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Huang X, Huang J, Li X, Fan J, Zhou D, Qu HQ, Glessner JT, Ji D, Jia Q, Ding Z, Wang N, Wei W, Lyu X, Li MJ, Liu Z, Liu W, Wei Y, Hakonarson H, Xia Q, Li J. Target genes regulated by CLEC16A intronic region associated with common variable immunodeficiency. J Allergy Clin Immunol 2024; 153:1668-1680. [PMID: 38191060 DOI: 10.1016/j.jaci.2023.12.023] [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: 08/17/2022] [Revised: 12/25/2023] [Accepted: 12/29/2023] [Indexed: 01/10/2024]
Abstract
BACKGROUND CLEC16A intron 19 has been identified as a candidate locus for common variable immunodeficiency (CVID). OBJECTIVES This study sought to elucidate the molecular mechanism by which variants at the CLEC16A intronic locus may contribute to the pathogenesis of CVID. METHODS The investigators performed fine-mapping of the CLEC16A locus in a CVID cohort, then deleted the candidate functional SNP in T-cell lines by the CRISPR-Cas9 technique and conducted RNA-sequencing to identify target gene(s). The interactions between the CLEC16A locus and its target genes were identified using circular chromosome conformation capture. The transcription factor complexes mediating the chromatin interactions were determined by proteomic approach. The molecular pathways regulated by the CLEC16A locus were examined by RNA-sequencing and reverse phase protein array. RESULTS This study showed that the CLEC16A locus is an enhancer regulating expression of multiple target genes including a distant gene ATF7IP2 through chromatin interactions. Distinct transcription factor complexes mediate the chromatin interactions in an allele-specific manner. Disruption of the CLEC16A locus affects the AKT signaling pathway, as well as the molecular response of CD4+ T cells to immune stimulation. CONCLUSIONS Through multiomics and targeted experimental approaches, this study elucidated the underlying target genes and signaling pathways involved in the genetic association of CLEC16A with CVID, and highlighted plausible molecular targets for developing novel therapeutics.
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Affiliation(s)
- Xubo Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Jinxia Huang
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Xiumei Li
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Jingxian Fan
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Desheng Zhou
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Hui-Qi Qu
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa
| | - Joseph T Glessner
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Dandan Ji
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Qi Jia
- International School of Information Science Engineering, Dalian University of Technology, Dalian, China
| | - Zhiyong Ding
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan, China
| | - Nan Wang
- Mills Institute for Personalized Cancer Care, Fynn Biotechnologies Ltd, Jinan, China
| | - Wei Wei
- Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China
| | - Xing Lyu
- Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China
| | - Mulin Jun Li
- Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Zhe Liu
- Department of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China
| | - Wei Liu
- Tianjin Children's Hospital (Tianjin University Children's Hospital), Tianjin, China; Tianjin Key Laboratory of Birth Defects for Prevention and Treatment, Tianjin, China
| | - Yongjie Wei
- Affiliated Cancer Hospital and Institute of Guangzhou Medical University, Guangzhou, China
| | - Hakon Hakonarson
- Center for Applied Genomics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Division of Human Genetics, The Children's Hospital of Philadelphia, Philadelphia, Pa; Department of Pediatrics, The Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pa
| | - Qianghua Xia
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Bioinformatics, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China.
| | - Jin Li
- Department of Cell Biology, The Province and Ministry Co-sponsored Collaborative Innovation Center for Medical Epigenetics, Key Laboratory of Immune Microenvironment and Disease (Ministry of Education), Tianjin Key Laboratory of Medical Epigenetics, Tianjin Institute of Immunology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, China; Department of Rheumatology and Immunology, Tianjin Medical University General Hospital, Tianjin, China.
