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Banda A, Impomeni O, Singh A, Baloch AR, Hu W, Jaijyan DK. Precision in Action: The Role of Clustered Regularly Interspaced Short Palindromic Repeats/Cas in Gene Therapies. Vaccines (Basel) 2024; 12:636. [PMID: 38932365 PMCID: PMC11209408 DOI: 10.3390/vaccines12060636] [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: 04/14/2024] [Revised: 05/21/2024] [Accepted: 06/04/2024] [Indexed: 06/28/2024] Open
Abstract
Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)-associated enzyme-CAS holds great promise for treating many uncured human diseases and illnesses by precisely correcting harmful point mutations and disrupting disease-causing genes. The recent Food and Drug Association (FDA) approval of the first CRISPR-based gene therapy for sickle cell anemia marks the beginning of a new era in gene editing. However, delivering CRISPR specifically into diseased cells in vivo is a significant challenge and an area of intense research. The identification of new CRISPR/Cas variants, particularly ultra-compact CAS systems with robust gene editing activities, paves the way for the low-capacity delivery vectors to be used in gene therapies. CRISPR/Cas technology has evolved beyond editing DNA to cover a wide spectrum of functionalities, including RNA targeting, disease diagnosis, transcriptional/epigenetic regulation, chromatin imaging, high-throughput screening, and new disease modeling. CRISPR/Cas can be used to engineer B-cells to produce potent antibodies for more effective vaccines and enhance CAR T-cells for the more precise and efficient targeting of tumor cells. However, CRISPR/Cas technology has challenges, including off-target effects, toxicity, immune responses, and inadequate tissue-specific delivery. Overcoming these challenges necessitates the development of a more effective and specific CRISPR/Cas delivery system. This entails strategically utilizing specific gRNAs in conjunction with robust CRISPR/Cas variants to mitigate off-target effects. This review seeks to delve into the intricacies of the CRISPR/Cas mechanism, explore progress in gene therapies, evaluate gene delivery systems, highlight limitations, outline necessary precautions, and scrutinize the ethical considerations associated with its application.
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Affiliation(s)
- Amrutha Banda
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Olivia Impomeni
- Department of Biology, The College of New Jersey, Ewing Township, NJ 08618, USA
| | - Aparana Singh
- Department of Chemistry, National Institute of Technology Agartala, Agartala 799046, India;
| | - Abdul Rasheed Baloch
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Wenhui Hu
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
| | - Dabbu Kumar Jaijyan
- Department of Anatomy and Neurobiology, School of Medicine, Virginia Commonwealth University, Richmond, VA 23284, USA;
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2
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Boulch M, Cazaux M, Cuffel A, Guerin MV, Garcia Z, Alonso R, Lemaître F, Beer A, Corre B, Menger L, Grandjean CL, Morin F, Thieblemont C, Caillat-Zucman S, Bousso P. Tumor-intrinsic sensitivity to the pro-apoptotic effects of IFN-γ is a major determinant of CD4 + CAR T-cell antitumor activity. NATURE CANCER 2023; 4:968-983. [PMID: 37248395 PMCID: PMC10368531 DOI: 10.1038/s43018-023-00570-7] [Citation(s) in RCA: 27] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Accepted: 04/27/2023] [Indexed: 05/31/2023]
Abstract
CD4+ T cells and CD4+ chimeric antigen receptor (CAR) T cells display highly variable antitumor activity in preclinical models and in patients; however, the mechanisms dictating how and when CD4+ T cells promote tumor regression are incompletely understood. With the help of functional intravital imaging, we report that interferon (IFN)-γ production but not perforin-mediated cytotoxicity was the dominant mechanism for tumor elimination by anti-CD19 CD4+ CAR T cells. Mechanistically, mouse or human CD4+ CAR T-cell-derived IFN-γ diffused extensively to act on tumor cells at distance selectively killing tumors sensitive to cytokine-induced apoptosis, including antigen-negative variants. In anti-CD19 CAR T-cell-treated patients exhibiting elevated CAR CD4:CD8 ratios, strong induction of serum IFN-γ was associated with increased survival. We propose that the sensitivity of tumor cells to the pro-apoptotic activity of IFN-γ is a major determinant of CD4+ CAR T-cell efficacy and may be considered to guide the use of CD4+ T cells during immunotherapy.
