans JF, Shendure J. Chromatin context-dependent regulation and epigenetic manipulation of prime editing. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.04.12.536587. [PMID: 37090511 PMCID: PMC10120711 DOI: 10.1101/2023.04.12.536587] [Citation(s) in RCA: 13] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Prime editing is a powerful means of introducing precise changes to specific locations in mammalian genomes. However, the widely varying efficiency of prime editing across target sites of interest has limited its adoption in the context of both basic research and clinical settings. Here, we set out to exhaustively characterize the impact of the cis- chromatin environment on prime editing efficiency. Using a newly developed and highly sensitive method for mapping the genomic locations of a randomly integrated "sensor", we identify specific epigenetic features that strongly correlate with the highly variable efficiency of prime editing across different genomic locations. Next, to assess the interaction of trans -acting factors with the cis -chromatin environment, we develop and apply a pooled genetic screening approach with which the impact of knocking down various DNA repair factors on prime editing efficiency can be stratified by cis -chromatin context. Finally, we demonstrate that we can dramatically modulate the efficiency of prime editing through epigenome editing, i.e. altering chromatin state in a locus-specific manner in order to increase or decrease the efficiency of prime editing at a target site. Looking forward, we envision that the insights and tools described here will broaden the range of both basic research and therapeutic contexts in which prime editing is useful.
Collapse
|
10
|
Yagyu S, Nakazawa Y. piggyBac-transposon-mediated CAR-T cells for the treatment of hematological and solid malignancies. Int J Clin Oncol 2023; 28:736-747. [PMID: 36859566 DOI: 10.1007/s10147-023-02319-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Accepted: 02/17/2023] [Indexed: 03/03/2023]
Abstract
Since the introduction of the use of chimeric antigen receptor T-cell therapy (CAR-T therapy) dramatically changed the therapeutic strategy for B cell tumors, various CAR-T cell products have been developed and applied to myeloid and solid tumors. Although viral vectors have been widely used to produce genetically engineered T cells, advances in genetic engineering have led to the development of methods for producing non-viral, gene-modified CAR-T cells. Recent progress has revealed that non-viral CAR-T cells have a significant impact not only on the simplicity of the production process and the accessibility of non-viral vectors but also on the function of the cells themselves. In this review, we focus on piggyBac-transposon-based CAR-T cells among non-viral, gene-modified CAR-T cells and discuss their characteristics, preclinical development, and recent clinical applications.
Collapse
Affiliation(s)
- Shigeki Yagyu
- Innovative Research and Liaison Organization, Shinshu University, 3-1-1, Asahi, Matsumoto, Nagano, Japan. .,Center for Advanced Research of Gene and Cell Therapy, Shinshu University, 3-1-1, Asahi, Matsumoto, Nagano, Japan. .,Department of Pediatrics, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, 465 Kajii-cho, Kawaramachihirokoji, Kamigyo-ku, Kyoto, Japan.
| | - Yozo Nakazawa
- Center for Advanced Research of Gene and Cell Therapy, Shinshu University, 3-1-1, Asahi, Matsumoto, Nagano, Japan.,Department of Pediatrics, Shinshu University School of Medicine, 3-1-1, Asahi, Matsumoto, Nagano, Japan.,Institute for Biomedical Sciences, Interdisciplinary Cluster for Cutting Edge Research, Shinshu University, 3-1-1, Asahi, Matsumoto, Nagano, Japan
| |
Collapse
|
11
|
Characterizing piggyBat-a transposase for genetic modification of T cells. Mol Ther Methods Clin Dev 2022; 25:250-263. [PMID: 35474955 PMCID: PMC9018555 DOI: 10.1016/j.omtm.2022.03.012] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 03/17/2022] [Indexed: 11/21/2022]
Abstract
Chimeric antigen receptor (CAR) T cells targeting CD19 have demonstrated remarkable efficacy in the treatment of B cell malignancies. Current CAR T cell manufacturing protocols are complex and costly due to their reliance on viral vectors. Non-viral systems of genetic modification, such as with transposase and transposon systems, offer a potential streamlined alternative for CAR T cell manufacture and are currently being evaluated in clinical trials. In this study, we utilized the previously described transposase from the little brown bat, designated piggyBat, for production of CD19-specific CAR T cells. PiggyBat demonstrates efficient CAR transgene delivery, with a relatively low variability in integration copy number across a range of manufacturing conditions as well as a similar integration site profile to super-piggyBac transposon and viral vectors. PiggyBat-generated CAR T cells demonstrate CD19-specific cytotoxic efficacy in vitro and in vivo. These data demonstrate that alternative, naturally occurring DNA transposons can be efficiently re-tooled to be exploited in real-world applications.
Collapse
|
12
|
Wada Y, Sato T, Hasegawa H, Matsudaira T, Nao N, Coler-Reilly ALG, Tasaka T, Yamauchi S, Okagawa T, Momose H, Tanio M, Kuramitsu M, Sasaki D, Matsumoto N, Yagishita N, Yamauchi J, Araya N, Tanabe K, Yamagishi M, Nakashima M, Nakahata S, Iha H, Ogata M, Muramatsu M, Imaizumi Y, Uchimaru K, Miyazaki Y, Konnai S, Yanagihara K, Morishita K, Watanabe T, Yamano Y, Saito M. RAISING is a high-performance method for identifying random transgene integration sites. Commun Biol 2022; 5:535. [PMID: 35654946 PMCID: PMC9163355 DOI: 10.1038/s42003-022-03467-w] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2021] [Accepted: 05/09/2022] [Indexed: 11/09/2022] Open
Abstract
Both natural viral infections and therapeutic interventions using viral vectors pose significant risks of malignant transformation. Monitoring for clonal expansion of infected cells is important for detecting cancer. Here we developed a novel method of tracking clonality via the detection of transgene integration sites. RAISING (Rapid Amplification of Integration Sites without Interference by Genomic DNA contamination) is a sensitive, inexpensive alternative to established methods. Its compatibility with Sanger sequencing combined with our CLOVA (Clonality Value) software is critical for those without access to expensive high throughput sequencing. We analyzed samples from 688 individuals infected with the retrovirus HTLV-1, which causes adult T-cell leukemia/lymphoma (ATL) to model our method. We defined a clonality value identifying ATL patients with 100% sensitivity and 94.8% specificity, and our longitudinal analysis also demonstrates the usefulness of ATL risk assessment. Future studies will confirm the broad applicability of our technology, especially in the emerging gene therapy sector.