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2
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Chen R, Lukianova E, van der Loeff IS, Spegarova JS, Willet JDP, James KD, Ryder EJ, Griffin H, IJspeert H, Gajbhiye A, Lamoliatte F, Marin-Rubio JL, Woodbine L, Lemos H, Swan DJ, Pintar V, Sayes K, Ruiz-Morales ER, Eastham S, Dixon D, Prete M, Prigmore E, Jeggo P, Boyes J, Mellor A, Huang L, van der Burg M, Engelhardt KR, Stray-Pedersen A, Erichsen HC, Gennery AR, Trost M, Adams DJ, Anderson G, Lorenc A, Trynka G, Hambleton S. NUDCD3 deficiency disrupts V(D)J recombination to cause SCID and Omenn syndrome. Sci Immunol 2024; 9:eade5705. [PMID: 38787962 DOI: 10.1126/sciimmunol.ade5705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2022] [Accepted: 04/24/2024] [Indexed: 05/26/2024]
Abstract
Inborn errors of T cell development present a pediatric emergency in which timely curative therapy is informed by molecular diagnosis. In 11 affected patients across four consanguineous kindreds, we detected homozygosity for a single deleterious missense variant in the gene NudC domain-containing 3 (NUDCD3). Two infants had severe combined immunodeficiency with the complete absence of T and B cells (T -B- SCID), whereas nine showed classical features of Omenn syndrome (OS). Restricted antigen receptor gene usage by residual T lymphocytes suggested impaired V(D)J recombination. Patient cells showed reduced expression of NUDCD3 protein and diminished ability to support RAG-mediated recombination in vitro, which was associated with pathologic sequestration of RAG1 in the nucleoli. Although impaired V(D)J recombination in a mouse model bearing the homologous variant led to milder immunologic abnormalities, NUDCD3 is absolutely required for healthy T and B cell development in humans.
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Affiliation(s)
- Rui Chen
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Elena Lukianova
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Ina Schim van der Loeff
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | | | - Joseph D P Willet
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Kieran D James
- Institute of Immunology and Immunotherapy, University of Birmingham. B15 2TT Birmingham, UK
| | - Edward J Ryder
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Helen Griffin
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Hanna IJspeert
- Department of Immunology, Erasmus University Medical Center, Rotterdam 3000 CA, Netherlands
| | - Akshada Gajbhiye
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Frederic Lamoliatte
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Jose L Marin-Rubio
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Lisa Woodbine
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Brighton, UK
| | - Henrique Lemos
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - David J Swan
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Valeria Pintar
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Kamal Sayes
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | | | - Simon Eastham
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - David Dixon
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Martin Prete
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Elena Prigmore
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Penny Jeggo
- Genome Damage and Stability Centre, University of Sussex, BN1 9RQ Brighton, UK
| | - Joan Boyes
- Faculty of Biological Sciences, University of Leeds, LS2 9JT Leeds, UK
| | - Andrew Mellor
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Lei Huang
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Mirjam van der Burg
- Department of Immunology, Erasmus University Medical Center, Rotterdam 3000 CA, Netherlands
| | - Karin R Engelhardt
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - Asbjørg Stray-Pedersen
- Norwegian National Unit for Newborn Screening, Division of Pediatric and Adolescent Medicine, Oslo University Hospital, Oslo 0424, Norway
| | - Hans Christian Erichsen
- Division of Pediatric and Adolescent Medicine, Oslo University Hospital and Institute of Clinical Medicine, University of Oslo, Oslo 0424, Norway
| | - Andrew R Gennery
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
| | - Matthias Trost
- Biosciences Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
| | - David J Adams
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Graham Anderson
- Institute of Immunology and Immunotherapy, University of Birmingham. B15 2TT Birmingham, UK
| | - Anna Lorenc
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Gosia Trynka
- Wellcome Sanger Institute, Wellcome Genome Campus, CB10 1SA Hinxton, UK
- Open Targets, Wellcome Genome Campus, CB10 1SA Hinxton, UK
| | - Sophie Hambleton
- Translational and Clinical Research Institute, Newcastle University, NE2 4HH Newcastle upon Tyne, UK
- Great North Children's Hospital, Newcastle upon Tyne Hospitals NHS Foundation Trust, NE1 4LP Newcastle upon Tyne, UK
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Xu F, Zheng C, Xu W, Zhang S, Liu S, Chen X, Yao K. Breaking genetic shackles: The advance of base editing in genetic disorder treatment. Front Pharmacol 2024; 15:1364135. [PMID: 38510648 PMCID: PMC10953296 DOI: 10.3389/fphar.2024.1364135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/01/2024] [Accepted: 02/26/2024] [Indexed: 03/22/2024] Open
Abstract
The rapid evolution of gene editing technology has markedly improved the outlook for treating genetic diseases. Base editing, recognized as an exceptionally precise genetic modification tool, is emerging as a focus in the realm of genetic disease therapy. We provide a comprehensive overview of the fundamental principles and delivery methods of cytosine base editors (CBE), adenine base editors (ABE), and RNA base editors, with a particular focus on their applications and recent research advances in the treatment of genetic diseases. We have also explored the potential challenges faced by base editing technology in treatment, including aspects such as targeting specificity, safety, and efficacy, and have enumerated a series of possible solutions to propel the clinical translation of base editing technology. In conclusion, this article not only underscores the present state of base editing technology but also envisions its tremendous potential in the future, providing a novel perspective on the treatment of genetic diseases. It underscores the vast potential of base editing technology in the realm of genetic medicine, providing support for the progression of gene medicine and the development of innovative approaches to genetic disease therapy.