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Affiliation(s)
- Morgane Boulch
- Institut Pasteur, Université de Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Marine Cazaux
- Institut Pasteur, Université de Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Alexis Cuffel
- Université de Paris Cité, Hôpital Saint-Louis, AP-HP Nord, Laboratoire d'Immunologie, Paris, France
- INSERM UMR976, Institut de Recherche St-Louis, Paris, France
| | - Marion V Guerin
- Institut Pasteur, Université de Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Zacarias Garcia
- Institut Pasteur, Université de Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Ruby Alonso
- Institut Pasteur, Université de Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Fabrice Lemaître
- Institut Pasteur, Université de Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Alexander Beer
- Institut Pasteur, Université de Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Béatrice Corre
- Institut Pasteur, Université de Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Laurie Menger
- Gustave Roussy, Villejuif, France; INSERM U1015, Villejuif, France
| | - Capucine L Grandjean
- Institut Pasteur, Université de Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Paris, France
| | - Florence Morin
- Université de Paris Cité, Hôpital Saint-Louis, AP-HP Nord, Laboratoire d'Immunologie, Paris, France
| | - Catherine Thieblemont
- Service d'Hémato-Oncologie, Hôpital Saint-Louis, AP-HP, Université de Paris Cité, Paris, France
| | - Sophie Caillat-Zucman
- Université de Paris Cité, Hôpital Saint-Louis, AP-HP Nord, Laboratoire d'Immunologie, Paris, France
- INSERM UMR976, Institut de Recherche St-Louis, Paris, France
| | - Philippe Bousso
- Institut Pasteur, Université de Paris Cité, INSERM U1223, Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Paris, France.
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3
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Edelstein J, Fritz M, Lai SK. Challenges and opportunities in gene editing of B cells. Biochem Pharmacol 2022; 206:115285. [PMID: 36241097 DOI: 10.1016/j.bcp.2022.115285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2022] [Revised: 09/28/2022] [Accepted: 09/30/2022] [Indexed: 01/29/2023]
Abstract
B cells have long been an underutilized target in immune cell engineering, despite a number of unique attributes that could address longstanding challenges in medicine. Notably, B cells evolved to secrete large quantities of antibodies for prolonged periods, making them suitable platforms for long-term protein delivery. Recent advances in gene editing technologies, such as CRISPR-Cas, have improved the precision and efficiency of engineering and expanded potential applications of engineered B cells. While most work on B cell editing has focused on ex vivo modification, a body of recent work has also advanced the possibility of in vivo editing applications. In this review, we will discuss both past and current approaches to B cell engineering, and its promising applications in immunology research and therapeutic gene editing.
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Affiliation(s)
- Jasmine Edelstein
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Marshall Fritz
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA
| | - Samuel K Lai
- Division of Pharmacoengineering and Molecular Pharmaceutics, Eshelman School of Pharmacy, University of North Carolina, Chapel Hill, NC, USA; Department of Biomedical Engineering, University of North Carolina, Chapel Hill, NC, USA; Department of Immunology and Microbiology, University of North Carolina, Chapel Hill, NC, USA.
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4
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Vincendeau E, Wei W, Zhang X, Planchais C, Yu W, Lenden-Hasse H, Cokelaer T, Pipoli da Fonseca J, Mouquet H, Adams DJ, Alt FW, Jackson SP, Balmus G, Lescale C, Deriano L. SHLD1 is dispensable for 53BP1-dependent V(D)J recombination but critical for productive class switch recombination. Nat Commun 2022; 13:3707. [PMID: 35764636 PMCID: PMC9240092 DOI: 10.1038/s41467-022-31287-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 06/13/2022] [Indexed: 11/21/2022] Open
Abstract
SHLD1 is part of the Shieldin (SHLD) complex, which acts downstream of 53BP1 to counteract DNA double-strand break (DSB) end resection and promote DNA repair via non-homologous end-joining (NHEJ). While 53BP1 is essential for immunoglobulin heavy chain class switch recombination (CSR), long-range V(D)J recombination and repair of RAG-induced DSBs in XLF-deficient cells, the function of SHLD during these processes remains elusive. Here we report that SHLD1 is dispensable for lymphocyte development and RAG-mediated V(D)J recombination, even in the absence of XLF. By contrast, SHLD1 is essential for restricting resection at AID-induced DSB ends in both NHEJ-proficient and NHEJ-deficient B cells, providing an end-protection mechanism that permits productive CSR by NHEJ and alternative end-joining. Finally, we show that this SHLD1 function is required for orientation-specific joining of AID-initiated DSBs. Our data thus suggest that 53BP1 promotes V(D)J recombination and CSR through two distinct mechanisms: SHLD-independent synapsis of V(D)J segments and switch regions within chromatin, and SHLD-dependent protection of AID-DSB ends against resection.