Collapse
Affiliation(s)
- Yusaku Wada
- Biotechnological Research Support Division, FASMAC Co., Ltd, Atsugi, Kanagawa, 243-0021, Japan
| | - Tomoo Sato
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8512, Japan
- Division of Neurology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Hiroo Hasegawa
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, 852-8501, Japan
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8501, Japan
| | - Takahiro Matsudaira
- Biotechnological Research Support Division, FASMAC Co., Ltd, Atsugi, Kanagawa, 243-0021, Japan
| | - Naganori Nao
- Division of International Research Promotion, International Institute for Zoonosis Control, Hokkaido University, Sapporo, 001-0020, Japan
- One Health Research Center, Hokkaido University, Sapporo, 060-0818, Japan
| | - Ariella L G Coler-Reilly
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8512, Japan
- Department of Internal Medicine, Division of Bone and Mineral Diseases, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | | | - Shunsuke Yamauchi
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, 852-8501, Japan
| | - Tomohiro Okagawa
- Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
| | - Haruka Momose
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo, 208-0011, Japan
| | - Michikazu Tanio
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo, 208-0011, Japan
| | - Madoka Kuramitsu
- Department of Safety Research on Blood and Biological Products, National Institute of Infectious Diseases, Tokyo, 208-0011, Japan
| | - Daisuke Sasaki
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, 852-8501, Japan
| | - Nariyoshi Matsumoto
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, 852-8501, Japan
| | - Naoko Yagishita
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8512, Japan
| | - Junji Yamauchi
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8512, Japan
| | - Natsumi Araya
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8512, Japan
| | - Kenichiro Tanabe
- Pathophysiology and Bioregulation, St. Marianna University Graduate School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Makoto Yamagishi
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Makoto Nakashima
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Shingo Nakahata
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Hidekatsu Iha
- Department of Microbiology, Faculty of Medicine, Oita University, Oita, 879-5593, Japan
| | - Masao Ogata
- Department of Hematology, Oita University Hospital, Oita, 879-5593, Japan
| | - Masamichi Muramatsu
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan
| | - Yoshitaka Imaizumi
- Department of Hematology, Nagasaki University Hospital, Nagasaki, 852-8501, Japan
| | - Kaoru Uchimaru
- Department of Computational Biology and Medical Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Tokyo, 108-8639, Japan
| | - Yasushi Miyazaki
- Department of Hematology, Nagasaki University Hospital, Nagasaki, 852-8501, Japan
- Atomic Bomb Disease and Hibakusha Medicine Unit, Atomic Bomb Disease Institute, Nagasaki University, Nagasaki, 852-8102, Japan
| | - Satoru Konnai
- Department of Advanced Pharmaceutics, Faculty of Veterinary Medicine, Hokkaido University, Hokkaido, 060-0818, Japan
- Department of Disease Control, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Hokkaido, 060-0818, Japan
| | - Katsunori Yanagihara
- Department of Laboratory Medicine, Nagasaki University Hospital, Nagasaki, 852-8501, Japan
- Department of Laboratory Medicine, Nagasaki University Graduate School of Biomedical Sciences, Nagasaki, 852-8501, Japan
| | - Kazuhiro Morishita
- Division of Tumor and Cellular Biochemistry, Department of Medical Sciences, University of Miyazaki, Miyazaki, 889-1692, Japan
| | - Toshiki Watanabe
- Department of Practical Management of Medical Information, St. Marianna University Graduate School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Yoshihisa Yamano
- Department of Rare Diseases Research, Institute of Medical Science, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8512, Japan
- Division of Neurology, Department of Internal Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, 216-8511, Japan
| | - Masumichi Saito
- Department of Virology II, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
- Center for Emergency Preparedness and Response, National Institute of Infectious Diseases, Tokyo, 162-8640, Japan.
| |
Collapse
|
13
|
Zhang X, Jin X, Sun R, Zhang M, Lu W, Zhao M. Gene knockout in cellular immunotherapy: Application and limitations. Cancer Lett 2022; 540:215736. [DOI: 10.1016/j.canlet.2022.215736] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 04/30/2022] [Accepted: 05/06/2022] [Indexed: 12/11/2022]
|
14
|
Ryu J, Chan W, Wettengel JM, Hanna CB, Burwitz BJ, Hennebold JD, Bimber BN. Rapid, accurate mapping of transgene integration in viable rhesus macaque embryos using enhanced-specificity tagmentation-assisted PCR. Mol Ther Methods Clin Dev 2022; 24:241-254. [PMID: 35211637 PMCID: PMC8829455 DOI: 10.1016/j.omtm.2022.01.009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 01/16/2022] [Indexed: 11/19/2022]
Abstract
Genome engineering is a powerful tool for in vitro research and the creation of novel model organisms and has growing clinical applications. Randomly integrating vectors, such as lentivirus- or transposase-based methods, are simple and easy to use but carry risks arising from insertional mutagenesis. Here we present enhanced-specificity tagmentation-assisted PCR (esTag-PCR), a rapid and accurate method for mapping transgene integration and copy number. Using stably transfected HepG2 cells, we demonstrate that esTag-PCR has higher integration site detection accuracy and efficiency than alternative tagmentation-based methods. Next, we performed esTag-PCR on rhesus macaque embryos derived from zygotes injected with piggyBac transposase and transposon/transgene plasmid. Using low-input trophectoderm biopsies, we demonstrate that esTag-PCR accurately maps integration events while preserving blastocyst viability. We used these high-resolution data to evaluate the performance of piggyBac-mediated editing of rhesus macaque embryos, demonstrating that increased concentration of transposon/transgene plasmid can increase the fraction of embryos with stable integration; however, the number of integrations per embryo also increases, which may be problematic for some applications. Collectively, esTag-PCR represents an important improvement to the detection of transgene integration, provides a method to validate and screen edited embryos before implantation, and represents an important advance in the creation of transgenic animal models.