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Affiliation(s)
- Fang Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Caiyan Zheng
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Weihui Xu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shiyao Zhang
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Shanshan Liu
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Xiaopeng Chen
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
| | - Kai Yao
- Institute of Visual Neuroscience and Stem Cell Engineering, Wuhan University of Science and Technology, Wuhan, China
- College of Life Sciences and Health, Wuhan University of Science and Technology, Wuhan, China
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4
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Zheng X, Huang C, Lin Y, Han B, Chen Y, Li C, Li J, Ding Y, Song X, Wang W, Liang W, Wu J, Wu J, Gao J, Wei C, Zhang X, Tu Z, Yan S. Generation of inactivated IL2RG and RAG1 monkeys with severe combined immunodeficiency using base editing. Signal Transduct Target Ther 2023; 8:327. [PMID: 37661226 PMCID: PMC10475462 DOI: 10.1038/s41392-023-01544-y] [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: 02/01/2023] [Revised: 06/03/2023] [Accepted: 06/16/2023] [Indexed: 09/05/2023] Open
Abstract
Severe combined immunodeficiency (SCID) encompasses a range of inherited disorders that lead to a profound deterioration of the immune system. Among the pivotal genes associated with SCID, RAG1 and IL2RG play crucial roles. IL2RG is essential for the development, differentiation, and functioning of T, B, and NK cells, while RAG1 critically contributes to adaptive immunity by facilitating V(D)J recombination during the maturation of lymphocytes. Animal models carrying mutations in these genes exhibit notable deficiencies in their immune systems. Non-human primates (NHPs) are exceptionally well-suited models for biomedical research due to their genetic and physiological similarities to humans. Cytosine base editors (CBEs) serve as powerful tools for precisely and effectively modifying single-base mutations in the genome. Their successful implementation has been demonstrated in human cells, mice, and crop species. This study outlines the creation of an immunodeficient monkey model by deactivating both the IL2RG and RAG1 genes using the CBE4max system. The base-edited monkeys exhibited a severely compromised immune system characterized by lymphopenia, atrophy of lymphoid organs, and a deficiency of mature T cells. Furthermore, these base-edited monkeys were capable of hosting and supporting the growth of human breast cancer cells, leading to tumor formation. In summary, we have successfully developed an immunodeficient monkey model with the ability to foster tumor growth using the CBE4max system. These immunodeficiency monkeys show tremendous potential as valuable tools for advancing biomedical and translational research.
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Affiliation(s)
- Xiao Zheng
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Chunhui Huang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Yingqi Lin
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Bofeng Han
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Yizhi Chen
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Caijuan Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Jiawei Li
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China
| | - Yongyan Ding
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Xichen Song
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Wei Wang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Weien Liang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Jianhao Wu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Jiaxi Wu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Jiale Gao
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Chengxi Wei
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Xudong Zhang
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China
| | - Zhuchi Tu
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China.
| | - Sen Yan
- Guangdong Key Laboratory of Non-human Primate Research, Guangdong-Hongkong-Macau Institute of CNS Regeneration, Jinan University, 510632, Guangzhou, China.
- Department of Pathophysiology, School of Medicine, Jinan University, 510632, Guangzhou, China.