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Affiliation(s)
- Estelle Vincendeau
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Wenming Wei
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Xuefei Zhang
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
- Biomedical Pioneering Innovation Center (BIOPIC) and Beijing Advanced Innovation Center for Genomics (ICG), Peking University, Beijing, 100871, China
| | - Cyril Planchais
- Institut Pasteur, Université de Paris, INSERM U1222, Laboratory of Humoral Immunology, 75015, Paris, France
| | - Wei Yu
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Hélène Lenden-Hasse
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France
| | - Thomas Cokelaer
- Institut Pasteur, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques, 75015, Paris, France
- Institut Pasteur, Hub de Bioinformatique et Biostatistique, Département de Biologie Computationnelle, 75015, Paris, France
| | - Juliana Pipoli da Fonseca
- Institut Pasteur, Plate-forme Technologique Biomics, Centre de Ressources et Recherches Technologiques, 75015, Paris, France
| | - Hugo Mouquet
- Institut Pasteur, Université de Paris, INSERM U1222, Laboratory of Humoral Immunology, 75015, Paris, France
| | - David J Adams
- Wellcome Trust Sanger Institute, Cambridge, CB10 1SA, UK
| | - Frederick W Alt
- Howard Hughes Medical Institute, Program in Cellular and Molecular Medicine at Boston Children's Hospital, Department of Genetics, Harvard Medical School, Boston, MA, 02115, USA
| | - Stephen P Jackson
- Wellcome Trust/Cancer Research UK Gurdon Institute, Department of Biochemistry, University of Cambridge, Cambridge, CB2 1QN, UK
| | - Gabriel Balmus
- UK Dementia Research Institute at University of Cambridge, Department of Clinical Neurosciences, University of Cambridge, Cambridge, CB2 0AH, UK
| | - Chloé Lescale
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France.
| | - Ludovic Deriano
- Institut Pasteur, Université Paris Cité, INSERM U1223, Équipe Labellisée Ligue Contre Le Cancer, Genome Integrity, Immunity and Cancer Unit, 75015, Paris, France.
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5
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Khazen R, Cazaux M, Lemaître F, Corre B, Garcia Z, Bousso P. Functional heterogeneity of cytotoxic T cells and tumor resistance to cytotoxic hits limit anti-tumor activity in vivo. EMBO J 2021; 40:e106658. [PMID: 33855732 PMCID: PMC8167356 DOI: 10.15252/embj.2020106658] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2020] [Revised: 02/19/2021] [Accepted: 02/26/2021] [Indexed: 01/17/2023] Open
Abstract
Cytotoxic T cells (CTLs) can eliminate tumor cells through the delivery of lethal hits, but the actual efficiency of this process in the tumor microenvironment is unclear. Here, we visualized the capacity of single CTLs to attack tumor cells in vitro and in vivo using genetically encoded reporters that monitor cell damage and apoptosis. Using two distinct malignant B-cell lines, we found that the majority of cytotoxic hits delivered by CTLs in vitro were sublethal despite proper immunological synapse formation, and associated with reversible calcium elevation and membrane damage in the targets. Through intravital imaging in the bone marrow, we established that the majority of CTL interactions with lymphoma B cells were either unproductive or sublethal. Functional heterogeneity of CTLs contributed to diverse outcomes during CTL-tumor contacts in vivo. In the therapeutic settings of anti-CD19 CAR T cells, the majority of CAR T cell-tumor interactions were also not associated with lethal hit delivery. Thus, differences in CTL lytic potential together with tumor cell resistance to cytotoxic hits represent two important bottlenecks for anti-tumor responses in vivo.