Collapse
Affiliation(s)
- Junghyun Ryu
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - William Chan
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jochen M. Wettengel
- Institute of Virology, Technical University of Munich/Helmholtz Zentrum München, München, 81675 Germany
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Carol B. Hanna
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Benjamin J. Burwitz
- Vaccine & Gene Therapy Institute, Oregon Health & Science University, Beaverton, OR 97006, USA
- Division of Pathobiology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
| | - Jon D. Hennebold
- Division of Reproductive & Developmental Sciences, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
- Department of Obstetrics & Gynecology, Oregon Health & Science University, Portland, OR 97239, USA
| | - Benjamin N. Bimber
- Division of Pathobiology, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
- Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA
- Corresponding author Benjamin N. Bimber, PhD, Division of Genetics, Oregon National Primate Research Center, Oregon Health & Science University, Beaverton, OR 97006, USA.
| |
Collapse
|
15
|
Suematsu M, Yagyu S, Nagao N, Kubota S, Shimizu Y, Tanaka M, Nakazawa Y, Imamura T. PiggyBac Transposon-Mediated CD19 Chimeric Antigen Receptor-T Cells Derived From CD45RA-Positive Peripheral Blood Mononuclear Cells Possess Potent and Sustained Antileukemic Function. Front Immunol 2022; 13:770132. [PMID: 35154098 PMCID: PMC8829551 DOI: 10.3389/fimmu.2022.770132] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/03/2021] [Accepted: 01/05/2022] [Indexed: 12/13/2022] Open
Abstract
The quality of chimeric antigen receptor (CAR)-T cell products, namely, memory and exhaustion markers, affects the long-term functionality of CAR-T cells. We previously reported that piggyBac (PB) transposon-mediated CD19 CAR-T cells exhibit a memory-rich phenotype that is characterized by the high proportion of CD45RA+/C-C chemokine receptor type 7 (CCR7)+ T-cell fraction. To further investigate the favorable phenotype of PB-CD19 CAR-T cells, we generated PB-CD19 CAR-T cells from CD45RA+ and CD45RA− peripheral blood mononuclear cells (PBMCs) (RA+ CAR and RA− CAR, respectively), and compared their phenotypes and antitumor activity. RA+ CAR-T cells showed better transient gene transfer efficiency 24 h after transduction and superior expansion capacity after 14 days of culture than those shown by RA− CAR-T cells. RA+ CAR-T cells exhibited dominant CD8 expression, decreased expression of the exhaustion marker programmed cell death protein-1 (PD-1) and T-cell senescence marker CD57, and enriched naïve/stem cell memory fraction, which are associated with the longevity of CAR-T cells. Transcriptome analysis showed that canonical exhaustion markers were downregulated in RA+ CAR-T, even after antigen stimulation. Although antigen stimulation could increase CAR expression, leading to tonic CAR signaling and exhaustion, the expression of CAR molecules on cell surface after antigen stimulation in RA+ CAR-T cells was controlled at a relatively lower level than that in RA− CAR-T cells. In the in vivo stress test, RA+ CAR-T cells achieved prolonged tumor control with expansion of CAR-T cells compared with RA− CAR-T cells. CAR-T cells were not detected in the control or RA− CAR-T cells but RA+ CAR-T cells were expanded even after 50 days of treatment, as confirmed by sequential bone marrow aspiration. Our results suggest that PB-mediated RA+ CAR-T cells exhibit a memory-rich phenotype and superior antitumor function, thus CD45RA+ PBMCs might be considered an efficient starting material for PB-CAR-T cell manufacturing. This novel approach will be beneficial for effective treatment of B cell malignancies.
Collapse
Affiliation(s)
- Masaya Suematsu
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | - Shigeki Yagyu
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| | - Nobuyoshi Nagao
- AGC Inc. Innovative Technology Laboratories, Yokohama, Japan
| | - Susumu Kubota
- AGC Inc. Materials Integration Laboratories, Yokohama, Japan
| | - Yuto Shimizu
- AGC Inc. Materials Integration Laboratories, Yokohama, Japan
| | - Miyuki Tanaka
- Department of Pediatrics, Shinshu University School of Medicine, Nagano, Japan
| | - Yozo Nakazawa
- Department of Pediatrics, Shinshu University School of Medicine, Nagano, Japan
| | - Toshihiko Imamura
- Department of Pediatrics, Kyoto Prefectural University of Medicine, Graduate School of Medical Science, Kyoto, Japan
| |
Collapse
|
16
|
Hu Y, Cao G, Chen X, Huang X, Asby N, Ankenbruck N, Rahman A, Thusu A, He Y, Riedell PA, Bishop MR, Schreiber H, Kline JP, Huang J. Antigen-Multimers: Specific, Sensitive, Precise, and Multifunctional High-Avidity CAR-Staining Reagents. MATTER 2021; 4:3917-3940. [PMID: 34901832 PMCID: PMC8654235 DOI: 10.1016/j.matt.2021.09.027] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Although chimeric antigen receptor (CAR) T-cell therapy has transformed cancer treatment, high-quality and universal CAR-staining reagents are urgently required to manufacture CAR T cells, predict therapy response, decipher CAR biology, and engineer new CARs. Here, we developed tetrameric and dodecameric forms of a multifunctional and extensible category of high-avidity CAR-staining reagents: antigen-multimers. Antigen-multimers detected CARs against CD19, HER2, and Tn-glycoside with significantly higher specificity, sensitivity, and precision than existing reagents. In addition to accurate CAR T-cell detection by flow cytometry, antigen-multimers also enabled ≥100-fold magnetic enrichment of rare CAR T cells, selective CAR T-cell stimulation, and high-dimensional CAR T-cell profiling by single-cell multi-omics analyses. Finally, antigen-multimers accurately captured clinical anti-CD19 CAR T cells from patients' cellular infusion products, post-infusion peripheral blood, and tumor biopsies. Antigen-multimers can be readily extended to other CAR systems by switching its antigen ligand. As such, antigen-multimers have broad clinical and research applications.