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Braams M, Pike-Overzet K, Staal FJT. The recombinase activating genes: architects of immune diversity during lymphocyte development. Front Immunol 2023; 14:1210818. [PMID: 37497222 PMCID: PMC10367010 DOI: 10.3389/fimmu.2023.1210818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Accepted: 06/19/2023] [Indexed: 07/28/2023] Open
Abstract
The mature lymphocyte population of a healthy individual has the remarkable ability to recognise an immense variety of antigens. Instead of encoding a unique gene for each potential antigen receptor, evolution has used gene rearrangements, also known as variable, diversity, and joining gene segment (V(D)J) recombination. This process is critical for lymphocyte development and relies on recombination-activating genes-1 (RAG1) and RAG2, here collectively referred to as RAG. RAG serves as powerful genome editing tools for lymphocytes and is strictly regulated to prevent dysregulation. However, in the case of dysregulation, RAG has been implicated in cases of cancer, autoimmunity and severe combined immunodeficiency (SCID). This review examines functional protein domains and motifs of RAG, describes advances in our understanding of the function and (dys)regulation of RAG, discuss new therapeutic options, such as gene therapy, for RAG deficiencies, and explore in vitro and in vivo methods for determining RAG activity and target specificity.
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Affiliation(s)
- Merijn Braams
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Karin Pike-Overzet
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
| | - Frank J. T. Staal
- Department of Immunology, Leiden University Medical Centre, Leiden, Netherlands
- Novo Nordisk Foundation Centre for Stem Cell Medicine (reNEW), Leiden University Medical Centre, Leiden, Netherlands
- Department of Paediatrics, Leiden University Medical Centre, Leiden, Netherlands
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6
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Sun S, Wijanarko K, Liani O, Strumila K, Ng ES, Elefanty AG, Stanley EG. Lymphoid cell development from fetal hematopoietic progenitors and human pluripotent stem cells. Immunol Rev 2023; 315:154-170. [PMID: 36939073 PMCID: PMC10952469 DOI: 10.1111/imr.13197] [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] [Indexed: 03/21/2023]
Abstract
Lymphoid cells encompass the adaptive immune system, including T and B cells and Natural killer T cells (NKT), and innate immune cells (ILCs), including Natural Killer (NK) cells. During adult life, these lineages are thought to derive from the differentiation of long-term hematopoietic stem cells (HSCs) residing in the bone marrow. However, during embryogenesis and fetal development, the ontogeny of lymphoid cells is both complex and multifaceted, with a large body of evidence suggesting that lymphoid lineages arise from progenitor cell populations antedating the emergence of HSCs. Recently, the application of single cell RNA-sequencing technologies and pluripotent stem cell-based developmental models has provided new insights into lymphoid ontogeny during embryogenesis. Indeed, PSC differentiation platforms have enabled de novo generation of lymphoid immune cells independently of HSCs, supporting conclusions drawn from the study of hematopoiesis in vivo. Here, we examine lymphoid development from non-HSC progenitor cells and technological advances in the differentiation of human lymphoid cells from pluripotent stem cells for clinical translation.
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Affiliation(s)
- Shicheng Sun
- Murdoch Children's Research InstituteThe Royal Children's HospitalParkvilleVictoriaAustralia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health SciencesUniversity of MelbourneParkvilleVictoriaAustralia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Kevin Wijanarko
- Murdoch Children's Research InstituteThe Royal Children's HospitalParkvilleVictoriaAustralia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health SciencesUniversity of MelbourneParkvilleVictoriaAustralia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Oniko Liani
- Murdoch Children's Research InstituteThe Royal Children's HospitalParkvilleVictoriaAustralia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health SciencesUniversity of MelbourneParkvilleVictoriaAustralia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Kathleen Strumila
- Murdoch Children's Research InstituteThe Royal Children's HospitalParkvilleVictoriaAustralia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health SciencesUniversity of MelbourneParkvilleVictoriaAustralia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Elizabeth S. Ng
- Murdoch Children's Research InstituteThe Royal Children's HospitalParkvilleVictoriaAustralia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health SciencesUniversity of MelbourneParkvilleVictoriaAustralia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Andrew G. Elefanty
