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Hovhannisyan Y, Li Z, Callon D, Suspène R, Batoumeni V, Canette A, Blanc J, Hocini H, Lefebvre C, El-Jahrani N, Kitsara M, L'honoré A, Kordeli E, Fornes P, Concordet JP, Tachdjian G, Rodriguez AM, Vartanian JP, Béhin A, Wahbi K, Joanne P, Agbulut O. Critical contribution of mitochondria in the development of cardiomyopathy linked to desmin mutation. Stem Cell Res Ther 2024; 15:10. [PMID: 38167524 PMCID: PMC10763022 DOI: 10.1186/s13287-023-03619-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Accepted: 12/18/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Beyond the observed alterations in cellular structure and mitochondria, the mechanisms linking rare genetic mutations to the development of heart failure in patients affected by desmin mutations remain unclear due in part, to the lack of relevant human cardiomyocyte models. METHODS To shed light on the role of mitochondria in these mechanisms, we investigated cardiomyocytes derived from human induced pluripotent stem cells carrying the heterozygous DESE439K mutation that were either isolated from a patient or generated by gene editing. To increase physiological relevance, cardiomyocytes were either cultured on an anisotropic micropatterned surface to obtain elongated and aligned cardiomyocytes, or as a cardiac spheroid to create a micro-tissue. Moreover, when applicable, results from cardiomyocytes were confirmed with heart biopsies of suddenly died patient of the same family harboring DESE439K mutation, and post-mortem heart samples from five control healthy donors. RESULTS The heterozygous DESE439K mutation leads to dramatic changes in the overall cytoarchitecture of cardiomyocytes, including cell size and morphology. Most importantly, mutant cardiomyocytes display altered mitochondrial architecture, mitochondrial respiratory capacity and metabolic activity reminiscent of defects observed in patient's heart tissue. Finally, to challenge the pathological mechanism, we transferred normal mitochondria inside the mutant cardiomyocytes and demonstrated that this treatment was able to restore mitochondrial and contractile functions of cardiomyocytes. CONCLUSIONS This work highlights the deleterious effects of DESE439K mutation, demonstrates the crucial role of mitochondrial abnormalities in the pathophysiology of desmin-related cardiomyopathy, and opens up new potential therapeutic perspectives for this disease.
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Affiliation(s)
- Yeranuhi Hovhannisyan
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Zhenlin Li
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Domitille Callon
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
- Department of Pathology, Academic Hospital of Reims, Reims, France
| | - Rodolphe Suspène
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Vivien Batoumeni
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
- Ksilink, Strasbourg, France
| | - Alexis Canette
- Service de Microscopie Électronique (IBPS-SME), Institut de Biologie Paris-Seine (IBPS), CNRS, Sorbonne Université, Paris, France
| | - Jocelyne Blanc
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Hakim Hocini
- INSERM U955, Equipe 16, Université Paris-Est Créteil, Créteil, France
| | - Cécile Lefebvre
- INSERM U955, Equipe 16, Université Paris-Est Créteil, Créteil, France
| | - Nora El-Jahrani
- INSERM U955, Equipe 16, Université Paris-Est Créteil, Créteil, France
| | - Maria Kitsara
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Aurore L'honoré
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Ekaterini Kordeli
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Paul Fornes
- Department of Pathology, Academic Hospital of Reims, Reims, France
| | - Jean-Paul Concordet
- INSERM U1154, CNRS UMR7196, Museum National d'Histoire Naturelle, Paris, France
| | - Gérard Tachdjian
- Laboratoire de Cytogénétique, Service d'Histologie-Embryologie-Cytogénétique, AP-HP, Hôpital Antoine Béclère, Université Paris Saclay, Clamart, France
| | - Anne-Marie Rodriguez
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France
| | - Jean-Pierre Vartanian
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université Paris Cité, Paris, France
| | - Anthony Béhin
- Reference Center for Muscle Diseases Paris-Est, Myology Institute, AP-HP, Pitié-Salpêtrière Hospital, Sorbonne Université, Paris, France
| | - Karim Wahbi
- Cardiology Department, AP-HP, Cochin Hospital, Université Paris Cité, Paris, France
| | - Pierre Joanne
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France.
| | - Onnik Agbulut
- UMR CNRS 8256, INSERM U1164, Biological Adaptation and Ageing, Institut de Biologie Paris-Seine (IBPS), Sorbonne Université, 7, Quai St Bernard (case 256), 75005, Paris, France.