Collapse
Affiliation(s)
- Yifei Hu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Pritzker School of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Guoshuai Cao
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Xiufen Chen
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
| | - Xiaodan Huang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Nicholas Asby
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Nicholas Ankenbruck
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Ali Rahman
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Ashima Thusu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
| | - Yanran He
- Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
| | - Peter A. Riedell
- Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- The David and Etta Jonas Center for Cellular Therapy, University of Chicago, Chicago, IL 60637, USA
| | - Michael R. Bishop
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- The David and Etta Jonas Center for Cellular Therapy, University of Chicago, Chicago, IL 60637, USA
| | - Hans Schreiber
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
- Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
- The David and Etta Jonas Center for Cellular Therapy, University of Chicago, Chicago, IL 60637, USA
- Department of Pathology, University of Chicago, Chicago, IL 60637, USA
| | - Justin P. Kline
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
- Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
- Department of Medicine, University of Chicago, Chicago, IL 60637, USA
- The David and Etta Jonas Center for Cellular Therapy, University of Chicago, Chicago, IL 60637, USA
| | - Jun Huang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL 60637, USA
- Committee on Immunology, University of Chicago, Chicago, IL 60637, USA
- Committee on Cancer Biology, University of Chicago, Chicago, IL 60637, USA
| |
Collapse
|
17
|
Micklethwaite KP, Gowrishankar K, Gloss BS, Li Z, Street JA, Moezzi L, Mach MA, Sutrave G, Clancy LE, Bishop DC, Louie RHY, Cai C, Foox J, MacKay M, Sedlazeck FJ, Blombery P, Mason CE, Luciani F, Gottlieb DJ, Blyth E. Investigation of product-derived lymphoma following infusion of piggyBac-modified CD19 chimeric antigen receptor T cells. Blood 2021; 138:1391-1405. [PMID: 33974080 PMCID: PMC8532197 DOI: 10.1182/blood.2021010858] [Citation(s) in RCA: 106] [Impact Index Per Article: 35.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 04/24/2021] [Indexed: 11/20/2022] Open
Abstract
We performed a phase 1 clinical trial to evaluate outcomes in patients receiving donor-derived CD19-specific chimeric antigen receptor (CAR) T cells for B-cell malignancy that relapsed or persisted after matched related allogeneic hemopoietic stem cell transplant. To overcome the cost and transgene-capacity limitations of traditional viral vectors, CAR T cells were produced using the piggyBac transposon system of genetic modification. Following CAR T-cell infusion, 1 patient developed a gradually enlarging retroperitoneal tumor due to a CAR-expressing CD4+ T-cell lymphoma. Screening of other patients led to the detection, in an asymptomatic patient, of a second CAR T-cell tumor in thoracic para-aortic lymph nodes. Analysis of the first lymphoma showed a high transgene copy number, but no insertion into typical oncogenes. There were also structural changes such as altered genomic copy number and point mutations unrelated to the insertion sites. Transcriptome analysis showed transgene promoter-driven upregulation of transcription of surrounding regions despite insulator sequences surrounding the transgene. However, marked global changes in transcription predominantly correlated with gene copy number rather than insertion sites. In both patients, the CAR T-cell-derived lymphoma progressed and 1 patient died. We describe the first 2 cases of malignant lymphoma derived from CAR gene-modified T cells. Although CAR T cells have an enviable record of safety to date, our results emphasize the need for caution and regular follow-up of CAR T recipients, especially when novel methods of gene transfer are used to create genetically modified immune therapies. This trial was registered at www.anzctr.org.au as ACTRN12617001579381.
Collapse
MESH Headings
- Aged
- DNA Transposable Elements
- Gene Expression Regulation, Neoplastic
- Gene Transfer Techniques
- Humans
- Immunotherapy, Adoptive/adverse effects
- Immunotherapy, Adoptive/methods
- Leukemia, B-Cell/genetics
- Leukemia, B-Cell/therapy
- Lymphoma/etiology
- Lymphoma/genetics
- Lymphoma, B-Cell/genetics
- Lymphoma, B-Cell/therapy
- Male
- Receptors, Antigen, T-Cell/genetics
- Receptors, Antigen, T-Cell/therapeutic use
- T-Lymphocytes/metabolism
- Transcriptome
- Transgenes
Collapse
Affiliation(s)
- Kenneth P Micklethwaite
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology-ICPMR Westmead, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Kavitha Gowrishankar
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Brian S Gloss
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Ziduo Li
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Janine A Street
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Leili Moezzi
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - Melanie A Mach
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Gaurav Sutrave
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Leighton E Clancy
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology-ICPMR Westmead, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
| | - David C Bishop
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Raymond H Y Louie
- Kirby Institute, University of New South Wales, Sydney. NSW, Australia
| | - Curtis Cai
- Kirby Institute, University of New South Wales, Sydney. NSW, Australia
| | - Jonathan Foox
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY
| | - Matthew MacKay
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY
| | - Fritz J Sedlazeck
- Human Genome Sequencing Center, College of Medicine, Baylor University, Houston, TX
| | - Piers Blombery
- Department of Pathology, Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- Clinical Haematology, The Royal Melbourne Hospital and Peter MacCallum Cancer Centre, Parkville, VIC, Australia
- Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, VIC, Australia
| | - Christopher E Mason
- Institute for Computational Biomedicine, Weill Cornell Medicine, New York, NY