- Murdoch Children's Research InstituteThe Royal Children's HospitalParkvilleVictoriaAustralia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health SciencesUniversity of MelbourneParkvilleVictoriaAustralia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research InstituteParkvilleVictoriaAustralia
| | - Edouard G. Stanley
- Murdoch Children's Research InstituteThe Royal Children's HospitalParkvilleVictoriaAustralia
- Department of Paediatrics, Faculty of Medicine, Dentistry and Health SciencesUniversity of MelbourneParkvilleVictoriaAustralia
- The Novo Nordisk Foundation Center for Stem Cell Medicine (reNEW), Murdoch Children's Research InstituteParkvilleVictoriaAustralia
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7
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Castiello MC, Brandas C, Capo V, Villa A. HyperIgE in hypomorphic recombination-activating gene defects. Curr Opin Immunol 2023; 80:102279. [PMID: 36529093 DOI: 10.1016/j.coi.2022.102279] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2022] [Accepted: 11/28/2022] [Indexed: 12/23/2022]
Abstract
Increased immunogloblulin-E (IgE) levels associated with eosinophilia represent a common finding observed in Omenn syndrome, a severe immunodeficiency caused by decreased V(D)J recombination, leading to restricted T- and B-cell receptor repertoire. V(D)J recombination is initiated by the lymphoid-restricted recombination-activating gene (RAG) recombinases. The lack of RAG proteins causes a block in lymphocyte differentiation, resulting in T-B- severe combined immunodeficiency. Conversely, hypomorphic mutations allow the generation of few T and B cells, leading to a spectrum of immunological phenotypes, in which immunodeficiency associates to inflammation, immune dysregulation, and autoimmunity. Elevated IgE levels are frequently observed in hypomorphic RAG patients. Here, we describe the role of RAG genes in lymphocyte differentiation and maintenance of immune tolerance.
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Affiliation(s)
- Maria Carmina Castiello
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy; Institute of Genetic and Biomedical Research, Milan Unit, National Research Council, Milan, Italy
| | - Chiara Brandas
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy; Translational and Molecular Medicine (DIMET), University of Milano-Bicocca, Monza, Italy
| | - Valentina Capo
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy; Institute of Genetic and Biomedical Research, Milan Unit, National Research Council, Milan, Italy
| | - Anna Villa
- San Raffaele Telethon Institute for Gene Therapy (SR-Tiget), IRCCS San Raffaele Scientific Institute, Milan, Italy; Institute of Genetic and Biomedical Research, Milan Unit, National Research Council, Milan, Italy.
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8
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Devaux CA, Pontarotti P, Nehari S, Raoult D. 'Cannibalism' of exogenous DNA sequences: The ancestral form of adaptive immunity which entails recognition of danger. Front Immunol 2022; 13:989707. [PMID: 36618387 PMCID: PMC9816338 DOI: 10.3389/fimmu.2022.989707] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 12/05/2022] [Indexed: 12/24/2022] Open
Abstract
Adaptive immunity is a sophisticated form of immune response capable of retaining the molecular memory of a very great diversity of target antigens (epitopes) as non-self. It is capable of reactivating itself upon a second encounter with an immunoglobulin or T-cell receptor antigen-binding site with a known epitope that had previously primed the host immune system. It has long been considered that adaptive immunity is a highly evolved form of non-self recognition that appeared quite late in speciation and complemented a more generalist response called innate immunity. Innate immunity offers a relatively non-specific defense (although mediated by sensors that could specifically recognize virus or bacteria compounds) and which does not retain a memory of the danger. But this notion of recent acquisition of adaptive immunity is challenged by the fact that another form of specific recognition mechanisms already existed in prokaryotes that may be able to specifically auto-protect against external danger. This recognition mechanism can be considered a primitive form of specific (adaptive) non-self recognition. It is based on the fact that many archaea and bacteria use a genome editing system that confers the ability to appropriate viral DNA sequences allowing prokaryotes to prevent host damage through a mechanism very similar to adaptive immunity. This is indistinctly called, 'endogenization of foreign DNA' or 'viral DNA predation' or, more pictorially 'DNA cannibalism'. For several years evidence has been accumulating, highlighting the crucial role of endogenization of foreign DNA in the fundamental processes related to adaptive immunity and leading to a change in the dogma that adaptive immunity appeared late in speciation.