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Affiliation(s)
- Roxana Khazen
- Dynamics of Immune Responses UnitInstitut Pasteur, Equipe Labellisée Ligue Contre le CancerINSERM U1223ParisFrance
| | - Marine Cazaux
- Dynamics of Immune Responses UnitInstitut Pasteur, Equipe Labellisée Ligue Contre le CancerINSERM U1223ParisFrance
- Université de ParisParisFrance
| | - Fabrice Lemaître
- Dynamics of Immune Responses UnitInstitut Pasteur, Equipe Labellisée Ligue Contre le CancerINSERM U1223ParisFrance
| | - Beatrice Corre
- Dynamics of Immune Responses UnitInstitut Pasteur, Equipe Labellisée Ligue Contre le CancerINSERM U1223ParisFrance
| | - Zacarias Garcia
- Dynamics of Immune Responses UnitInstitut Pasteur, Equipe Labellisée Ligue Contre le CancerINSERM U1223ParisFrance
| | - Philippe Bousso
- Dynamics of Immune Responses UnitInstitut Pasteur, Equipe Labellisée Ligue Contre le CancerINSERM U1223ParisFrance
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6
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Tyrosine kinase inhibitors protect the salivary gland from radiation damage by increasing DNA double-strand break repair. J Biol Chem 2021; 296:100401. [PMID: 33571522 PMCID: PMC7973138 DOI: 10.1016/j.jbc.2021.100401] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 11/23/2022] Open
Abstract
We have previously shown that the tyrosine kinase inhibitors (TKIs) dasatinib and imatinib can protect salivary glands from irradiation (IR) damage without impacting tumor therapy. However, how they induce this protection is unknown. Here we show that TKIs mediate radioprotection by increasing the repair of DNA double-stranded breaks. DNA repair in IR-treated parotid cells, but not oral cancer cells, occurs more rapidly following pretreatment with imatinib or dasatinib and is accompanied by faster formation of DNA damage-induced foci. Similar results were observed in the parotid glands of mice pretreated with imatinib prior to IR, suggesting that TKIs "prime" cells for DNA repair. Mechanistically, we observed that TKIs increased IR-induced activation of DNA-PK, but not ATM. Pretreatment of parotid cells with the DNA-PK inhibitor NU7441 reversed the increase in DNA repair induced by TKIs. Reporter assays specific for homologous recombination (HR) or nonhomologous end joining (NHEJ) verified regulatation of both DNA repair pathways by imatinib. Moreover, TKIs also increased basal and IR-induced expression of genes associated with NHEJ (DNA ligase 4, Artemis, XLF) and HR (Rad50, Rad51 and BRCA1); depletion of DNA ligase 4 or BRCA1 reversed the increase in DNA repair mediated by TKIs. In addition, TKIs increased activation of the ERK survival pathway in parotid cells, and ERK was required for the increased survival of TKI-treated cells. Our studies demonstrate a dual mechanism by which TKIs provide radioprotection of the salivary gland tissues and support exploration of TKIs clinically in head and neck cancer patients undergoing IR therapy.
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Engineered B cells expressing an anti-HIV antibody enable memory retention, isotype switching and clonal expansion. Nat Commun 2020; 11:5851. [PMID: 33203857 PMCID: PMC7673991 DOI: 10.1038/s41467-020-19649-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Accepted: 10/15/2020] [Indexed: 11/26/2022] Open
Abstract
HIV viremia can be controlled by chronic antiretroviral therapy. As a potentially single-shot alternative, B cells engineered by CRISPR/Cas9 to express anti-HIV broadly neutralizing antibodies (bNAbs) are capable of secreting high antibody titers. Here, we show that, upon immunization of mice, adoptively transferred engineered B cells home to germinal centers (GC) where they predominate over the endogenous response and differentiate into memory and plasma cells while undergoing class switch recombination (CSR). Immunization with a high affinity antigen increases accumulation in GCs and CSR rates. Boost immunization increases the rate of engineered B cells in GCs and antibody secretion, indicating memory retention. Finally, antibody sequences of engineered B cells in the spleen show patterns of clonal selection. Therefore, B cells can be engineered into what could be a living and evolving drug. Chronic antiretroviral therapy does not eradicate HIV infection. Here, the authors describe a potentially one-shot alternative by engineering B cells to express anti-HIV antibodies and undergo memory retention, isotype switching and clonal expansion