- The Bin Talal Bin Abdulaziz Alsaud Institute for Computational Biomedicine, New York, NY
- The Feil Family Brain and Mind Research Institute, New York, NY; and
- The WorldQuant Initiative for Quantitative Prediction, New York, NY
| | - Fabio Luciani
- Kirby Institute, University of New South Wales, Sydney. NSW, Australia
| | - David J Gottlieb
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| | - Emily Blyth
- Blood Transplant and Cell Therapies Program, Department of Haematology, Westmead Hospital, Sydney, NSW, Australia
- Blood Transplant and Cell Therapies Laboratory, NSW Health Pathology-ICPMR Westmead, Sydney, NSW, Australia
- Westmead Institute for Medical Research, Sydney, NSW, Australia
- Sydney Medical School, Faculty of Medicine and Health, University of Sydney, Sydney, NSW, Australia
| |
Collapse
|
18
|
Zhao Y, Yang X, Li S, Zhang B, Li S, Wang X, Wang Y, Jia C, Chang Y, Wei W. sTNFRII-Fc modification protects human UC-MSCs against apoptosis/autophagy induced by TNF-α and enhances their efficacy in alleviating inflammatory arthritis. Stem Cell Res Ther 2021; 12:535. [PMID: 34627365 PMCID: PMC8502322 DOI: 10.1186/s13287-021-02602-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/07/2021] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Tumor necrosis factor (TNF)-α inhibitors represented by Etanercept (a fusion protein containing soluble TNF receptor II (sTNFRII) and the Fc segment of human IgG1) play a pivotal role in Rheumatoid arthritis (RA) treatment. However, long-term use increases the risk of infection and tumors for their systemic inhibition of TNF-α, which disrupts the regular physiological function of this molecular. Mesenchymal stem cells (MSCs)-based delivery system provides new options for RA treatment with their "homing" and immune-regulation capacities, whereas inflammatory environment (especially TNF-α) is not conducive to MSCs' therapeutic effects by inducing apoptosis/autophagy. Here, we constructed a strain of sTNFRII-Fc-expressing MSCs (sTNFRII-MSC), aiming to offset the deficiency of those two interventions. METHODS Constructed sTNFRII-Fc lentiviral vector was used to infect human umbilical cord-derived MSCs, and sTNFRII-MSC stable cell line was generated by monoclonal cultivation. In vitro and vivo characteristics of sTNFRII-MSC were assessed by coculture assay and an acute inflammatory model in NOD/SCID mice. The sTNFRII-MSC were transplanted into CIA model, pathological and immunological indicators were detected to evaluate the therapeutic effects of sTNFRII-MSC. The distribution of sTNFRII-MSC was determined by immunofluorescence assay. Apoptosis and autophagy were analyzed by flow cytometry, western blot and immunofluorescence. RESULTS sTNFRII-Fc secreted by sTNFRII-MSC present biological activity both in vitro and vivo. sTNFRII-MSC transplantation effectively alleviates mice collagen-induced arthritis (CIA) via migrating to affected area, protecting articular cartilage destruction, modulating immune balance and sTNFRII-MSC showed prolonged internal retention via resisting apoptosis/autophagy induced by TNF-α. CONCLUSION sTNFRII-Fc modification protects MSCs against apoptosis/autophagy induced by TNF-α, in addition to releasing sTNFRII-Fc neutralizing TNF-α to block relevant immune-inflammation cascade, and thus exert better therapeutic effects in alleviating inflammatory arthritis.
Collapse
Affiliation(s)
- Yingjie Zhao
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Ministry of Education, Hefei, 230032, China.,Department of Clinical Pharmacology, The Second Hospital of Anhui Medical University, Hefei, 230601, China
| | - Xuezhi Yang
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Ministry of Education, Hefei, 230032, China
| | - Siyu Li
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Ministry of Education, Hefei, 230032, China
| | - Bingjie Zhang
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Ministry of Education, Hefei, 230032, China
| | - Susu Li
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Ministry of Education, Hefei, 230032, China
| | - Xinwei Wang
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Ministry of Education, Hefei, 230032, China
| | - Yueye Wang
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Ministry of Education, Hefei, 230032, China
| | - Chengyan Jia
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Ministry of Education, Hefei, 230032, China
| | - Yan Chang
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Ministry of Education, Hefei, 230032, China.
| | - Wei Wei
- Key Laboratory of Anti-Inflammatory and Immune Medicine, Anhui Collaborative Innovation Center of Anti-Inflammatory and Immune Medicine, Institute of Clinical Pharmacology, Anhui Medical University, Ministry of Education, Hefei, 230032, China.
| |
Collapse
|
19
|
Kang M, Lee SH, Kwon M, Byun J, Kim D, Kim C, Koo S, Kwon SP, Moon S, Jung M, Hong J, Go S, Song SY, Choi JH, Hyeon T, Oh YK, Park HH, Kim BS. Nanocomplex-Mediated In Vivo Programming to Chimeric Antigen Receptor-M1 Macrophages for Cancer Therapy. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2021; 33:e2103258. [PMID: 34510559 DOI: 10.1002/adma.202103258] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 08/06/2021] [Indexed: 06/13/2023]
Abstract
Chimeric antigen receptor-T (CAR-T) cell immunotherapy has shown impressive clinical outcomes for hematologic malignancies. However, its broader applications are challenged due to its complex ex vivo cell-manufacturing procedures and low therapeutic efficacy against solid tumors. The limited therapeutic effects are partially due to limited CAR-T cell infiltration to solid tumors and inactivation of CAR-T cells by the immunosuppressive tumor microenvironment. Here, a facile approach is presented to in vivo program macrophages, which can intrinsically penetrate solid tumors, into CAR-M1 macrophages displaying enhanced cancer-directed phagocytosis and anti-tumor activity. In vivo injected nanocomplexes of macrophage-targeting nanocarriers and CAR-interferon-γ-encoding plasmid DNA induce CAR-M1 macrophages that are capable of CAR-mediated cancer phagocytosis, anti-tumor immunomodulation, and inhibition of solid tumor growth. Together, this study describes an off-the-shelf CAR-macrophage therapy that is effective for solid tumors and avoids the complex and costly processes of ex vivo CAR-cell manufacturing.