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Affiliation(s)
- Christian A. Devaux
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France,Department of Biological Sciences, Centre National de la Recherche Scientifique, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France,*Correspondence: Christian A. Devaux,
| | - Pierre Pontarotti
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France,Department of Biological Sciences, Centre National de la Recherche Scientifique, Centre National de la Recherche Scientifique (CNRS)-SNC5039, Marseille, France
| | - Sephora Nehari
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France
| | - Didier Raoult
- Aix-Marseille University, Institut de recherche pour le développement (IRD), Assistance Publique Hôpitaux de Marseille (APHM), MEPHI, Institut Hospitalo-universitaire (IHU)-Méditerranée Infection, Marseille, France
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9
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Janssen AWF, Louisse J, Rijkers D, Pinckaers NET, Hoekstra SA, Hoogenboom RLAP, Peijnenburg AACM, Beekmann K. Perfluoroalkyl substances (PFASs) decrease the expression of recombination-activating genes (RAG1 and RAG2) in human B lymphoma Namalwa cells. Arch Toxicol 2022; 97:10.1007/s00204-022-03405-z. [PMID: 36326898 PMCID: PMC9859925 DOI: 10.1007/s00204-022-03405-z] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Accepted: 10/24/2022] [Indexed: 11/06/2022]
Abstract
Per- and polyfluoroalkyl substances (PFASs) are omnipresent and have been shown to induce a wide range of adverse effects, including hepatotoxicity, developmental toxicity and immunotoxicity. So far, little information is available about the mechanisms underlying the toxicity of PFASs, including those related to their immunotoxicity. Reported immunotoxic effects of PFASs include decreased antibody responses in experimental animals and humans, indicating that PFASs may, among others, affect B cell function. In the present study, we first assessed the effects of PFOA on the transcriptome of the human Namalwa B cell line using RNA seq analysis. Gene expression changes, analyzed using Ingenuity Pathway Analysis, pointed to various cellular processes affected by PFOA, including 'B cell development' and 'Primary immunodeficiency signaling'. Interestingly, PFOA decreased the expression of RAG1 and RAG2, genes involved in immunoglobulin and T cell receptor V(D)J recombination. As a next step, time- and concentration-dependent changes in the expression of RAG1 and RAG2 upon exposure to PFOA, PFNA, PFHxS and PFOS were studied through RT-qPCR analysis. Analysis with the concentration-response modeling software PROAST resulted in the following potency ranking: PFNA > PFOA > PFOS > PFHxS. Altogether, the present in vitro study provides insights into the effects of selected PFASs on B cells, identifying RAG1 and RAG2 expression as possible relevant targets that may play a role in the immunotoxicity of PFASs.
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Affiliation(s)
- Aafke W F Janssen
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands.
| | - Jochem Louisse
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands
| | - Deborah Rijkers
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands
| | - Nicole E T Pinckaers
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands
| | - Sjoerdtje A Hoekstra
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands
| | - Ron L A P Hoogenboom
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands
| | - Ad A C M Peijnenburg
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands
| | - Karsten Beekmann
- Wageningen Food Safety Research (WFSR), Wageningen University and Research, Akkermaalsbos 2, 6708 WB, Wageningen, The Netherlands
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Hennessy C, Deptula M, Issa F. Research Highlights. Transplantation 2022; 106:1888-1889. [PMID: 37779302 DOI: 10.1097/tp.0000000000004362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Conor Hennessy
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
| | - Milena Deptula
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
- Laboratory of Tissue Engineering and Regenerative Medicine, Division of Embryology, Medical University of Gdansk, Gdansk, Poland
| | - Fadi Issa
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, United Kingdom
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11
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Pan C, Zhao A, Li M. Atopic Dermatitis-like Genodermatosis: Disease Diagnosis and Management. Diagnostics (Basel) 2022; 12:diagnostics12092177. [PMID: 36140582 PMCID: PMC9498295 DOI: 10.3390/diagnostics12092177] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2022] [Revised: 07/23/2022] [Accepted: 08/15/2022] [Indexed: 11/29/2022] Open
Abstract
Eczema is a classical characteristic not only in atopic dermatitis but also in various genodermatosis. Patients suffering from primary immunodeficiency diseases such as hyper-immunoglobulin E syndromes, Wiskott-Aldrich syndrome, immune dysregulation, polyendocrinopathy, enteropathy, X-linked syndrome, STAT5B deficiency, Omenn syndrome, atypical complete DiGeorge syndrome; metabolic disorders such as acrodermatitis enteropathy, multiple carboxylase deficiency, prolidase deficiency; and other rare syndromes like severe dermatitis, multiple allergies and metabolic wasting syndrome, Netherton syndrome, and peeling skin syndrome frequently perform with eczema-like lesions. These genodermatosis may be misguided in the context of eczematous phenotype. Misdiagnosis of severe disorders unavoidably affects appropriate treatment and leads to irreversible outcomes for patients, which underlines the importance of molecular diagnosis and genetic analysis. Here we conclude clinical manifestations, molecular mechanism, diagnosis and management of several eczema-related genodermatosis and provide accessible advice to physicians.