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Abstract
According to the endosymbiotic theory, most of the DNA of the original bacterial endosymbiont has been lost or transferred to the nucleus, leaving a much smaller (∼16 kb in mammals), circular molecule that is the present-day mitochondrial DNA (mtDNA). The ability of mtDNA to escape mitochondria and integrate into the nuclear genome was discovered in budding yeast, along with genes that regulate this process. Mitochondria have emerged as key regulators of innate immunity, and it is now recognized that mtDNA released into the cytoplasm, outside of the cell, or into circulation activates multiple innate immune signaling pathways. Here, we first review the mechanisms through which mtDNA is released into the cytoplasm, including several inducible mitochondrial pores and defective mitophagy or autophagy. Next, we cover how the different forms of released mtDNA activate specific innate immune nucleic acid sensors and inflammasomes. Finally, we discuss how intracellular and extracellular mtDNA release, including circulating cell-free mtDNA that promotes systemic inflammation, are implicated in human diseases, bacterial and viral infections, senescence and aging.
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Affiliation(s)
- Laura E Newman
- Salk Institute for Biological Studies, La Jolla, California, USA;
| | - Gerald S Shadel
- Salk Institute for Biological Studies, La Jolla, California, USA;
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3
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Khalfi P, Suspène R, Raymond KA, Caval V, Caignard G, Berry N, Thiers V, Combredet C, Rufie C, Rigaud S, Ghozlane A, Volant S, Komarova AV, Tangy F, Vartanian JP. Antagonism of ALAS1 by the Measles Virus V protein contributes to degradation of the mitochondrial network and promotes interferon response. PLoS Pathog 2023; 19:e1011170. [PMID: 36802406 PMCID: PMC9983871 DOI: 10.1371/journal.ppat.1011170] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2022] [Revised: 03/03/2023] [Accepted: 02/01/2023] [Indexed: 02/23/2023] Open
Abstract
Viruses have evolved countless mechanisms to subvert and impair the host innate immune response. Measles virus (MeV), an enveloped, non-segmented, negative-strand RNA virus, alters the interferon response through different mechanisms, yet no viral protein has been described as directly targeting mitochondria. Among the crucial mitochondrial enzymes, 5'-aminolevulinate synthase (ALAS) is an enzyme that catalyzes the first step in heme biosynthesis, generating 5'-aminolevulinate from glycine and succinyl-CoA. In this work, we demonstrate that MeV impairs the mitochondrial network through the V protein, which antagonizes the mitochondrial enzyme ALAS1 and sequesters it to the cytosol. This re-localization of ALAS1 leads to a decrease in mitochondrial volume and impairment of its metabolic potential, a phenomenon not observed in MeV deficient for the V gene. This perturbation of the mitochondrial dynamics demonstrated both in culture and in infected IFNAR-/- hCD46 transgenic mice, causes the release of mitochondrial double-stranded DNA (mtDNA) in the cytosol. By performing subcellular fractionation post infection, we demonstrate that the most significant source of DNA in the cytosol is of mitochondrial origin. Released mtDNA is then recognized and transcribed by the DNA-dependent RNA polymerase III. The resulting double-stranded RNA intermediates will be captured by RIG-I, ultimately initiating type I interferon production. Deep sequencing analysis of cytosolic mtDNA editing divulged an APOBEC3A signature, primarily analyzed in the 5'TpCpG context. Finally, in a negative feedback loop, APOBEC3A an interferon inducible enzyme will orchestrate the catabolism of mitochondrial DNA, decrease cellular inflammation, and dampen the innate immune response.