Collapse
Affiliation(s)
- Mikyung Kang
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seong Ho Lee
- Department of Smart Health Science and Technology, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Miji Kwon
- Department of Smart Health Science and Technology, Kangwon National University, Chuncheon, 24341, Republic of Korea
| | - Junho Byun
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Dongyoon Kim
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Cheesue Kim
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sagang Koo
- Center for Nanoparticle Research, Institute of Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sung Pil Kwon
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Sangjun Moon
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Mungyo Jung
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jihye Hong
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seokhyeong Go
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Seuk Young Song
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
| | - Jae Hyun Choi
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Taeghwan Hyeon
- Center for Nanoparticle Research, Institute of Basic Science (IBS), Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, and Institute of Chemical Processes, Seoul National University, Seoul, 08826, Republic of Korea
| | - Yu-Kyoung Oh
- College of Pharmacy and Research Institute of Pharmaceutical Sciences, Seoul National University, Seoul, 08826, Republic of Korea
| | - Hee Ho Park
- Department of Bioengineering, Hanyang University, Seoul, 04763, Republic of Korea
- Education and Research Group for Biopharmaceutical Innovation Leader, Hanyang University, Seoul, 04763, Republic of Korea
| | - Byung-Soo Kim
- Interdisciplinary Program for Bioengineering, Seoul National University, Seoul, 08826, Republic of Korea
- School of Chemical and Biological Engineering, Seoul National University, Seoul, 08826, Republic of Korea
- Institute of Chemical Processes, Institute of Engineering Research, BioMAX, Seoul National University, Seoul, 08826, Republic of Korea
| |
Collapse
|
20
|
Applications of piggyBac Transposons for Genome Manipulation in Stem Cells. Stem Cells Int 2021; 2021:3829286. [PMID: 34567130 PMCID: PMC8460389 DOI: 10.1155/2021/3829286] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Accepted: 08/16/2021] [Indexed: 12/20/2022] Open
Abstract
Transposons are mobile genetic elements in the genome. The piggyBac (PB) transposon system is increasingly being used for stem cell research due to its high transposition efficiency and seamless excision capacity. Over the past few decades, forward genetic screens based on PB transposons have been successfully established to identify genes associated with drug resistance and stem cell-related characteristics. Moreover, PB transposon is regarded as a promising gene therapy vector and has been used in some clinically relevant stem cells. Here, we review the recent progress on the basic biology of PB, highlight its applications in current stem cell research, and discuss its advantages and challenges.
Collapse
|
21
|
Zhang P, Ganesamoorthy D, Nguyen SH, Au R, Coin LJ, Tey SK. Nanopore sequencing as a scalable, cost-effective platform for analyzing polyclonal vector integration sites following clinical T cell therapy. J Immunother Cancer 2021; 8:jitc-2019-000299. [PMID: 32527930 PMCID: PMC7292043 DOI: 10.1136/jitc-2019-000299] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/28/2020] [Indexed: 11/21/2022] Open
Abstract
Background Analysis of vector integration sites in gene-modified cells can provide critical information on clonality and potential biological impact on nearby genes. Current short-read next-generation sequencing methods require specialized instruments and large batch runs. Methods We used nanopore sequencing to analyze the vector integration sites of T cells transduced by the gammaretroviral vector, SFG.iCasp9.2A.ΔCD19. DNA from oligoclonal cell lines and polyclonal clinical samples were restriction enzyme digested with two 6-cutters, NcoI and BspHI; and the flanking genomic DNA amplified by inverse PCR or cassette ligation PCR. Following nested PCR and barcoding, the amplicons were sequenced on the Oxford Nanopore platform. Reads were filtered for quality, trimmed, and aligned. Custom tool was developed to cluster reads and merge overlapping clusters. Results Both inverse PCR and cassette ligation PCR could successfully amplify flanking genomic DNA, with cassette ligation PCR showing less bias. The 4.8 million raw reads were grouped into 12,186 clusters and 6410 clones. The 3′long terminal repeat (LTR)-genome junction could be resolved within a 5-nucleotide span for a majority of clusters and within one nucleotide span for clusters with ≥5 reads. The chromosomal distributions of the insertional sites and their predilection for regions proximate to transcription start sites were consistent with previous reports for gammaretroviral vector integrants as analyzed by short-read next-generation sequencing. Conclusion Our study shows that it is feasible to use nanopore sequencing to map polyclonal vector integration sites. The assay is scalable and requires minimum capital, which together enable cost-effective and timely analysis. Further refinement is required to reduce amplification bias and improve single nucleotide resolution.
Collapse
Affiliation(s)
- Ping Zhang
- Department of Immunology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Devika Ganesamoorthy
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Son Hoang Nguyen
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia
| | - Raymond Au
- Department of Immunology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia
| | - Lachlan J Coin
- Institute for Molecular Bioscience, University of Queensland, Brisbane, Queensland, Australia.,Department of Clinical Pathology, The University of Melbourne, Melbourne, Victoria, Australia.,Department of Infectious Disease, Imperial College London, London, London, UK
| | - Siok-Keen Tey
- Department of Immunology, QIMR Berghofer Medical Research Institute, Herston, Queensland, Australia .,Department of Haematology and Bone Marrow Transplantation, Royal Brisbane and Women's Hospital, Herston, Queensland, Australia.,Faculty of Medicine, University of Queensland, Brisbane, Queensland, Australia
| |
Collapse
|
22
|
Development of CAR T-cell lymphoma in two of ten patients effectively treated with piggyBac modified CD19 CAR T-cells. Blood 2021; 138:1504-1509. [PMID: 34010392 DOI: 10.1182/blood.2021010813] [Citation(s) in RCA: 90] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 04/13/2021] [Indexed: 11/20/2022] Open
Abstract
CD19-specific chimeric antigen receptor (CAR19) T-cells effectively induce remission of B-cell malignancy, but the cost and complexity of production using viral vectors is a factor limiting widespread application. Furthermore, the small cargo capacity of viral vectors may hamper future development of more heavily engineered CAR T-cells. We demonstrated the feasibility of generating CAR19 T-cells from HLA-matched donors of sibling allogeneic hematopoietic stem cell transplant (HSCT) patients via a simple and inexpensive method using the high-capacity piggyBac transposon. A cohort of 10 patients with relapsed or refractory B-cell acute lymphoblastic leukemia or aggressive lymphoma following HSCT were the first human subjects to receive piggyBac-generated CAR19 T-cells. Treatment with intra-patient escalating doses of CAR19 T-cells was effective, with all 9 evaluable patients achieving complete remission. At a median follow-up of 18.0 months, 5 patients remained in complete remission of B-cell malignancy. One patient died of viral sepsis. Four patients developed cytokine release syndrome of maximum grade 2, and no neurotoxicity or new graft-versus-host disease occurred. However, two patients developed malignant CAR19 T-cell tumors, one of whom was successfully treated; one patient died of the secondary tumor. The piggyBac system represents a feasible alternative to viral vectors for the generation of effective CAR19 T-cells, but its oncogenic potential in the context of the described production process will need to be addressed before any further clinical use is possible. This trial was registered at www.anzctr.org.au as ACTRN12617001579381.