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8
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Repair of G1 induced DNA double-strand breaks in S-G2/M by alternative NHEJ. Nat Commun 2020; 11:5239. [PMID: 33067475 PMCID: PMC7567796 DOI: 10.1038/s41467-020-19060-w] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
The alternative non-homologous end-joining (NHEJ) pathway promotes DNA double-strand break (DSB) repair in cells deficient for NHEJ or homologous recombination, suggesting that it operates at all stages of the cell cycle. Here, we use an approach in which DNA breaks can be induced in G1 cells and their repair tracked, enabling us to show that joining of DSBs is not functional in G1-arrested XRCC4-deficient cells. Cell cycle entry into S-G2/M restores DSB repair by Pol θ-dependent and PARP1-independent alternative NHEJ with repair products bearing kilo-base long DNA end resection, micro-homologies and chromosome translocations. We identify a synthetic lethal interaction between XRCC4 and Pol θ under conditions of G1 DSBs, associated with accumulation of unresolved DNA ends in S-G2/M. Collectively, our results support the conclusion that the repair of G1 DSBs progressing to S-G2/M by alternative NHEJ drives genomic instability and represent an attractive target for future DNA repair-based cancer therapies. Depending on the cell cycle stage, cells can repair their genome via different pathways. Here the authors reveal mechanistic insights into repair of double strand breaks induced during G1 in an error-prone manner by Pol θ-dependent and PARP1-independent alt NHEJ during the SG2/M phases of the cell cycle
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9
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Beck C, Castañeda-Zegarra S, Huse C, Xing M, Oksenych V. Mediator of DNA Damage Checkpoint Protein 1 Facilitates V(D)J Recombination in Cells Lacking DNA Repair Factor XLF. Biomolecules 2019; 10:biom10010060. [PMID: 31905950 PMCID: PMC7023129 DOI: 10.3390/biom10010060] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Revised: 12/23/2019] [Accepted: 12/24/2019] [Indexed: 11/16/2022] Open
Abstract
DNA double-strand breaks (DSBs) trigger the Ataxia telangiectasia mutated (ATM)-dependent DNA damage response (DDR), which consists of histone H2AX, MDC1, RNF168, 53BP1, PTIP, RIF1, Rev7, and Shieldin. Early stages of B and T lymphocyte development are dependent on recombination activating gene (RAG)-induced DSBs that form the basis for further V(D)J recombination. Non-homologous end joining (NHEJ) pathway factors recognize, process, and ligate DSBs. Based on numerous loss-of-function studies, DDR factors were thought to be dispensable for the V(D)J recombination. In particular, mice lacking Mediator of DNA Damage Checkpoint Protein 1 (MDC1) possessed nearly wild-type levels of mature B and T lymphocytes in the spleen, thymus, and bone marrow. NHEJ factor XRCC4-like factor (XLF)/Cernunnos is functionally redundant with ATM, histone H2AX, and p53-binding protein 1 (53BP1) during the lymphocyte development in mice. Here, we genetically inactivated MDC1, XLF, or both MDC1 and XLF in murine vAbl pro-B cell lines and, using chromosomally integrated substrates, demonstrated that MDC1 stimulates the V(D)J recombination in cells lacking XLF. Moreover, combined inactivation of MDC1 and XLF in mice resulted in synthetic lethality. Together, these findings suggest that MDC1 and XLF are functionally redundant during the mouse development, in general, and the V(D)J recombination, in particular.