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Affiliation(s)
- Pierre Khalfi
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- Sorbonne Université, Complexité du Vivant, ED515, Paris, France
| | - Rodolphe Suspène
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Kyle A. Raymond
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- Sorbonne Université, Complexité du Vivant, ED515, Paris, France
| | - Vincent Caval
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| | | | - Noémie Berry
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- Sorbonne Université, Complexité du Vivant, ED515, Paris, France
- UMR1161 Virologie, ANSES-INRAE-ENVA, Maisons-Alfort, France
| | - Valérie Thiers
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Chantal Combredet
- Vaccines Innovation Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Claude Rufie
- Vaccines Innovation Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Stéphane Rigaud
- Image Analysis Hub, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Amine Ghozlane
- Bioinformatics and Biostatistics HUB, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Stevenn Volant
- Bioinformatics and Biostatistics HUB, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Anastassia V. Komarova
- Interactomics, RNA and Immunity Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Frédéric Tangy
- Vaccines Innovation Laboratory, Institut Pasteur, Université de Paris Cité, Paris, France
| | - Jean-Pierre Vartanian
- Virus and Cellular Stress Unit, Department of Virology, Institut Pasteur, Université de Paris Cité, Paris, France
- * E-mail:
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4
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Berry N, Suspène R, Caval V, Khalfi P, Beauclair G, Rigaud S, Blanc H, Vignuzzi M, Wain-Hobson S, Vartanian JP. Herpes Simplex Virus Type 1 Infection Disturbs the Mitochondrial Network, Leading to Type I Interferon Production through the RNA Polymerase III/RIG-I Pathway. mBio 2021; 12:e0255721. [PMID: 34809467 PMCID: PMC8609356 DOI: 10.1128/mbio.02557-21] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2021] [Accepted: 10/19/2021] [Indexed: 11/20/2022] Open
Abstract
Viruses have evolved a plethora of mechanisms to impair host innate immune responses. Herpes simplex virus type 1 (HSV-1), a double-stranded linear DNA virus, impairs the mitochondrial network and dynamics predominantly through the UL12.5 gene. We demonstrated that HSV-1 infection induced a remodeling of mitochondrial shape, resulting in a fragmentation of the mitochondria associated with a decrease in their volume and an increase in their sphericity. This damage leads to the release of mitochondrial DNA (mtDNA) to the cytosol. By generating a stable THP-1 cell line expressing the DNase I-mCherry fusion protein and a THP-1 cell line specifically depleted of mtDNA upon ethidium bromide treatment, we showed that cytosolic mtDNA contributes to type I interferon and APOBEC3A upregulation. This was confirmed by using an HSV-1 strain (KOS37 UL98-SPA) with a deletion of the UL12.5 gene that impaired its ability to induce mtDNA stress. Furthermore, by using an inhibitor of RNA polymerase III, we demonstrated that upon HSV-1 infection, cytosolic mtDNA enhanced type I interferon induction through the RNA polymerase III/RIG-I pathway. APOBEC3A was in turn induced by interferon. Deep sequencing analyses of cytosolic mtDNA mutations revealed an APOBEC3A signature predominantly in the 5'TpCpG context. These data demonstrate that upon HSV-1 infection, the mitochondrial network is disrupted, leading to the release of mtDNA and ultimately to its catabolism through APOBEC3-induced mutations. IMPORTANCE Herpes simplex virus 1 (HSV-1) impairs the mitochondrial network through the viral protein UL12.5. This leads to the fusion of mitochondria and simultaneous release of mitochondrial DNA (mtDNA) in a mouse model. We have shown that released mtDNA is recognized as a danger signal, capable of stimulating signaling pathways and inducing the production of proinflammatory cytokines. The expression of the human cytidine deaminase APOBEC3A is highly upregulated by interferon responses. This enzyme catalyzes the deamination of cytidine to uridine in single-stranded DNA substrates, resulting in the catabolism of edited DNA. Using human cell lines deprived of mtDNA and viral strains deficient in UL12, we demonstrated the implication of mtDNA in the production of interferon and APOBEC3A expression during viral infection. We have shown that HSV-1 induces mitochondrial network fragmentation in a human model and confirmed the implication of RNA polymerase III/RIG-I signaling in the capture of cytosolic mtDNA.