Collapse
|
23
|
Sandoval-Villegas N, Nurieva W, Amberger M, Ivics Z. Contemporary Transposon Tools: A Review and Guide through Mechanisms and Applications of Sleeping Beauty, piggyBac and Tol2 for Genome Engineering. Int J Mol Sci 2021; 22:ijms22105084. [PMID: 34064900 PMCID: PMC8151067 DOI: 10.3390/ijms22105084] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2021] [Revised: 04/30/2021] [Accepted: 05/05/2021] [Indexed: 01/19/2023] Open
Abstract
Transposons are mobile genetic elements evolved to execute highly efficient integration of their genes into the genomes of their host cells. These natural DNA transfer vehicles have been harnessed as experimental tools for stably introducing a wide variety of foreign DNA sequences, including selectable marker genes, reporters, shRNA expression cassettes, mutagenic gene trap cassettes, and therapeutic gene constructs into the genomes of target cells in a regulated and highly efficient manner. Given that transposon components are typically supplied as naked nucleic acids (DNA and RNA) or recombinant protein, their use is simple, safe, and economically competitive. Thus, transposons enable several avenues for genome manipulations in vertebrates, including transgenesis for the generation of transgenic cells in tissue culture comprising the generation of pluripotent stem cells, the production of germline-transgenic animals for basic and applied research, forward genetic screens for functional gene annotation in model species and therapy of genetic disorders in humans. This review describes the molecular mechanisms involved in transposition reactions of the three most widely used transposon systems currently available (Sleeping Beauty, piggyBac, and Tol2), and discusses the various parameters and considerations pertinent to their experimental use, highlighting the state-of-the-art in transposon technology in diverse genetic applications.
Collapse
Affiliation(s)
| | | | | | - Zoltán Ivics
- Correspondence: ; Tel.: +49-6103-77-6000; Fax: +49-6103-77-1280
| |
Collapse
|
24
|
Abstract
The Vanderbilt O'Brien Kidney Center (VOKC) is one of the eight National Institutes of Health P30-funded centers in the United States. The mission of these core-based centers is to provide technical and conceptual support to enhance and facilitate research in the field of kidney diseases. The goal of the VOKC is to provide support to understand mechanisms and identify potential therapies for acute and chronic kidney disease. The services provided by the VOKC are meant to help the scientific community to have the right support and tools as well as to select the right animal model, statistical analysis, and clinical study design to perform innovative research and translate discoveries into personalized care to prevent, diagnose, and cure kidney disease. To achieve these goals, the VOKC has in place a program to foster collaborative investigation into critical questions of kidney disease, to personalize diagnosis and treatment of kidney disease, and to disseminate information about kidney disease and the benefits of VOKC services and research. The VOKC is complemented by state-of-the-art cores and an education and outreach program whose goals are to provide an educational platform to enhance the study of kidney disease, to publicize information about services available through the VOKC, and to provide information about kidney disease to patients and other interested members of the community. In this review, we highlight the major services and contributions of the VOKC.
Collapse
Affiliation(s)
- Ambra Pozzi
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt Center for Kidney Disease, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Veterans Affairs, Nashville, Tennessee
| | - Raymond C Harris
- Division of Nephrology and Hypertension, Department of Medicine, Vanderbilt University School of Medicine, Nashville, Tennessee.,Vanderbilt Center for Kidney Disease, Vanderbilt University School of Medicine, Nashville, Tennessee.,Department of Veterans Affairs, Nashville, Tennessee
| |
Collapse
|
25
|
Overhauling CAR T Cells to Improve Efficacy, Safety and Cost. Cancers (Basel) 2020; 12:cancers12092360. [PMID: 32825533 PMCID: PMC7564591 DOI: 10.3390/cancers12092360] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2020] [Revised: 08/06/2020] [Accepted: 08/10/2020] [Indexed: 12/13/2022] Open
Abstract
Gene therapy is now surpassing 30 years of clinical experience and in that time a variety of approaches has been applied for the treatment of a wide range of pathologies. While the promise of gene therapy was over-stated in the 1990’s, the following decades were met with polar extremes between demonstrable success and devastating setbacks. Currently, the field of gene therapy is enjoying the rewards of overcoming the hurdles that come with turning new ideas into safe and reliable treatments, including for cancer. Among these modalities, the modification of T cells with chimeric antigen receptors (CAR-T cells) has met with clear success and holds great promise for the future treatment of cancer. We detail a series of considerations for the improvement of the CAR-T cell approach, including the design of the CAR, routes of gene transfer, introduction of CARs in natural killer and other cell types, combining the CAR approach with checkpoint blockade or oncolytic viruses, improving pre-clinical models as well as means for reducing cost and, thus, making this technology more widely available. While CAR-T cells serve as a prime example of translating novel ideas into effective treatments, certainly the lessons learned will serve to accelerate the current and future development of gene therapy drugs.
Collapse
|
26
|
Abstract
Chimeric antigen receptor-T (CAR-T) cell therapy is a promising frontier of immunoengineering and cancer immunotherapy. Methods that detect, quantify, track, and visualize the CAR, have catalyzed the rapid advancement of CAR-T cell therapy from preclinical models to clinical adoption. For instance, CAR-staining/labeling agents have enabled flow cytometry analysis, imaging applications, cell sorting, and high-dimensional clinical profiling. Molecular assays, such as quantitative polymerase chain reaction, integration site analysis, and RNA-sequencing, have characterized CAR transduction, expression, and in vivo CAR-T cell expansion kinetics. In vitro visualization methods, including confocal and total internal reflection fluorescence microscopy, have captured the molecular details underlying CAR immunological synapse formation, signaling, and cytotoxicity. In vivo tracking methods, including two-photon microscopy, bioluminescence imaging, and positron emission tomography scanning, have monitored CAR-T cell biodistribution across blood, tissue, and tumor. Here, we review the plethora of CAR detection methods, which can operate at the genomic, transcriptomic, proteomic, and organismal levels. For each method, we discuss: (1) what it measures; (2) how it works; (3) its scientific and clinical importance; (4) relevant examples of its use; (5) specific protocols for CAR detection; and (6) its strengths and weaknesses. Finally, we consider current scientific and clinical needs in order to provide future perspectives for improved CAR detection.
