1
|
Carrero D, Pascual-Torner M, Álvarez-Puente D, Quesada V, García-Gómez C, López-Otín C. Insights into aging mechanisms from comparative genomics in orange and silver roughies. Sci Rep 2024; 14:19748. [PMID: 39187546 PMCID: PMC11347708 DOI: 10.1038/s41598-024-70642-w] [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: 12/13/2023] [Accepted: 08/20/2024] [Indexed: 08/28/2024] Open
Abstract
The demersal fish orange roughy (Hoplostethus atlanticus) can live for up to 250 years, twenty times more than its congener silver roughy (Hoplostethus mediterraneus). Studies of Hoplostethus have focused mainly on its ecology and conservation due to its vulnerability to commercial fishing. In this work, we present the de novo genomes of orange and silver roughies and explore the genomic mechanisms that could contribute to such differential longevities. Using comparative genomics on a list of more than 400 genes, we identified gene candidates with differential residue changes in Hoplostethus that are related to genomic instability, disabled macroautophagy and intercellular communication. We hypothesized that these mechanisms could have been selected as adaptations to the deep environment and, as an epiphenomenon of these mechanisms, may have contributed to an extension of the lifespan of H. atlanticus.
Collapse
Affiliation(s)
- Dido Carrero
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, Spain
| | - Maria Pascual-Torner
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, Spain.
- Observatorio Marino de Asturias, Departamento de Biología de Organismos y Sistemas, Universidad de Oviedo, Oviedo, Spain.
| | - Diana Álvarez-Puente
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, Spain
| | - Víctor Quesada
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, Spain
| | - Claudia García-Gómez
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, Spain
| | - Carlos López-Otín
- Departamento de Bioquímica y Biología Molecular, Instituto Universitario de Oncología, Ciberonc, Universidad de Oviedo, Oviedo, Spain
| |
Collapse
|
2
|
Amor-Guéret M. Loss of cytidine deaminase expression as a potential attempt to counteract the process of carcinogenesis by reducing basal PARP-1 activity and increasing tau levels. Biochim Biophys Acta Mol Basis Dis 2024; 1870:167213. [PMID: 38714266 DOI: 10.1016/j.bbadis.2024.167213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2023] [Revised: 04/01/2024] [Accepted: 05/01/2024] [Indexed: 05/09/2024]
Abstract
Cytidine deaminase (CDA) is a pyrimidine salvage pathway enzyme that catalyzes the hydrolytic deamination of free cytidine and deoxycytidine to uridine and deoxyuridine, respectively. Our team discovered that CDA deficiency is associated with several aspects of genetic instability, such as increased sister chromatid exchange and ultrafine anaphase bridge frequencies. Based on these results, we sought (1) to determine how CDA deficiency contributes to genetic instability, (2) to explore the possible relationships between CDA deficiency and carcinogenesis, and (3) to develop a new anticancer treatment targeting CDA-deficient tumors. This review summarizes our major findings indicating that CDA deficiency is associated with a genetic instability that does not confer an increased cancer risk. In light of our results and published data, I propose a novel hypothesis that loss of CDA, by reducing basal PARP-1 activity and increasing Tau levels, may reflect an attempt to prevent, slow or reverse the process of carcinogenesis.
Collapse
Affiliation(s)
- Mounira Amor-Guéret
- Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France; CNRS UMR 3348, Centre Universitaire, 91405 Orsay, France; Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405 Orsay, France.
| |
Collapse
|
3
|
Xu B, Sui Q, Hu H, Hu X, Zhou X, Qian C, Li N. SAMHD1 Attenuates Acute Inflammation by Maintaining Mitochondrial Function in Macrophages via Interaction with VDAC1. Int J Mol Sci 2023; 24:ijms24097888. [PMID: 37175593 PMCID: PMC10177872 DOI: 10.3390/ijms24097888] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2023] [Revised: 04/15/2023] [Accepted: 04/20/2023] [Indexed: 05/15/2023] Open
Abstract
Over-activation of Toll-like receptor 4 (TLR4) is the key mechanism in Gram-negative bacterial infection-induced sepsis. SAM and HD domain-containing deoxynucleoside triphosphate triphosphohydrolase 1 (SAMHD1) inhibits multiple viruses, but whether it plays a role during bacterial invasion remains unelucidated. Monocyte-macrophage specific Samhd1 knockout (Samhd1-/-) mice and Samhd1-/- macrophage cell line RAW264.7 were constructed and used as research models to evaluate the role of SAMHD1 in TLR4-activated inflammation. In vivo, LPS-challenged Samhd1-/- mice showed higher serum inflammatory factors, accompanied with more severe inflammation infiltration and lower survival rate. In vitro, Samhd1-/- peritoneal macrophages had more activated TLR4 pathway upon LPS-stimulation, accompanied with mitochondrial depolarization and dysfunction and a higher tendency to be M1-polarized. These results could be rescued by overexpressing full-length wild-type SAMHD1 or its phospho-mimetic T634D mutant into Samhd1-/- RAW264.7 cells, whereas the mutants, dNTP hydrolase-function-deprived H238A and phospho-ablative T634A, did not exert the same effect. Lastly, co-IP and immunofluorescence assays confirmed that SAMHD1 interacted with an outer mitochondrial membrane-localized protein, voltage-dependent anion channel-1 (VDAC1). SAMHD1 inhibits TLR4-induced acute inflammation and M1 polarization of macrophages by interacting with VDAC1 and maintaining mitochondria function, which outlines a novel regulatory mechanism of TLR signaling upon LPS stimulation.