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Affiliation(s)
- Noémie Berry
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
- Sorbonne Université, Complexité du Vivant, Paris, France
| | | | - Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
| | - Pierre Khalfi
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France
- Sorbonne Université, Complexité du Vivant, Paris, France
| | | | | | - Hervé Blanc
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, Paris, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, Institut Pasteur, CNRS UMR 3569, Paris, France
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5
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Cinat D, Coppes RP, Barazzuol L. DNA Damage-Induced Inflammatory Microenvironment and Adult Stem Cell Response. Front Cell Dev Biol 2021; 9:729136. [PMID: 34692684 PMCID: PMC8531638 DOI: 10.3389/fcell.2021.729136] [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: 06/22/2021] [Accepted: 08/18/2021] [Indexed: 12/14/2022] Open
Abstract
Adult stem cells ensure tissue homeostasis and regeneration after injury. Due to their longevity and functional requirements, throughout their life stem cells are subject to a significant amount of DNA damage. Genotoxic stress has recently been shown to trigger a cascade of cell- and non-cell autonomous inflammatory signaling pathways, leading to the release of pro-inflammatory factors and an increase in the amount of infiltrating immune cells. In this review, we discuss recent evidence of how DNA damage by affecting the microenvironment of stem cells present in adult tissues and neoplasms can affect their maintenance and long-term function. We first focus on the importance of self-DNA sensing in immunity activation, inflammation and secretion of pro-inflammatory factors mediated by activation of the cGAS-STING pathway, the ZBP1 pathogen sensor, the AIM2 and NLRP3 inflammasomes. Alongside cytosolic DNA, the emerging roles of cytosolic double-stranded RNA and mitochondrial DNA are discussed. The DNA damage response can also initiate mechanisms to limit division of damaged stem/progenitor cells by inducing a permanent state of cell cycle arrest, known as senescence. Persistent DNA damage triggers senescent cells to secrete senescence-associated secretory phenotype (SASP) factors, which can act as strong immune modulators. Altogether these DNA damage-mediated immunomodulatory responses have been shown to affect the homeostasis of tissue-specific stem cells leading to degenerative conditions. Conversely, the release of specific cytokines can also positively impact tissue-specific stem cell plasticity and regeneration in addition to enhancing the activity of cancer stem cells thereby driving tumor progression. Further mechanistic understanding of the DNA damage-induced immunomodulatory response on the stem cell microenvironment might shed light on age-related diseases and cancer, and potentially inform novel treatment strategies.
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Affiliation(s)
- Davide Cinat
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Robert P Coppes
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
| | - Lara Barazzuol
- Department of Biomedical Sciences of Cells and Systems, University Medical Center Groningen, University of Groningen, Groningen, Netherlands.,Department of Radiation Oncology, University Medical Center Groningen, University of Groningen, Groningen, Netherlands
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6
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Caval V, Suspène R, Khalfi P, Gaillard J, Caignard G, Vitour D, Roingeard P, Vartanian JP, Wain-Hobson S. Frame-shifted APOBEC3A encodes two alternative proapoptotic proteins that target the mitochondrial network. J Biol Chem 2021; 297:101081. [PMID: 34403699 PMCID: PMC8424220 DOI: 10.1016/j.jbc.2021.101081] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 08/04/2021] [Accepted: 08/12/2021] [Indexed: 12/02/2022] Open
Abstract
The human APOBEC3A (A3A) cytidine deaminase is a powerful DNA mutator enzyme recognized as a major source of somatic mutations in tumor cell genomes. However, there is a discrepancy between APOBEC3A mRNA levels after interferon stimulation in myeloid cells and A3A detection at the protein level. To understand this difference, we investigated the expression of two novel alternative “A3Alt” proteins encoded in the +1-shifted reading frame of the APOBEC3A gene. A3Alt-L and its shorter isoform A3Alt-S appear to be transmembrane proteins targeted to the mitochondrial compartment that induce membrane depolarization and apoptosis. Thus, the APOBEC3A gene represents a new example wherein a single gene encodes two proapoptotic proteins, A3A cytidine deaminases that target the genome and A3Alt proteins that target mitochondria.
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Affiliation(s)
- Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France.