Collapse
Affiliation(s)
- Yifei Hu
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
- Pritzker School of Medicine, University of Chicago, Chicago, IL, United States
| | - Jun Huang
- Pritzker School of Molecular Engineering, University of Chicago, Chicago, IL, United States
| |
Collapse
|
27
|
Straetemans T, Janssen A, Jansen K, Doorn R, Aarts T, van Muyden ADD, Simonis M, Bergboer J, de Witte M, Sebestyen Z, Kuball J. TEG001 Insert Integrity from Vector Producer Cells until Medicinal Product. Mol Ther 2019; 28:561-571. [PMID: 31882320 DOI: 10.1016/j.ymthe.2019.11.030] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2019] [Revised: 11/19/2019] [Accepted: 11/26/2019] [Indexed: 12/20/2022] Open
Abstract
Despite extensive usage of gene therapy medicinal products (GTMPs) in clinical studies and recent approval of chimeric antigen receptor (CAR) T cell therapy, little information has been made available on the precise molecular characterization and possible variations in terms of insert integrity and vector copy numbers of different GTMPs during the complete production chain. Within this context, we characterize αβT cells engineered to express a defined γδT cell engineered to express a defined γδT receptor (TEG) currently used in a first-in-human clinical study (NTR6541). Utilizing targeted locus amplification in combination with next generation sequencing for the vector producer clone and TEG001 products, we report on five single-nucleotide variants and nine intact vector copies integrated in the producer clone. The vector copy number in TEG001 cells was on average a factor 0.72 (SD 0.11) below that of the producer cell clone. All nucleotide variants were transferred to TEG001 without having an effect on cellular proliferation during extensive in vitro culture. Based on an environmental risk assessment of the five nucleotide variants present in the non-coding viral region of the TEG001 insert, there was no altered environmental impact of TEG001 cells. We conclude that TEG001 cells do not have an increased risk for malignant transformation in vivo.
Collapse
Affiliation(s)
- Trudy Straetemans
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| | - Anke Janssen
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Koen Jansen
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Ruud Doorn
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Tineke Aarts
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Anna D D van Muyden
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | | | | | - Moniek de Witte
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Zsolt Sebestyen
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands
| | - Jurgen Kuball
- Department of Hematology, Center of Translational Immunology, University Medical Center Utrecht, Utrecht University, Utrecht, the Netherlands.
| |
Collapse
|
28
|
Wang P, Qin W, Liu T, Jiang D, Cui L, Liu X, Fang Y, Tang X, Jin H, Qian Q. PiggyBac-engineered T cells expressing a glypican-3-specific chimeric antigen receptor show potent activities against hepatocellular carcinoma. Immunobiology 2019; 225:151850. [PMID: 31522780 DOI: 10.1016/j.imbio.2019.09.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 08/08/2019] [Accepted: 09/03/2019] [Indexed: 12/24/2022]
Abstract
Glypican-3 (GPC3) is an attractive target for chimeric antigen receptor (CAR)-T cell therapy, as it is overexpressed in most hepatocellular carcinoma (HCC) tissues but shows restricted expression in healthy adult tissues. Herein, we generated GPC3-specific CAR-T cells for HCC therapy by electroporation with plasmid DNA encoding the piggyBac (PB) transposon and the hyperactive piggyBac transposase simultaneously instead of by commonly-used viral vectors. Our results demonstrated that GPC3CAR gene was efficiently integrated into the genome of T cells utilizing the PB transposon system. Upon stimulation with GPC3 antigen, GPC3CAR-T cells could be effectively activated, proliferate strongly and secrete high levels of cytokines. It also was demonstrated that GPC3CAR-T cells displayed potent cytotoxicity against GPC3-positive HCC cell lines in vitro by using real-time cell analyser (RTCA) system and the JuLI™ Stage Cell History Recorder. More importantly, in a Huh-7 xenograft mouse model, GPC3CAR-T cells significantly reduced the tumour burden companied with the secretion of high levels of IFN-γ. Moreover, T cells in mice treated with GPC3CAR-T cells could infiltrate into tumour tissues and persist as effector memory T cells (TEM). Overall, our study suggests that the use of PB system-based GPC3CAR-T cell therapy could be a promising clinical strategy for patients with HCC.
Collapse
Affiliation(s)
- Pei Wang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Wenxia Qin
- Shanghai Cell Therapy Research Institute, Shanghai Cell Therapy Group, Shanghai 201805, China
| | - Tao Liu
- Shanghai Cell Therapy Research Institute, Shanghai Cell Therapy Group, Shanghai 201805, China
| | - Duqing Jiang
- Shanghai Cell Therapy Research Institute, Shanghai Cell Therapy Group, Shanghai 201805, China
| | - Lianzhen Cui
- Shanghai Cell Therapy Research Institute, Shanghai Cell Therapy Group, Shanghai 201805, China
| | - Xiangzhen Liu
- Shanghai Cell Therapy Research Institute, Shanghai Cell Therapy Group, Shanghai 201805, China
| | - Yuan Fang
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - Xi Tang
- Shanghai Cell Therapy Research Institute, Shanghai Cell Therapy Group, Shanghai 201805, China
| | - Huajun Jin
- Shanghai Cell Therapy Research Institute, Shanghai Cell Therapy Group, Shanghai 201805, China; Eastern Hepatobiliary Surgery Hospital, The Second Military University, Shanghai 201805, China.
| | - Qijun Qian
- College of Life Sciences and Medicine, Zhejiang Sci-Tech University, Hangzhou 310018, China; Shanghai Cell Therapy Research Institute, Shanghai Cell Therapy Group, Shanghai 201805, China; Eastern Hepatobiliary Surgery Hospital, The Second Military University, Shanghai 201805, China.
| |
Collapse
|