Collapse
Affiliation(s)
- Bowen Xu
- National Key Laboratory of Immunity & Inflammation, Institute of Immunology, Naval Medical University, Shanghai 200433, China
| | - Qianyi Sui
- National Key Laboratory of Immunity & Inflammation, Institute of Immunology, Naval Medical University, Shanghai 200433, China
| | - Han Hu
- National Key Laboratory of Immunity & Inflammation, Institute of Immunology, Naval Medical University, Shanghai 200433, China
- Faculty of Anesthesiology, Changhai Hospital, Naval Medical University, Shanghai 200433, China
| | - Xiangjia Hu
- National Key Laboratory of Immunity & Inflammation, Institute of Immunology, Naval Medical University, Shanghai 200433, China
| | - Xuchang Zhou
- National Key Laboratory of Immunity & Inflammation, Institute of Immunology, Naval Medical University, Shanghai 200433, China
- School of Sport Medicine and Rehabilitation, Beijing Sport University, Beijing 100084, China
| | - Cheng Qian
- National Key Laboratory of Immunity & Inflammation, Institute of Immunology, Naval Medical University, Shanghai 200433, China
| | - Nan Li
- National Key Laboratory of Immunity & Inflammation, Institute of Immunology, Naval Medical University, Shanghai 200433, China
| |
Collapse
|
4
|
Onclercq-Delic R, Buhagiar-Labarchède G, Leboucher S, Larcher T, Ledevin M, Machon C, Guitton J, Amor-Guéret M. Cytidine deaminase deficiency in mice enhances genetic instability but limits the number of chemically induced colon tumors. Cancer Lett 2023; 555:216030. [PMID: 36496104 DOI: 10.1016/j.canlet.2022.216030] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 12/13/2022]
Abstract
Cytidine deaminase (CDA) catalyzes the deamination of cytidine (C) and deoxycytidine (dC) to uridine and deoxyuridine, respectively. We recently showed that CDA deficiency leads to genomic instability, a hallmark of cancers. We therefore investigated whether constitutive CDA inactivation conferred a predisposition to cancer development. We developed a novel mouse model of Cda deficiency by generating Cda-knockout mice. Cda+/+ and Cda-/- mice did not differ in lifetime phenotypic or behavioral characteristics, or in the frequency or type of spontaneous cancers. However, the frequency of chemically induced tumors in the colon was significantly lower in Cda-/- mice. An analysis of primary kidney cells from Cda-/- mice revealed an excess of C and dC associated with significantly higher frequencies of sister chromatid exchange and ultrafine anaphase bridges and lower Parp-1 activity than in Cda+/+ cells. Our results suggest that, despite inducing genetic instability, an absence of Cda limits the number of chemically induced tumors. These results raise questions about whether a decrease in basal Parp-1 activity can protect against inflammation-driven tumorigenesis; we discuss our findings in light of published data for the Parp-1-deficient mouse model.
Collapse
Affiliation(s)
- Rosine Onclercq-Delic
- Institut Curie, PSL Research University, UMR 3348, 91405, Orsay, France; CNRS UMR 3348, Centre Universitaire, 91405, Orsay, France; Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405, Orsay, France
| | - Géraldine Buhagiar-Labarchède
- Institut Curie, PSL Research University, UMR 3348, 91405, Orsay, France; CNRS UMR 3348, Centre Universitaire, 91405, Orsay, France; Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405, Orsay, France
| | - Sophie Leboucher
- Institut Curie, PSL Research University, UMR 3348, 91405, Orsay, France; CNRS UMR 3348, Centre Universitaire, 91405, Orsay, France; Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405, Orsay, France
| | | | | | - Christelle Machon
- Laboratoire de Biochimie et Toxicologie, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre-Bénite, France; Laboratoire de Chimie Analytique, ISPB, Faculté de Pharmacie, Université Lyon 1, Université de Lyon, Lyon, France
| | - Jérôme Guitton
- Laboratoire de Biochimie et Toxicologie, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre-Bénite, France; Laboratoire de Toxicologie, ISPB, Faculté de Pharmacie, Université Lyon 1, Université de Lyon, Lyon, France
| | - Mounira Amor-Guéret
- Institut Curie, PSL Research University, UMR 3348, 91405, Orsay, France; CNRS UMR 3348, Centre Universitaire, 91405, Orsay, France; Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405, Orsay, France.
| |
Collapse
|
5
|
Cytidine deaminase activity increases in the blood of breast cancer patients. Sci Rep 2022; 12:14062. [PMID: 35982128 PMCID: PMC9388666 DOI: 10.1038/s41598-022-18462-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 08/12/2022] [Indexed: 11/09/2022] Open
Abstract
Cytidine deaminase (CDA), an enzyme of the pyrimidine salvage pathway, deaminates cytidine, deoxycytidine and analogs, such as gemcitabine. Constitutive low levels of CDA activity have been reported in the blood of patients with hematological malignancies or suffering from gemcitabine toxicity. We previously reported that cellular CDA deficiency leads to genetic instability. We therefore hypothesized that constitutive CDA deficiency might confer a predisposition to cancer. We analyzed CDA activity and expression in blood samples from breast cancer (BC) patients with a suspected predisposition to the disease, and in healthy controls. Contrary to our hypothesis, we found that both CDA activity and mRNA levels were higher in blood samples from BC patients than in those from controls, and that this difference was not due to excess neutrophils. CDA activity levels were significantly higher in the serum samples of BC patients treated by radiotherapy (RT) than in those of untreated healthy controls, and hormone therapy in RT-treated BC patients was associated with significantly lower levels of CDA activity. A preliminary analysis of CDA activity in the serum of the very few BC patients who had undergone no treatment other than surgery suggested that the increase in CDA activity might be due to the breast cancer itself. Our findings raise important questions, which should lead to studies to elucidate the origin and significance of the increase in CDA activity in the serum of BC patients, and the impact of hormone therapy.
Collapse
|
6
|
Mameri H, Buhagiar-Labarchède G, Fontaine G, Corcelle C, Barette C, Onclercq-Delic R, Beauvineau C, Mahuteau-Betzer F, Amor-Guéret M. Cytidine deaminase deficiency in tumor cells is associated with sensitivity to a naphthol derivative and a decrease in oncometabolite levels. Cell Mol Life Sci 2022; 79:465. [PMID: 35925417 PMCID: PMC9352748 DOI: 10.1007/s00018-022-04487-9] [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: 05/02/2022] [Revised: 07/01/2022] [Accepted: 07/13/2022] [Indexed: 11/19/2022]
Abstract
Identifying new molecular targets for novel anticancer treatments is a major challenge in clinical cancer research. We have shown that cytidine deaminase (CDA) expression is downregulated in about 60% of cancer cells and tissues. In this study, we aimed to develop a new anticancer treatment specifically inhibiting the growth of CDA-deficient tumor cells. High-throughput screening of a chemical library led to the identification of a naphthol derivative, X55, targeting CDA-deficient tumor cells preferentially, without affecting the growth of non-tumoral cells regardless of CDA expression status. Metabolomic profiling revealed that CDA-deficient HeLa cells differed markedly from control HeLa cells. X55 treatment had a moderate effect on control cells, but greatly disturbed the metabolome of CDA-deficient HeLa cells, worsening the deregulation of many metabolites. In particular, the levels of the three oncometabolites, fumarate, succinate and 2-hydroxyglutarate, were significantly lower in CDA-depleted cells, and this decrease in levels was exacerbated by X55 treatment, revealing an unexpected link between CDA deficiency, mitochondrial function and X55 response. Finally, we identified strong downregulation of MAPT (encoding Tau, a microtubule associated protein) expression as a reliable predictive marker for tumor cell X55 sensitivity.
Collapse
Affiliation(s)
- Hamza Mameri
- Institut Curie, PSL Research University, CNRS UMR 3348, 91405, Orsay, France.,CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France.,Université Paris-Saclay, CNRS UMR 3348, 91405, Orsay, France.,Present address: UMR 1208 IATE, Montpellier University, INRAE, Institut Agro, 34060, Montpellier, France
| | - Géraldine Buhagiar-Labarchède
- Institut Curie, PSL Research University, CNRS UMR 3348, 91405, Orsay, France.,CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France.,Université Paris-Saclay, CNRS UMR 3348, 91405, Orsay, France
| | - Gaëlle Fontaine
- Institut Curie, PSL Research University, CNRS UMR 3348, 91405, Orsay, France.,CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France.,Université Paris-Saclay, CNRS UMR 3348, 91405, Orsay, France
| | - Céline Corcelle
- Institut Curie, PSL Research University, CNRS UMR 9187, INSERM U1196, 91405, Orsay, France.,CNRS UMR 9187, INSERM, U1196, Centre Universitaire, Bât. 110, 91405, Orsay, France.,Université Paris-Saclay, CNRS UMR 9187, INSERM U1196, 91405, Orsay, France
| | - Caroline Barette
- CEA/IRIG/Gen & Chem, Univ. Grenoble Alpes, 38000, Grenoble, France
| | - Rosine Onclercq-Delic
- Institut Curie, PSL Research University, CNRS UMR 3348, 91405, Orsay, France.,CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France.,Université Paris-Saclay, CNRS UMR 3348, 91405, Orsay, France
| | - Claire Beauvineau
- Institut Curie, PSL Research University, CNRS UMR 9187, INSERM U1196, 91405, Orsay, France.,CNRS UMR 9187, INSERM, U1196, Centre Universitaire, Bât. 110, 91405, Orsay, France.,Université Paris-Saclay, CNRS UMR 9187, INSERM U1196, 91405, Orsay, France
| | - Florence Mahuteau-Betzer
- Institut Curie, PSL Research University, CNRS UMR 9187, INSERM U1196, 91405, Orsay, France. .,CNRS UMR 9187, INSERM, U1196, Centre Universitaire, Bât. 110, 91405, Orsay, France. .,Université Paris-Saclay, CNRS UMR 9187, INSERM U1196, 91405, Orsay, France.
| | - Mounira Amor-Guéret
- Institut Curie, PSL Research University, CNRS UMR 3348, 91405, Orsay, France. .,CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France. .,Université Paris-Saclay, CNRS UMR 3348, 91405, Orsay, France.
| |
Collapse
|
7
|
Donne R, Saroul-Ainama M, Cordier P, Hammoutene A, Kabore C, Stadler M, Nemazanyy I, Galy-Fauroux I, Herrag M, Riedl T, Chansel-Da Cruz M, Caruso S, Bonnafous S, Öllinger R, Rad R, Unger K, Tran A, Couty JP, Gual P, Paradis V, Celton-Morizur S, Heikenwalder M, Revy P, Desdouets C. Replication stress triggered by nucleotide pool imbalance drives DNA damage and cGAS-STING pathway activation in NAFLD. Dev Cell 2022; 57:1728-1741.e6. [PMID: 35768000 DOI: 10.1016/j.devcel.2022.06.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 04/22/2022] [Accepted: 06/07/2022] [Indexed: 12/25/2022]
Abstract
Non-alcoholic steatotic liver disease (NAFLD) is the most common cause of chronic liver disease worldwide. NAFLD has a major effect on the intrinsic proliferative properties of hepatocytes. Here, we investigated the mechanisms underlying the activation of DNA damage response during NAFLD. Proliferating mouse NAFLD hepatocytes harbor replication stress (RS) with an alteration of the replication fork's speed and activation of ATR pathway, which is sufficient to cause DNA breaks. Nucleotide pool imbalance occurring during NAFLD is the key driver of RS. Remarkably, DNA lesions drive cGAS/STING pathway activation, a major component of cells' intrinsic immune response. The translational significance of this study was reiterated by showing that lipid overload in proliferating HepaRG was sufficient to induce RS and nucleotide pool imbalance. Moreover, livers from NAFLD patients displayed nucleotide pathway deregulation and cGAS/STING gene alteration. Altogether, our findings shed light on the mechanisms by which damaged NAFLD hepatocytes might promote disease progression.
Collapse
Affiliation(s)
- Romain Donne
- Team Proliferation, Stress and Liver Physiopathology, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, 75006 Paris, France
| | - Maëva Saroul-Ainama
- Team Proliferation, Stress and Liver Physiopathology, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, 75006 Paris, France
| | - Pierre Cordier
- Team Proliferation, Stress and Liver Physiopathology, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, 75006 Paris, France
| | - Adel Hammoutene
- Université Paris-Cité, Centre de recherche sur l'inflammation, INSERM U1149, CNRS, ERL8252, 75018 Paris, France
| | - Christelle Kabore
- Team Proliferation, Stress and Liver Physiopathology, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, 75006 Paris, France
| | - Mira Stadler
- Division of Chronic Inflammation and Cancer (F180), German Cancer Research Center, Heidelberg, Germany
| | - Ivan Nemazanyy
- Platform for Metabolic Analyses, Structure Fédérative de Recherche Necker, INSERM US24/CNRS UMS 3633, Paris, France
| | - Isabelle Galy-Fauroux
- Team Proliferation, Stress and Liver Physiopathology, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, 75006 Paris, France
| | - Mounia Herrag
- Laboratory of Genome Dynamics in the Immune System, Labellisé Ligue, INSERM UMR 1163, Université Paris-Cité, Institut Imagine, Paris, France
| | - Tobias Riedl
- Division of Chronic Inflammation and Cancer (F180), German Cancer Research Center, Heidelberg, Germany
| | - Marie Chansel-Da Cruz
- Laboratory of Genome Dynamics in the Immune System, Labellisé Ligue, INSERM UMR 1163, Université Paris-Cité, Institut Imagine, Paris, France
| | - Stefano Caruso
- Functional Genomics of Solid Tumors Team, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, Université Paris 13, Labex Immuno-Oncology, Équipe Labellisée Ligue Contre le Cancer, Paris, France
| | | | - Rupert Öllinger
- Institute of Molecular Oncology and Functional Genomics, Rechts der Isar University Hospital, Munich, Germany
| | - Roland Rad
- Institute of Molecular Oncology and Functional Genomics, Rechts der Isar University Hospital, Munich, Germany
| | - Kristian Unger
- Research Unit of Radiation Cytogenetics, Helmholtz Zentrum München, Neuherberg, Germany
| | - Albert Tran
- Université Côte d'Azur, INSERM, U1065, C3M, CHU, Nice, France
| | - Jean-Pierre Couty
- Team Proliferation, Stress and Liver Physiopathology, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, 75006 Paris, France
| | - Philippe Gual
- Université Côte d'Azur, INSERM, U1065, C3M, CHU, Nice, France
| | - Valérie Paradis
- Université Paris-Cité, Centre de recherche sur l'inflammation, INSERM U1149, CNRS, ERL8252, 75018 Paris, France; Service d'Anatomie Pathologique, Hôpital Beaujon, Assistance Publique-Hôpitaux de Paris, Clichy, France
| | - Séverine Celton-Morizur
- Team Proliferation, Stress and Liver Physiopathology, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, 75006 Paris, France
| | - Mathias Heikenwalder
- Division of Chronic Inflammation and Cancer (F180), German Cancer Research Center, Heidelberg, Germany
| | - Patrick Revy
- Laboratory of Genome Dynamics in the Immune System, Labellisé Ligue, INSERM UMR 1163, Université Paris-Cité, Institut Imagine, Paris, France
| | - Chantal Desdouets
- Team Proliferation, Stress and Liver Physiopathology, Centre de Recherche des Cordeliers, INSERM, Sorbonne Université, Université Paris-Cité, 75006 Paris, France.
| |
Collapse
|
8
|
Yi R, Xie L, Wang X, Shen C, Chen X, Qiao L. Multi-Omic Profiling of Multi-Biosamples Reveals the Role of Amino Acid and Nucleotide Metabolism in Endometrial Cancer. Front Oncol 2022; 12:861142. [PMID: 35574395 PMCID: PMC9099206 DOI: 10.3389/fonc.2022.861142] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 04/01/2022] [Indexed: 11/15/2022] Open
Abstract
Background Endometrial cancer (EC) is one of the most common gynecological cancers. The traditional diagnosis of EC relies on histopathology, which, however, is invasive and may arouse tumor spread. There have been many studies aiming to find the metabolomic biomarkers of EC to improve the early diagnosis of cancer in a non-invasive or minimally invasive way, which can also provide valuable information for understanding the disease. However, most of these studies only analyze a single type of sample by metabolomics, and cannot provide a comprehensive view of the altered metabolism in EC patients. Our study tries to gain a pathway-based view of multiple types of samples for understanding metabolomic disorders in EC by combining metabolomics and proteomics. Methods Forty-four EC patients and forty-three controls were recruited for the research. We collected endometrial tissue, urine, and intrauterine brushing samples. Untargeted metabolomics and untargeted proteomics were both performed on the endometrial tissue samples, while only untargeted metabolomics was performed on the urine and intrauterine brushing samples. Results By integrating the differential metabolites and proteins between EC patients and controls detected in the endometrial tissue samples, we identified several EC-related significant pathways, such as amino acid metabolism and nucleotide metabolism. The significance of these pathways and the potential of metabolite biomarker-based diagnosis were then further verified by using urine and intrauterine brushing samples. It was found that the regulation of metabolites involved in the significant pathways showed similar trends in the intrauterine brushings and the endometrial tissue samples, while opposite trends in the urine and the endometrial tissue samples. Conclusions With multi-omics characterization of multi-biosamples, the metabolomic changes related to EC are illustrated in a pathway-based way. The network of altered metabolites and related proteins provides a comprehensive view of altered metabolism in the endometrial tissue samples. The verification of these critical pathways by using urine and intrauterine brushing samples provides evidence for the possible non-invasive or minimally invasive biopsy for EC diagnosis in the future.
Collapse
Affiliation(s)
- Runqiu Yi
- Department of Chemistry, Shanghai Stomatological Hospital, and Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, China
| | - Liying Xie
- Department of Chemistry, Shanghai Stomatological Hospital, and Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, China
| | | | | | - Xiaojun Chen
- Department of Chemistry, Shanghai Stomatological Hospital, and Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, China
- *Correspondence: Liang Qiao, ; Xiaojun Chen,
| | - Liang Qiao
- Department of Chemistry, Shanghai Stomatological Hospital, and Obstetrics and Gynecology Hospital of Fudan University, Fudan University, Shanghai, China
- *Correspondence: Liang Qiao, ; Xiaojun Chen,
| |
Collapse
|
9
|
Li Y, Luo W, Zhang H, Wang C, Yu C, Jiang Z, Zhang W. Antitumor Mechanism of Hydroxycamptothecin via the Metabolic Perturbation of Ribonucleotide and Deoxyribonucleotide in Human Colorectal Carcinoma Cells. Molecules 2021; 26:4902. [PMID: 34443490 PMCID: PMC8398164 DOI: 10.3390/molecules26164902] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2021] [Revised: 08/06/2021] [Accepted: 08/09/2021] [Indexed: 12/12/2022] Open
Abstract
Hydroxycamptothecin (SN38) is a natural plant extract isolated from Camptotheca acuminate. It has a broad spectrum of anticancer activity through inhibition of DNA topoisomerase I, which could affect DNA synthesis and lead to DNA damage. Thus, the action of SN38 against cancers could inevitably affect endogenous levels of ribonucleotide (RNs) and deoxyribonucleotide (dRNs) that play critical roles in many biological processes, especially in DNA synthesis and repair. However, the exact impact of SN38 on RNs and dRNs is yet to be fully elucidated. In this study, we evaluated the anticancer effect and associated mechanism of SN38 in human colorectal carcinoma HCT 116 cells. As a result, SN38 could decrease the cell viability and induce DNA damage in a concentration-dependent manner. Furthermore, cell cycle arrest and intracellular nucleotide metabolism were perturbed due to DNA damage response, of which ATP, UTP, dATP, and TTP may be the critical metabolites during the whole process. Combined with the expression of deoxyribonucleoside triphosphates synthesis enzymes, our results demonstrated that the alteration and imbalance of deoxyribonucleoside triphosphates caused by SN38 was mainly due to the de novo nucleotide synthesis at 24 h, and subsequently the salvage pathways at 48 h. The unique features of SN38 suggested that it might be recommended as an effective supplementary drug with an anticancer effect.
Collapse
Affiliation(s)
- Yan Li
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Wendi Luo
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Huixia Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Caiyun Wang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Caiyuan Yu
- Faculty of Agroforestry and Medicine, The Open University of China, Beijing 100039, China;
| | - Zhihong Jiang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| | - Wei Zhang
- State Key Laboratory of Quality Research in Chinese Medicines, Macau Institute for Applied Research in Medicine and Health, Macau University of Science and Technology, Taipa, Macau 999078, China; (Y.L.); (W.L.); (H.Z.); (C.W.)
| |
Collapse
|
10
|
Ababou M. Bloom syndrome and the underlying causes of genetic instability. Mol Genet Metab 2021; 133:35-48. [PMID: 33736941 DOI: 10.1016/j.ymgme.2021.03.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Revised: 02/01/2021] [Accepted: 03/06/2021] [Indexed: 11/27/2022]
Abstract
Autosomal hereditary recessive diseases characterized by genetic instability are often associated with cancer predisposition. Bloom syndrome (BS), a rare genetic disorder, with <300 cases reported worldwide, combines both. Indeed, patients with Bloom's syndrome are 150 to 300 times more likely to develop cancers than normal individuals. The wide spectrum of cancers developed by BS patients suggests that early initial events occur in BS cells which may also be involved in the initiation of carcinogenesis in the general population and these may be common to several cancers. BS is caused by mutations of both copies of the BLM gene, encoding the RecQ BLM helicase. This review discusses the different aspects of BS and the different cellular functions of BLM in genome surveillance and maintenance through its major roles during DNA replication, repair, and transcription. BLM's activities are essential for the stabilization of centromeric, telomeric and ribosomal DNA sequences, and the regulation of innate immunity. One of the key objectives of this work is to establish a link between BLM functions and the main clinical phenotypes observed in BS patients, as well as to shed new light on the correlation between the genetic instability and diseases such as immunodeficiency and cancer. The different potential implications of the BLM helicase in the tumorigenic process and the use of BLM as new potential target in the field of cancer treatment are also debated.
Collapse
Affiliation(s)
- Mouna Ababou
- Laboratory of Human Pathologies Biology, Department of Biology, Faculty of Sciences, University Mohammed V, Rabat, Morocco; Genomic Center of Human Pathologies, Faculty of medicine and Pharmacy, University Mohammed V, Rabat, Morocco.
| |
Collapse
|
11
|
Straube H, Niehaus M, Zwittian S, Witte CP, Herde M. Enhanced nucleotide analysis enables the quantification of deoxynucleotides in plants and algae revealing connections between nucleoside and deoxynucleoside metabolism. THE PLANT CELL 2021; 33:270-289. [PMID: 33793855 PMCID: PMC8136904 DOI: 10.1093/plcell/koaa028] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/04/2020] [Accepted: 11/12/2020] [Indexed: 05/02/2023]
Abstract
Detecting and quantifying low-abundance (deoxy)ribonucleotides and (deoxy)ribonucleosides in plants remains difficult; this is a major roadblock for the investigation of plant nucleotide (NT) metabolism. Here, we present a method that overcomes this limitation, allowing the detection of all deoxy- and ribonucleotides as well as the corresponding nucleosides from the same plant sample. The method is characterized by high sensitivity and robustness enabling the reproducible detection and absolute quantification of these metabolites even if they are of low abundance. Employing the new method, we analyzed Arabidopsis thaliana null mutants of CYTIDINE DEAMINASE, GUANOSINE DEAMINASE, and NUCLEOSIDE HYDROLASE 1, demonstrating that the deoxyribonucleotide (dNT) metabolism is intricately interwoven with the catabolism of ribonucleosides (rNs). In addition, we discovered a function of rN catabolic enzymes in the degradation of deoxyribonucleosides in vivo. We also determined the concentrations of dNTs in several mono- and dicotyledonous plants, a bryophyte, and three algae, revealing a correlation of GC to AT dNT ratios with genomic GC contents. This suggests a link between the genome and the metabolome previously discussed but not experimentally addressed. Together, these findings demonstrate the potential of this new method to provide insight into plant NT metabolism.
Collapse
Affiliation(s)
- Henryk Straube
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Markus Niehaus
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Sarah Zwittian
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Claus-Peter Witte
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
| | - Marco Herde
- Department of Molecular Nutrition and Biochemistry of Plants, Leibniz Universität Hannover, Hannover 30419, Germany
- Author for correspondence:
| |
Collapse
|
12
|
Willaume S, Rass E, Fontanilla-Ramirez P, Moussa A, Wanschoor P, Bertrand P. A Link between Replicative Stress, Lamin Proteins, and Inflammation. Genes (Basel) 2021; 12:genes12040552. [PMID: 33918867 PMCID: PMC8070205 DOI: 10.3390/genes12040552] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2021] [Revised: 03/23/2021] [Accepted: 04/08/2021] [Indexed: 12/12/2022] Open
Abstract
Double-stranded breaks (DSB), the most toxic DNA lesions, are either a consequence of cellular metabolism, programmed as in during V(D)J recombination, or induced by anti-tumoral therapies or accidental genotoxic exposure. One origin of DSB sources is replicative stress, a major source of genome instability, especially when the integrity of the replication forks is not properly guaranteed. To complete stalled replication, restarting the fork requires complex molecular mechanisms, such as protection, remodeling, and processing. Recently, a link has been made between DNA damage accumulation and inflammation. Indeed, defects in DNA repair or in replication can lead to the release of DNA fragments in the cytosol. The recognition of this self-DNA by DNA sensors leads to the production of inflammatory factors. This beneficial response activating an innate immune response and destruction of cells bearing DNA damage may be considered as a novel part of DNA damage response. However, upon accumulation of DNA damage, a chronic inflammatory cellular microenvironment may lead to inflammatory pathologies, aging, and progression of tumor cells. Progress in understanding the molecular mechanisms of DNA damage repair, replication stress, and cytosolic DNA production would allow to propose new therapeutical strategies against cancer or inflammatory diseases associated with aging. In this review, we describe the mechanisms involved in DSB repair, the replicative stress management, and its consequences. We also focus on new emerging links between key components of the nuclear envelope, the lamins, and DNA repair, management of replicative stress, and inflammation.
Collapse
|
13
|
Silveira SC, Buhagiar-Labarchède G, Onclercq-Delic R, Gemble S, Bou Samra E, Mameri H, Duchambon P, Machon C, Guitton J, Amor-Guéret M. A decrease in NAMPT activity impairs basal PARP-1 activity in cytidine deaminase deficient-cells, independently of NAD .. Sci Rep 2020; 10:13907. [PMID: 32807821 PMCID: PMC7431583 DOI: 10.1038/s41598-020-70874-6] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2020] [Accepted: 08/03/2020] [Indexed: 11/09/2022] Open
Abstract
Cytidine deaminase (CDA) deficiency causes pyrimidine pool disequilibrium. We previously reported that the excess cellular dC and dCTP resulting from CDA deficiency jeopardizes genome stability, decreasing basal poly(ADP-ribose) polymerase 1 (PARP-1) activity and increasing ultrafine anaphase bridge (UFB) formation. Here, we investigated the mechanism underlying the decrease in PARP-1 activity in CDA-deficient cells. PARP-1 activity is dependent on intracellular NAD+ concentration. We therefore hypothesized that defects of the NAD+ salvage pathway might result in decreases in PARP-1 activity. We found that the inhibition or depletion of nicotinamide phosphoribosyltransferase (NAMPT), the rate-limiting enzyme in the NAD+ salvage biosynthesis pathway, mimicked CDA deficiency, resulting in a decrease in basal PARP-1 activity, regardless of NAD+ levels. Furthermore, the expression of exogenous wild-type NAMPT fully restored basal PARP-1 activity and prevented the increase in UFB frequency in CDA-deficient cells. No such effect was observed with the catalytic mutant. Our findings demonstrate that (1) the inhibition of NAMPT activity in CDA-proficient cells lowers basal PARP-1 activity, and (2) the expression of exogenous wild-type NAMPT, but not of the catalytic mutant, fully restores basal PARP-1 activity in CDA-deficient cells; these results strongly suggest that basal PARP-1 activity in CDA-deficient cells decreases due to a reduction of NAMPT activity.
Collapse
Affiliation(s)
- Sandra Cunha Silveira
- Institut Curie, UMR 3348, PSL Research University, 91405, Orsay, France.,CNRS UMR 3348, Centre Universitaire, 91405, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405, Orsay, France
| | - Géraldine Buhagiar-Labarchède
- Institut Curie, UMR 3348, PSL Research University, 91405, Orsay, France.,CNRS UMR 3348, Centre Universitaire, 91405, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405, Orsay, France
| | - Rosine Onclercq-Delic
- Institut Curie, UMR 3348, PSL Research University, 91405, Orsay, France.,CNRS UMR 3348, Centre Universitaire, 91405, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405, Orsay, France
| | - Simon Gemble
- Institut Curie, UMR 3348, PSL Research University, 91405, Orsay, France.,CNRS UMR 3348, Centre Universitaire, 91405, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405, Orsay, France
| | - Elias Bou Samra
- Institut Curie, UMR 3348, PSL Research University, 91405, Orsay, France.,CNRS UMR 3348, Centre Universitaire, 91405, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405, Orsay, France
| | - Hamza Mameri
- Institut Curie, UMR 3348, PSL Research University, 91405, Orsay, France.,CNRS UMR 3348, Centre Universitaire, 91405, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405, Orsay, France
| | - Patricia Duchambon
- Protein Expression and Purification Core Facility, Institut Curie, PSL Research University, 75248, Paris, France.,Université Paris Sud, Université Paris-Saclay, Centre Universitaire, UMR 9187 - INSERM U1196, 91405, Orsay, France
| | - Christelle Machon
- Laboratoire de Biochimie et Toxicologie, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre-Bénite, France.,Laboratoire de Chimie Analytique, ISPB, Faculté de Pharmacie, Université Lyon 1, Université de Lyon, Lyon, France
| | - Jérôme Guitton
- Laboratoire de Biochimie et Toxicologie, Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Pierre-Bénite, France.,Laboratoire de Toxicologie, ISPB, Faculté de Pharmacie, Université Lyon 1, Université de Lyon, Lyon, France
| | - Mounira Amor-Guéret
- Institut Curie, UMR 3348, PSL Research University, 91405, Orsay, France. .,CNRS UMR 3348, Centre Universitaire, 91405, Orsay, France. .,Université Paris Sud, Université Paris-Saclay, Centre Universitaire, UMR 3348, 91405, Orsay, France.
| |
Collapse
|
14
|
Tian J, Xue W, Yin H, Zhang N, Zhou J, Long Z, Wu C, Liang Z, Xie K, Li S, Li L, Wu Z, Daria V, Zhao Y, Wang F, Wang M. Differential Metabolic Alterations and Biomarkers Between Gastric Cancer and Colorectal Cancer: A Systematic Review and Meta-Analysis. Onco Targets Ther 2020; 13:6093-6108. [PMID: 32612370 PMCID: PMC7323803 DOI: 10.2147/ott.s247393] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2020] [Accepted: 06/09/2020] [Indexed: 12/21/2022] Open
Abstract
Purpose Numerous metabolomics studies have been conducted to detect the metabolic mechanisms and biomarkers related to gastric cancer and colorectal cancer. Because of the common metabolic features between gastric cancer and colorectal cancer, a differential diagnosis is difficult. Here, we performed a systematic review and meta-analysis to identify differential metabolic biomarkers between these two types of cancers. Materials and Methods PubMed, Embase, and ScienceDirect were searched to identify all metabolomics studies of gastric cancer and colorectal cancer published up to September 2018. Differential metabolites or altered pathways were extracted. The intersections and differences for these metabolites and pathways between gastric cancer and colorectal cancer were compared. Candidate biomarker sets for diagnosis were proposed from biofluid or feces by comparing them with tumor tissues. Results Totally, 24 and 65 studies were included in gastric cancer and colorectal cancer, and 223 and 472 differential metabolites were extracted, respectively. Eight pathways were reproducibly enriched in blood, tissue and urine in gastric cancer, while, 11 pathways were reproducibly enriched in blood, urine, feces and tissue in colorectal cancer. Candidate metabolic biomarker sets in blood, urine, or feces for these two cancers were proposed. We found 27 pathways (categorized into eight classifications) common to both cancers, five pathways involving 35 metabolites enriched only in gastric cancer, and eight pathways involving 54 metabolites enriched only in colorectal cancer. Conclusion The altered metabolic pathways showed signatures of abnormal metabolism in gastric cancer and colorectal cancer; the potential metabolic biomarkers proposed in this study have important implications for the prospective validation of gastric cancer and colorectal cancer.
Collapse
Affiliation(s)
- Jingshen Tian
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Weinan Xue
- Department of Colorectal Surgery, The Tumor Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Huihui Yin
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Nannan Zhang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Junde Zhou
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Zhiping Long
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Chengwei Wu
- Department of Colorectal Surgery, The Second Affiliated Hospital of Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Zhengzi Liang
- Department of Colorectal Surgery, The Affiliated Hospital of Guizhou Medical University, Guiyang, Guizhou Province, People's Republic of China
| | - Kun Xie
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Shuo Li
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Liangliang Li
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Zhen Wu
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Volontovich Daria
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Yashuang Zhao
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Fan Wang
- Department of Epidemiology, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| | - Maoqing Wang
- National Key Disciplines of Nutrition and Food Hygiene, Department of Nutrition and Food Hygiene, School of Public Health, Harbin Medical University, Harbin, Heilongjiang Province, People's Republic of China
| |
Collapse
|
15
|
Martínez-Arribas B, Requena CE, Pérez-Moreno G, Ruíz-Pérez LM, Vidal AE, González-Pacanowska D. DCTPP1 prevents a mutator phenotype through the modulation of dCTP, dTTP and dUTP pools. Cell Mol Life Sci 2020; 77:1645-1660. [PMID: 31377845 PMCID: PMC7162842 DOI: 10.1007/s00018-019-03250-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 07/05/2019] [Accepted: 07/23/2019] [Indexed: 12/02/2022]
Abstract
To maintain dNTP pool homeostasis and preserve genetic integrity of nuclear and mitochondrial genomes, the synthesis and degradation of DNA precursors must be precisely regulated. Human all-alpha dCTP pyrophosphatase 1 (DCTPP1) is a dNTP pyrophosphatase with high affinity for dCTP and 5'-modified dCTP derivatives, but its contribution to overall nucleotide metabolism is controversial. Here, we identify a central role for DCTPP1 in the homeostasis of dCTP, dTTP and dUTP. Nucleotide pools and the dUTP/dTTP ratio are severely altered in DCTPP1-deficient cells, which exhibit an accumulation of uracil in genomic DNA, the activation of the DNA damage response and both a mitochondrial and nuclear hypermutator phenotype. Notably, DNA damage can be reverted by incubation with thymidine, dUTPase overexpression or uracil-DNA glycosylase suppression. Moreover, DCTPP1-deficient cells are highly sensitive to down-regulation of nucleoside salvage. Our data indicate that DCTPP1 is crucially involved in the provision of dCMP for thymidylate biosynthesis, introducing a new player in the regulation of pyrimidine dNTP levels and the maintenance of genomic integrity.
Collapse
Affiliation(s)
- Blanca Martínez-Arribas
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Cristina E Requena
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
- MRC London Institute of Medical Sciences, Du Cane Road, London, W12 0NN, UK
- Institute of Clinical Sciences, Imperial College London, Du Cane Road, London, W12 0NN, UK
| | - Guiomar Pérez-Moreno
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Luis M Ruíz-Pérez
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Antonio E Vidal
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina "López-Neyra", Consejo Superior de Investigaciones Científicas (CSIC), Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain.
| |
Collapse
|
16
|
SAMHD1 Functions and Human Diseases. Viruses 2020; 12:v12040382. [PMID: 32244340 PMCID: PMC7232136 DOI: 10.3390/v12040382] [Citation(s) in RCA: 42] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2020] [Revised: 03/27/2020] [Accepted: 03/28/2020] [Indexed: 12/12/2022] Open
Abstract
Deoxynucleoside triphosphate (dNTP) molecules are essential for the replication and maintenance of genomic information in both cells and a variety of viral pathogens. While the process of dNTP biosynthesis by cellular enzymes, such as ribonucleotide reductase (RNR) and thymidine kinase (TK), has been extensively investigated, a negative regulatory mechanism of dNTP pools was recently found to involve sterile alpha motif (SAM) domain and histidine-aspartate (HD) domain-containing protein 1, SAMHD1. When active, dNTP triphosphohydrolase activity of SAMHD1 degrades dNTPs into their 2'-deoxynucleoside (dN) and triphosphate subparts, steadily depleting intercellular dNTP pools. The differential expression levels and activation states of SAMHD1 in various cell types contributes to unique dNTP pools that either aid (i.e., dividing T cells) or restrict (i.e., nondividing macrophages) viral replication that consumes cellular dNTPs. Genetic mutations in SAMHD1 induce a rare inflammatory encephalopathy called Aicardi-Goutières syndrome (AGS), which phenotypically resembles viral infection. Recent publications have identified diverse roles for SAMHD1 in double-stranded break repair, genome stability, and the replication stress response through interferon signaling. Finally, a series of SAMHD1 mutations were also reported in various cancer cell types while why SAMHD1 is mutated in these cancer cells remains to investigated. Here, we reviewed a series of studies that have begun illuminating the highly diverse roles of SAMHD1 in virology, immunology, and cancer biology.
Collapse
|
17
|
Santoriello C, Sporrij A, Yang S, Flynn RA, Henriques T, Dorjsuren B, Custo Greig E, McCall W, Stanhope ME, Fazio M, Superdock M, Lichtig A, Adatto I, Abraham BJ, Kalocsay M, