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Balducci E, Steimlé T, Smith C, Villarese P, Feroul M, Payet-Bornet D, Kaltenbach S, Couronné L, Lhermitte L, Touzart A, Dourthe ME, Simonin M, Baruchel A, Dombret H, Ifrah N, Boissel N, Nadel B, Macintyre E, Cieslak A, Asnafi V. TREC mediated oncogenesis in human immature T lymphoid malignancies preferentially involves ZFP36L2. Mol Cancer 2023; 22:108. [PMID: 37430263 DOI: 10.1186/s12943-023-01794-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2023] [Accepted: 05/25/2023] [Indexed: 07/12/2023] Open
Abstract
The reintegration of excised signal joints resulting from human V(D)J recombination was described as a potent source of genomic instability in human lymphoid cancers. However, such molecular events have not been recurrently reported in clinical patient lymphoma/leukemia samples. Using a specifically designed NGS-capture pipeline, we here demonstrated the reintegration of T-cell receptor excision circles (TRECs) in 20/1533 (1.3%) patients with T-cell acute lymphoblastic leukemia (T-ALL) and T-cell lymphoblastic lymphoma (T-LBL). Remarkably, the reintegration of TREC recurrently targeted the tumor suppressor gene, ZFP36L2, in 17/20 samples. Thus, our data identified a new and hardly detectable mechanism of gene deregulation in lymphoid cancers providing new insights in human oncogenesis.
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Affiliation(s)
- Estelle Balducci
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
| | - Thomas Steimlé
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
- TAGC, UMR 1090, Aix-Marseille University, INSERM, Marseille, France
| | - Charlotte Smith
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
| | - Patrick Villarese
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
| | - Mélanie Feroul
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
| | | | - Sophie Kaltenbach
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
| | - Lucile Couronné
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
| | - Ludovic Lhermitte
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
| | - Aurore Touzart
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
| | - Marie-Emilie Dourthe
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
| | - Mathieu Simonin
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
| | - André Baruchel
- Department of Pediatric Hematology and Immunology, University Hospital Robert Debré, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France
- Institut Universitaire d'Hématologie, EA-3518, University Hospital Saint-Louis, Assistance Publique des Hôpitaux de Paris (APHP), Paris, France
| | - Hervé Dombret
- Université Paris Diderot, Institut Universitaire d'Hématologie, EA-3518, Assistance Publique-Hôpitaux de Paris, University Hospital Saint-Louis, 75010, Paris, France
| | - Norbert Ifrah
- PRES LUNAM, CHU Angers Service Des Maladies du Sang, INSERM U 892, 49933, Angers, France
| | - Nicolas Boissel
- Université Paris Diderot, Institut Universitaire d'Hématologie, EA-3518, Assistance Publique-Hôpitaux de Paris, University Hospital Saint-Louis, 75010, Paris, France
| | - Bertrand Nadel
- Aix Marseille Université, CNRS, INSERM, CIML, Marseille, France
| | - Elizabeth Macintyre
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France
| | - Agata Cieslak
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France.
| | - Vahid Asnafi
- Laboratory of Onco-Hematology, Necker Children's Hospital, Assistance Publique-Hôpitaux de Paris (AP-HP), Paris, France.
- Université Paris Cité, CNRS, INSERM U1151, Institut Necker Enfants Malades (INEM), Paris, France.