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Affiliation(s)
- Carole Beck
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Sergio Castañeda-Zegarra
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Camilla Huse
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Mengtan Xing
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
| | - Valentyn Oksenych
- Department of Clinical and Molecular Medicine (IKOM), Norwegian University of Science and Technology (NTNU), 7491 Trondheim, Norway
- St. Olavs Hospital, Trondheim University Hospital, Clinic of Medicine, Postboks 3250 Sluppen, 7006 Trondheim, Norway
- Department of Biosciences and Nutrition (BioNuT), Karolinska Institutet, 14183 Huddinge, Sweden
- Correspondence:
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10
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Yahia-Cherbal H, Rybczynska M, Lovecchio D, Stephen T, Lescale C, Placek K, Larghero J, Rogge L, Bianchi E. NFAT primes the human RORC locus for RORγt expression in CD4 + T cells. Nat Commun 2019; 10:4698. [PMID: 31619674 PMCID: PMC6795897 DOI: 10.1038/s41467-019-12680-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2018] [Accepted: 09/24/2019] [Indexed: 02/07/2023] Open
Abstract
T helper 17 (Th17) cells have crucial functions in mucosal immunity and the pathogenesis of several chronic inflammatory diseases. The lineage-specific transcription factor, RORγt, encoded by the RORC gene modulates Th17 polarization and function, as well as thymocyte development. Here we define several regulatory elements at the human RORC locus in thymocytes and peripheral CD4+ T lymphocytes, with CRISPR/Cas9-guided deletion of these genomic segments supporting their role in RORγt expression. Mechanistically, T cell receptor stimulation induces cyclosporine A-sensitive histone modifications and P300/CBP acetylase recruitment at these elements in activated CD4+ T cells. Meanwhile, NFAT proteins bind to these regulatory elements and activate RORγt transcription in cooperation with NF-kB. Our data thus demonstrate that NFAT specifically regulate RORγt expression by binding to the RORC locus and promoting its permissive conformation. The master transcription factor RORγt, encoded by the RORC gene, controls the polarization of CD4+ T cells expressing interleukin-17 (Th17). Here the authors describe several regulatory elements at the RORC locus that are recognized by NFAT and NFkB to induce a permissive epigenetic configuration of the RORC gene for RORγt expression and Th17 differentiation.
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Affiliation(s)
- Hanane Yahia-Cherbal
- Institut Pasteur, Immunoregulation Unit, Department of Immunology, Paris, France.,Université Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, Paris, France
| | - Magda Rybczynska
- Institut Pasteur, Immunoregulation Unit, Department of Immunology, Paris, France.,Laboratoire Colloides et Matériaux Divisés, École supérieure de Physique et de Chimie industrielles, Paris, France
| | - Domenica Lovecchio
- Institut Pasteur, Immunoregulation Unit, Department of Immunology, Paris, France
| | - Tharshana Stephen
- Institut Pasteur, Unité de Technologie et Service Cytométrie et Biomarqueurs (UTechS CB), Centre de recherche translationnelle (CRT), Paris, France
| | - Chloé Lescale
- Institut Pasteur, Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Paris, France
| | - Katarzyna Placek
- Institut Pasteur, Immunoregulation Unit, Department of Immunology, Paris, France.,Immunology and Metabolism, LIMES Institute, University of Bonn, Bonn, Germany
| | - Jérome Larghero
- Assistance Publique-Hopitaux de Paris, Hôpital Saint-Louis, Cell Therapy Unit and Cord Blood Bank; CIC de Biothérapies, CBT501, Paris, France
| | - Lars Rogge
- Institut Pasteur, Immunoregulation Unit, Department of Immunology, Paris, France
| | - Elisabetta Bianchi
- Institut Pasteur, Immunoregulation Unit, Department of Immunology, Paris, France.
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Milo I, Bedora-Faure M, Garcia Z, Thibaut R, Périé L, Shakhar G, Deriano L, Bousso P. The immune system profoundly restricts intratumor genetic heterogeneity. Sci Immunol 2019; 3:3/29/eaat1435. [PMID: 30470696 DOI: 10.1126/sciimmunol.aat1435] [Citation(s) in RCA: 71] [Impact Index Per Article: 14.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2018] [Revised: 08/03/2018] [Accepted: 10/18/2018] [Indexed: 12/14/2022]
Abstract
Tumors develop under the selective pressure of the immune system. However, it remains critical to establish how the immune system affects the clonal heterogeneity of tumors that often display cell-to-cell variation in genetic alterations and antigenic expression. To address these questions, we introduced a multicolor barcoding strategy to study the growth of a MYC-driven B cell lymphoma harboring a large degree of intratumor genetic diversity. Using intravital imaging, we visualized that lymphoma subclones grow as patches of sessile cells in the bone marrow, creating a spatially compartmentalized architecture for tumor diversity. Using multicolor barcoding and whole-exome sequencing, we demonstrated that immune responses strongly restrict intratumor genomic diversity and favor clonal dominance, a process mediated by the selective elimination of more immunogenic cells and amplified by epitope spreading. Anti-PD-1 treatment also narrowed intratumor diversity. Our results provide direct evidence that immune pressure shapes the level of intratumor genetic heterogeneity and have important implications for the design of therapeutic strategies.
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Affiliation(s)
- Idan Milo
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, 75015 Paris, France.,INSERM U1223, 75015 Paris, France
| | - Marie Bedora-Faure
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Zacarias Garcia
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, 75015 Paris, France.,INSERM U1223, 75015 Paris, France
| | - Ronan Thibaut
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, 75015 Paris, France.,INSERM U1223, 75015 Paris, France.,University Paris Diderot, Sorbonne Paris Cité, Cellule Pasteur, rue du Dr Roux, 75015 Paris, France
| | - Leïla Périé
- Institut Curie, PSL Research University, CNRS UMR168, 11 rue Pierre et Marie Curie, 75005 Paris, France.,Sorbonne Universités, UPMC University Paris 06, 4 place Jussieu, 75005 Paris, France
| | - Guy Shakhar
- Department of Immunology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015 Paris, France
| | - Philippe Bousso
- Dynamics of Immune Responses Unit, Equipe Labellisée Ligue Contre le Cancer, Institut Pasteur, 75015 Paris, France. .,INSERM U1223, 75015 Paris, France
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12
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Galindo-Campos MA, Bedora-Faure M, Farrés J, Lescale C, Moreno-Lama L, Martínez C, Martín-Caballero J, Ampurdanés C, Aparicio P, Dantzer F, Cerutti A, Deriano L, Yélamos J. Coordinated signals from the DNA repair enzymes PARP-1 and PARP-2 promotes B-cell development and function. Cell Death Differ 2019; 26:2667-2681. [PMID: 30996287 DOI: 10.1038/s41418-019-0326-5] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Revised: 03/22/2019] [Accepted: 03/25/2019] [Indexed: 02/07/2023] Open
Abstract
Poly (ADP-ribose) polymerase (PARP)-1 and PARP-2 regulate the function of various DNA-interacting proteins by transferring ADP-ribose emerging from catalytic cleavage of cellular β-NAD+. Hence, mice lacking PARP-1 or PARP-2 show DNA perturbations ranging from altered DNA integrity to impaired DNA repair. These effects stem from the central role that PARP-1 and PARP-2 have on the cellular response to DNA damage. Failure to mount a proper response culminates in cell death. Accordingly, PARP inhibitors are emerging as promising drugs in cancer therapy. However, the full impact of these inhibitors on immunity, including B-cell antibody production, remains elusive. Given that mice carrying dual PARP-1 and PARP-2 deficiency develop early embryonic lethality, we crossed PARP-1-deficient mice with mice carrying a B-cell-conditional PARP-2 gene deletion. We found that the resulting dually PARP-1 and PARP-2-deficient mice had perturbed bone-marrow B-cell development as well as profound peripheral depletion of transitional and follicular but not marginal zone B-cells. Of note, bone-marrow B-cell progenitors and peripheral mature B-cells were conserved in mice carrying either PARP-1 or PARP-2 deficiency. In dually PARP-1 and PARP-2-deficient mice, B-cell lymphopenia was associated with increased DNA damage and accentuated death in actively proliferating B-cells. Moreover, dual PARP-1 and PARP-2 deficiency impaired antibody responses to T-independent carbohydrate but not to T-dependent protein antigens. Notwithstanding the pivotal role of PARP-1 and PARP-2 in DNA repair, combined PARP-1 and PARP-2 deficiency did not perturb the DNA-editing processes required for the generation of a protective antibody repertoire, including Ig V(D)J gene recombination and IgM-to-IgG class switching. These findings provide key information as to the potential impact of PARP inhibitors on humoral immunity, which will facilitate the development of safer PARP-targeting regimens against cancer.
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Affiliation(s)
- Miguel A Galindo-Campos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Marie Bedora-Faure
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015, Paris, France
| | - Jordi Farrés
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Chloé Lescale
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015, Paris, France
| | - Lucia Moreno-Lama
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Carlos Martínez
- Experimental Pathology Unit, IMIB-LAIB-Arrixaca, Murcia, Spain
| | | | - Coral Ampurdanés
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Pedro Aparicio
- Department of Biochemistry, Molecular Biology and Immunology, University of Murcia, Murcia, Spain
| | - Françoise Dantzer
- Biotechnology and Cell Signaling, UMR7242-CNRS, Laboratory of Excellence Medalis, ESBS, Illkirch, France
| | - Andrea Cerutti
- Catalan Institute for Research and Advanced Studies (ICREA), Barcelona, Spain.,Inflammatory and Cardiovascular Disorders Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain
| | - Ludovic Deriano
- Genome Integrity, Immunity and Cancer Unit, Equipe Labellisée Ligue Contre le Cancer, Department of Immunology, Department of Genomes and Genetics, Institut Pasteur, 75015, Paris, France.
| | - José Yélamos
- Cancer Research Program, Hospital del Mar Medical Research Institute (IMIM), Barcelona, Spain. .,Department of Immunology, Hospital del Mar, Barcelona, Spain.
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13
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Wu CAM, Roth TL, Baglaenko Y, Ferri DM, Brauer P, Zuniga-Pflucker JC, Rosbe KW, Wither JE, Marson A, Allen CDC. Genetic engineering in primary human B cells with CRISPR-Cas9 ribonucleoproteins. J Immunol Methods 2018; 457:33-40. [PMID: 29614266 DOI: 10.1016/j.jim.2018.03.009] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2018] [Revised: 03/24/2018] [Accepted: 03/26/2018] [Indexed: 12/27/2022]
Abstract
Genome editing in human cells with targeted nucleases now enables diverse experimental and therapeutic genome engineering applications, but extension to primary human B cells remains limited. Here we report a method for targeted genetic engineering in primary human B cells, utilizing electroporation of CRISPR-Cas9 ribonucleoproteins (RNPs) to introduce gene knockout mutations at protein-coding loci with high efficiencies that in some cases exceeded 80%. Further, we demonstrate knock-in editing of targeted nucleotides with efficiency exceeding 10% through co-delivery of oligonucleotide templates for homology directed repair. We delivered Cas9 RNPs in two distinct in vitro culture systems to achieve editing in both undifferentiated B cells and activated B cells undergoing differentiation, reflecting utility in diverse experimental conditions. In summary, we demonstrate a powerful and scalable research tool for functional genetic studies of human B cell biology that may have further applications in engineered B cell therapeutics.
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Affiliation(s)
- Chung-An M Wu
- Cardiovascular Research Institute, Sandler Asthma Basic Research Center, 555 Mission Bay Blvd S, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Theodore L Roth
- Department of Microbiology and Immunology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA
| | - Yuriy Baglaenko
- Krembil Research Institute, 60 Leonard Ave, University Health Network, Toronto, Ontario, Canada; Department of Immunology, 60 Leonard Ave, University of Toronto, Toronto, Ontario, Canada
| | - Dario M Ferri
- Krembil Research Institute, 60 Leonard Ave, University Health Network, Toronto, Ontario, Canada; Department of Immunology, 60 Leonard Ave, University of Toronto, Toronto, Ontario, Canada
| | - Patrick Brauer
- Department of Immunology, 60 Leonard Ave, University of Toronto, Toronto, Ontario, Canada; Sunnybrook Research Institute, 2075 Bayview Ave, University of Toronto, Toronto, Ontario, Canada
| | - Juan Carlos Zuniga-Pflucker
- Department of Immunology, 60 Leonard Ave, University of Toronto, Toronto, Ontario, Canada; Sunnybrook Research Institute, 2075 Bayview Ave, University of Toronto, Toronto, Ontario, Canada
| | - Kristina W Rosbe
- Department of Otolaryngology, 550 16th St, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Joan E Wither
- Krembil Research Institute, 60 Leonard Ave, University Health Network, Toronto, Ontario, Canada; Department of Immunology, 60 Leonard Ave, University of Toronto, Toronto, Ontario, Canada; Department of Medicine, 60 Leonard Ave, University of Toronto, Toronto, Ontario, Canada.
| | - Alexander Marson
- Department of Microbiology and Immunology, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Department of Medicine, Diabetes Center, Helen Diller Family Comprehensive Cancer Center, 513 Parnassus Ave, University of California, San Francisco, CA 94143, USA; Innovative Genomics Institute, 2151 Berkeley Way, University of California, Berkeley, Berkeley, CA 94720, USA; Chan Zuckerberg Biohub, 499 Illinois St, San Francisco, CA 94158, USA.
| | - Christopher D C Allen
- Cardiovascular Research Institute, Sandler Asthma Basic Research Center, 555 Mission Bay Blvd S, University of California, San Francisco, San Francisco, CA 94143, USA; Department of Anatomy, 555 Mission Bay Blvd S, University of California, San Francisco, San Francisco, CA 94143, USA.
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