| | | | - Pierre Khalfi
- Molecular Retrovirology Unit, Institut Pasteur, Paris, France; Sorbonne Université, Complexité du Vivant, ED515, Paris, France
| | - Julien Gaillard
- Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, Inserm-U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France; Plate-Forme IBiSA des Microscopies, PPF ASB, Université de Tours and CHRU de Tours, Tours, France
| | - Grégory Caignard
- UMR Virologie, INRAE, Ecole Nationale Vétérinaire d'Alfort, Laboratoire de santé animale d'Alfort, Anses, Université Paris-Est, Maisons-Alfort, France
| | - Damien Vitour
- UMR Virologie, INRAE, Ecole Nationale Vétérinaire d'Alfort, Laboratoire de santé animale d'Alfort, Anses, Université Paris-Est, Maisons-Alfort, France
| | - Philippe Roingeard
- Morphogenèse et Antigénicité du VIH et des Virus des Hépatites, Inserm-U1259 MAVIVH, Université de Tours and CHRU de Tours, Tours, France; Plate-Forme IBiSA des Microscopies, PPF ASB, Université de Tours and CHRU de Tours, Tours, France
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APOBECs orchestrate genomic and epigenomic editing across health and disease. Trends Genet 2021; 37:1028-1043. [PMID: 34353635 DOI: 10.1016/j.tig.2021.07.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Revised: 07/03/2021] [Accepted: 07/05/2021] [Indexed: 12/17/2022]
Abstract
APOBEC proteins can deaminate cytosine residues in DNA and RNA. This can lead to somatic mutations, DNA breaks, RNA modifications, or DNA demethylation in a selective manner. APOBECs function in various cellular compartments and recognize different nucleic acid motifs and structures. They orchestrate a wide array of genomic and epigenomic modifications, thereby affecting various cellular functions positively or negatively, including immune editing, viral and retroelement restriction, DNA damage responses, DNA demethylation, gene expression, and tissue homeostasis. Furthermore, the cumulative increase in genomic and epigenomic editing with aging could also, at least in part, be attributed to APOBEC function. We synthesize our cumulative understanding of APOBEC activity in a unifying overview and discuss their genomic and epigenomic impact in physiological, pathological, and technological contexts.
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8
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Perez-Bercoff D, Laude H, Lemaire M, Hunewald O, Thiers V, Vignuzzi M, Blanc H, Poli A, Amoura Z, Caval V, Suspène R, Hafezi F, Mathian A, Vartanian JP, Wain-Hobson S. Sustained high expression of multiple APOBEC3 cytidine deaminases in systemic lupus erythematosus. Sci Rep 2021; 11:7893. [PMID: 33846459 PMCID: PMC8041901 DOI: 10.1038/s41598-021-87024-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2020] [Accepted: 03/23/2021] [Indexed: 12/13/2022] Open
Abstract
APOBEC3 (A3) enzymes are best known for their role as antiviral restriction factors and as mutagens in cancer. Although four of them, A3A, A3B, A3F and A3G, are induced by type-1-interferon (IFN-I), their role in inflammatory conditions is unknown. We thus investigated the expression of A3, and particularly A3A and A3B because of their ability to edit cellular DNA, in Systemic Lupus Erythematosus (SLE), a chronic inflammatory disease characterized by high IFN-α serum levels. In a cohort of 57 SLE patients, A3A and A3B, but also A3C and A3G, were upregulated ~ 10 to 15-fold (> 1000-fold for A3B) compared to healthy controls, particularly in patients with flares and elevated serum IFN-α levels. Hydroxychloroquine, corticosteroids and immunosuppressive treatment did not reverse A3 levels. The A3AΔ3B polymorphism, which potentiates A3A, was detected in 14.9% of patients and in 10% of controls, and was associated with higher A3A mRNA expression. A3A and A3B mRNA levels, but not A3C or A3G, were correlated positively with dsDNA breaks and negatively with lymphopenia. Exposure of SLE PBMCs to IFN-α in culture induced massive and sustained A3A levels by 4 h and led to massive cell death. Furthermore, the rs2853669 A > G polymorphism in the telomerase reverse transcriptase (TERT) promoter, which disrupts an Ets-TCF-binding site and influences certain cancers, was highly prevalent in SLE patients, possibly contributing to lymphopenia. Taken together, these findings suggest that high baseline A3A and A3B levels may contribute to cell frailty, lymphopenia and to the generation of neoantigens in SLE patients. Targeting A3 expression could be a strategy to reverse cell death and the generation of neoantigens.