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Christie SM, Fijen C, Rothenberg E. V(D)J Recombination: Recent Insights in Formation of the Recombinase Complex and Recruitment of DNA Repair Machinery. Front Cell Dev Biol 2022; 10:886718. [PMID: 35573672 PMCID: PMC9099191 DOI: 10.3389/fcell.2022.886718] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Accepted: 04/01/2022] [Indexed: 11/13/2022] Open
Abstract
V(D)J recombination is an essential mechanism of the adaptive immune system, producing a diverse set of antigen receptors in developing lymphocytes via regulated double strand DNA break and subsequent repair. DNA cleavage is initiated by the recombinase complex, consisting of lymphocyte specific proteins RAG1 and RAG2, while the repair phase is completed by classical non-homologous end joining (NHEJ). Many of the individual steps of this process have been well described and new research has increased the scale to understand the mechanisms of initiation and intermediate stages of the pathway. In this review we discuss 1) the regulatory functions of RAGs, 2) recruitment of RAGs to the site of recombination and formation of a paired complex, 3) the transition from a post-cleavage complex containing RAGs and cleaved DNA ends to the NHEJ repair phase, and 4) the potential redundant roles of certain factors in repairing the break. Regulatory (non-core) domains of RAGs are not necessary for catalytic activity, but likely influence recruitment and stabilization through interaction with modified histones and conformational changes. To form long range paired complexes, recent studies have found evidence in support of large scale chromosomal contraction through various factors to utilize diverse gene segments. Following the paired cleavage event, four broken DNA ends must now make a regulated transition to the repair phase, which can be controlled by dynamic conformational changes and post-translational modification of the factors involved. Additionally, we examine the overlapping roles of certain NHEJ factors which allows for prevention of genomic instability due to incomplete repair in the absence of one, but are lethal in combined knockouts. To conclude, we focus on the importance of understanding the detail of these processes in regards to off-target recombination or deficiency-mediated clinical manifestations.
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Affiliation(s)
- Shaun M. Christie
- *Correspondence: Shaun M. Christie, ; Carel Fijen, ; Eli Rothenberg,
| | - Carel Fijen
- *Correspondence: Shaun M. Christie, ; Carel Fijen, ; Eli Rothenberg,
| | - Eli Rothenberg
- *Correspondence: Shaun M. Christie, ; Carel Fijen, ; Eli Rothenberg,
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Chen ELY, Brauer PM, Martinez EC, Huang X, Yu N, Anderson MK, Li Y, Zúñiga-Pflücker JC. Cutting Edge: TCR-β Selection Is Required at the CD4 +CD8 + Stage of Human T Cell Development. THE JOURNAL OF IMMUNOLOGY 2021; 206:2271-2276. [PMID: 33941655 DOI: 10.4049/jimmunol.2100141] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 03/18/2021] [Indexed: 12/25/2022]
Abstract
T cell development is predicated on the successful rearrangement of the TCR gene loci, which encode for Ag-specific receptors. Recombination-activating gene (RAG) 2 is required for TCR gene rearrangements, which occur during specific stages of T cell development. In this study, we differentiated human pluripotent stem cells with a CRISPR/Cas9-directed deletion of the RAG2 gene (RAG2-KO) to elucidate the requirement for the TCR β-chain in mediating β-selection during human T cell development. In stark contrast to mice, human RAG2-KO T lineage progenitors progressed to the CD4+CD8+ double-positive (DP) stage in the absence of TCRβ rearrangements. Nonetheless, RAG2-KO DPs retrovirally transduced to express a rearranged TCR β-chain showed increased survival and proliferation as compared with control-transduced RAG2-KO DPs. Furthermore, transcriptomic analysis showed that TCRβ- and control-transduced RAG2-KO DPs differed in gene pathways related to survival and proliferation. Our results provide important insights as to the distinct requirement for the TCR β-chain during human T cell development.
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Affiliation(s)
- Edward L Y Chen
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Sunnybrook Research Institute, Toronto, Ontario, Canada
| | | | | | - Xiaotian Huang
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing, China
| | - Ning Yu
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing, China
| | - Michele K Anderson
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada.,Sunnybrook Research Institute, Toronto, Ontario, Canada
| | - Yang Li
- Department of Cell Biology, School of Basic Medical Sciences, Peking University Stem Cell Research Center, Peking University, Beijing, China
| | - Juan Carlos Zúñiga-Pflücker
- Department of Immunology, University of Toronto, Toronto, Ontario, Canada .,Sunnybrook Research Institute, Toronto, Ontario, Canada
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