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Affiliation(s)
- Chaolan Pan
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Anqi Zhao
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
| | - Ming Li
- Department of Dermatology, Xinhua Hospital, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Institute of Dermatology, Shanghai Jiaotong University School of Medicine, Shanghai 200092, China
- Department of Dermatology, The Children’s Hospital of Fudan University, Shanghai 200092, China
- Correspondence: ; Tel.: +86-2125078571
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12
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Luo S, Qiao R, Zhang X. DNA Damage Response and Repair in Adaptive Immunity. Front Cell Dev Biol 2022; 10:884873. [PMID: 35663402 PMCID: PMC9157429 DOI: 10.3389/fcell.2022.884873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2022] [Accepted: 03/31/2022] [Indexed: 11/16/2022] Open
Abstract
The diversification of B-cell receptor (BCR), as well as its secreted product, antibody, is a hallmark of adaptive immunity, which has more specific roles in fighting against pathogens. The antibody diversification is from recombination-activating gene (RAG)-initiated V(D)J recombination, activation-induced cytidine deaminase (AID)-initiated class switch recombination (CSR), and V(D)J exon somatic hypermutation (SHM). The proper repair of RAG- and AID-initiated DNA lesions and double-strand breaks (DSBs) is required for promoting antibody diversification, suppressing genomic instability, and oncogenic translocations. DNA damage response (DDR) factors and DSB end-joining factors are recruited to the RAG- and AID-initiated DNA lesions and DSBs to coordinately resolve them for generating productive recombination products during antibody diversification. Recently, cohesin-mediated loop extrusion is proposed to be the underlying mechanism of V(D)J recombination and CSR, which plays essential roles in promoting the orientation-biased deletional end-joining . Here, we will discuss the mechanism of DNA damage repair in antibody diversification.
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Affiliation(s)
- Sha Luo
- Biomedical Pioneering Innovation Center, Innovation Center for Genomics, Peking University, Beijing, China
- Academy for Advanced Interdisciplinery Studies, Peking University, Beijing, China
| | - Ruolin Qiao
- Biomedical Pioneering Innovation Center, Innovation Center for Genomics, Peking University, Beijing, China
- Academy for Advanced Interdisciplinery Studies, Peking University, Beijing, China
| | - Xuefei Zhang
- Biomedical Pioneering Innovation Center, Innovation Center for Genomics, Peking University, Beijing, China
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Liu Y, Yin J, Gan T, Liu M, Xin C, Zhang W, Hu J. PEM-seq comprehensively quantifies DNA repair outcomes during gene-editing and DSB repair. STAR Protoc 2022; 3:101088. [PMID: 35462794 PMCID: PMC9019705 DOI: 10.1016/j.xpro.2021.101088] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The repair products of double-stranded DNA breaks (DSBs) are crucial for investigating the mechanism underlying DNA damage repair as well as evaluating the safety and efficiency of gene-editing; however, a comprehensively quantitative assay remains to be established. Here, we describe the step-by-step instructions of the primer extension-mediated sequencing (PEM-seq), followed by the framework of data processing and statistical analysis. PEM-seq presents a full spectrum of repair outcomes for both genome-editing-induced and endogenous DSBs in mouse and human cells. For complete details on the use and execution of this profile, please refer to Gan et al. (2021), Yin et al. (2019), Liu et al. (2021a), and Zhang et al. (2021). PEM-seq comprehensively quantifies DSB repair outcomes PEM-seq evaluates the efficiency and safety of genome-editing tools PEM-seq studies the impact of DNA damage response pathways on DSB repair PEM-seq identifies endogenous DNA damage sites and DNA fragment integrations
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