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Affiliation(s)
- Danielle Perez-Bercoff
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg.
| | - Hélène Laude
- ICAReB Platform, 28 rue du Docteur Roux, 75724, Paris Cedex 15, France
- Viral Populations and Pathogenesis Unit, UMR 3569, CNRS, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Morgane Lemaire
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Oliver Hunewald
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Valérie Thiers
- Molecular Retrovirology Unit, UMR 3569, Institut Pasteur, CNRS, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Marco Vignuzzi
- Viral Populations and Pathogenesis Unit, UMR 3569, CNRS, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Hervé Blanc
- Viral Populations and Pathogenesis Unit, UMR 3569, CNRS, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Aurélie Poli
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Zahir Amoura
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre D'Immunologie Et Des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Vincent Caval
- Departement de Virologie, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Rodolphe Suspène
- Departement de Virologie, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - François Hafezi
- Department of Infection and Immunity, Luxembourg Institute of Health, 29 rue Henri Koch, 4354, Esch-sur-Alzette, Luxembourg
| | - Alexis Mathian
- Sorbonne Université, Assistance Publique-Hôpitaux de Paris, Groupement Hospitalier Pitié-Salpêtrière, French National Referral Center for Systemic Lupus Erythematosus, Antiphospholipid Antibody Syndrome and Other Autoimmune Disorders, Service de Médecine Interne 2, Institut E3M, Inserm UMRS, Centre D'Immunologie Et Des Maladies Infectieuses (CIMI-Paris), Paris, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, UMR 3569, Institut Pasteur, CNRS, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
- Departement de Virologie, Institut Pasteur, 28 rue du Dr. Roux, 75724, Paris Cedex 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, UMR 3569, Institut Pasteur, CNRS, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
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Brezgin S, Kostyusheva A, Ponomareva N, Volia V, Goptar I, Nikiforova A, Shilovskiy I, Smirnov V, Kostyushev D, Chulanov V. Clearing of Foreign Episomal DNA from Human Cells by CRISPRa-Mediated Activation of Cytidine Deaminases. Int J Mol Sci 2020; 21:ijms21186865. [PMID: 32962129 PMCID: PMC7557733 DOI: 10.3390/ijms21186865] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2020] [Revised: 09/07/2020] [Accepted: 09/16/2020] [Indexed: 02/06/2023] Open
Abstract
Restriction of foreign DNA is a fundamental defense mechanism required for maintaining genomic stability and proper function of mammalian cells. APOBEC cytidine deaminases are crucial effector molecules involved in clearing pathogenic DNA of viruses and other microorganisms and improperly localized self-DNA (DNA leakages). Mastering the expression of APOBEC provides the crucial means both for developing novel therapeutic approaches for combating infectious and non-infectious diseases and for numerous research purposes. In this study, we report successful application of a CRISPRa approach to effectively and specifically overexpress APOBEC3A and APOBEC3B deaminases and describe their effects on episomal and integrated foreign DNA. This method increased target gene transcription by >6–50-fold in HEK293T cells. Furthermore, CRISPRa-mediated activation of APOBEC3A/APOBEC3B suppressed episomal but not integrated foreign DNA. Episomal GC-rich DNA was rapidly destabilized and destroyed by CRISPRa-induced APOBEC3A/APOBEC3B, while the remaining DNA templates harbored frequent deaminated nucleotides. To conclude, the CRISPRa approach could be readily utilized for manipulating innate immunity and investigating the effects of the key effector molecules on foreign nucleic acids.
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Affiliation(s)
- Sergey Brezgin
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
- Department of Molecular Immunology, Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia; (I.S.); (V.S.)
| | - Anastasiya Kostyusheva
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
| | - Natalia Ponomareva
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
| | - Viktoriia Volia
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
| | - Irina Goptar
- Izmerov Research Institute of Occupational Health, 105275 Moscow, Russia; (I.G.); (A.N.)
| | - Anastasiya Nikiforova
- Izmerov Research Institute of Occupational Health, 105275 Moscow, Russia; (I.G.); (A.N.)
| | - Igor Shilovskiy
- Department of Molecular Immunology, Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia; (I.S.); (V.S.)
| | - Valery Smirnov
- Department of Molecular Immunology, Institute of Immunology, Federal Medical Biological Agency, 115522 Moscow, Russia; (I.S.); (V.S.)
| | - Dmitry Kostyushev
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
- Correspondence:
| | - Vladimir Chulanov
- Department of Molecular Biology and Immunopathology of Infectious Diseases, National Medical Research Center for Tuberculosis and Infectious Diseases, 127994 Moscow, Russia; (S.B.); (A.K.); (N.P.); (V.V.); (V.C.)
- Department of Infectious Diseases, Sechenov First Moscow State Medical University, 119146 Moscow, Russia
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10
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Swiatczak B. Genomic Stress Responses Drive Lymphocyte Evolvability: An Ancient and Ubiquitous Mechanism. Bioessays 2020; 42:e2000032. [PMID: 32767393 DOI: 10.1002/bies.202000032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2020] [Revised: 07/03/2020] [Indexed: 12/15/2022]
Abstract
Somatic diversification of antigen receptor genes depends on the activity of enzymes whose homologs participate in a mutagenic DNA repair in unicellular species. Indeed, by engaging error-prone polymerases, gap filling molecules and altered mismatch repair pathways, lymphocytes utilize conserved components of genomic stress response systems, which can already be found in bacteria and archaea. These ancient systems of mutagenesis and repair act to increase phenotypic diversity of microbial cell populations and operate to enhance their ability to produce fit variants during stress. Coopted by lymphocytes, the ancient mutagenic processing systems retained their diversification functions instilling the adaptive immune cells with enhanced evolvability and defensive capacity to resist infection and damage. As reviewed here, the ubiquity and conserved character of specialized variation-generating mechanisms from bacteria to lymphocytes highlight the importance of these mechanisms for evolution of life in general.
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Affiliation(s)
- Bartlomiej Swiatczak
- Department of History of Science and Scientific Archeology, University of Science and Technology of China, 96 Jinzhai Rd., Hefei, 230026, China
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11
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Caval V, Jiao W, Berry N, Khalfi P, Pitré E, Thiers V, Vartanian JP, Wain-Hobson S, Suspène R. Mouse APOBEC1 cytidine deaminase can induce somatic mutations in chromosomal DNA. BMC Genomics 2019; 20:858. [PMID: 31726973 PMCID: PMC6854741 DOI: 10.1186/s12864-019-6216-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Background APOBEC1 (A1) enzymes are cytidine deaminases involved in RNA editing. In addition to this activity, a few A1 enzymes have been shown to be active on single stranded DNA. As two human ssDNA cytidine deaminases APOBEC3A (A3A), APOBEC3B (A3B) and related enzymes across the spectrum of placental mammals have been shown to introduce somatic mutations into nuclear DNA of cancer genomes, we explored the mutagenic threat of A1 cytidine deaminases to chromosomal DNA. Results Molecular cloning and expression of various A1 enzymes reveal that the cow, pig, dog, rabbit and mouse A1 have an intracellular ssDNA substrate specificity. However, among all the enzymes studied, mouse A1 appears to be singular, being able to introduce somatic mutations into nuclear DNA with a clear 5’TpC editing context, and to deaminate 5-methylcytidine substituted DNA which are characteristic features of the cancer related mammalian A3A and A3B enzymes. However, mouse A1 activity fails to elicit formation of double stranded DNA breaks, suggesting that mouse A1 possess an attenuated nuclear DNA mutator phenotype reminiscent of human A3B. Conclusions At an experimental level mouse APOBEC1 is remarkable among 12 mammalian A1 enzymes in that it represents a source of somatic mutations in mouse genome, potentially fueling oncogenesis. While the order Rodentia is bereft of A3A and A3B like enzymes it seems that APOBEC1 may well substitute for it, albeit remaining much less active. This modifies the paradigm that APOBEC3 and AID enzymes are the sole endogenous mutator enzymes giving rise to off-target editing of mammalian genomes.
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Affiliation(s)
- Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.
| | - Wenjuan Jiao
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Noémie Berry
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Pierre Khalfi
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Emmanuelle Pitré
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Valérie Thiers
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Rodolphe Suspène
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
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12
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Tao L, Jiang Z, Xu M, Xu T, Liu Y. Induction of APOBEC3C Facilitates the Genotoxic Stress-Mediated Cytotoxicity of Artesunate. Chem Res Toxicol 2019; 32:2526-2537. [DOI: 10.1021/acs.chemrestox.9b00358] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Li Tao
- College of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, China
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Zhuangzhuang Jiang
- College of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, China
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Min Xu
- College of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, China
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Tingting Xu
- College of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, China
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
| | - Yanqing Liu
- College of Medicine, Yangzhou University, Yangzhou, Jiangsu 225001, China
- The State Administration of Traditional Chinese Medicine Key Laboratory of Toxic Pathogens-Based Therapeutic Approaches of Gastric Cancer, Yangzhou University, Yangzhou, Jiangsu 225009, China
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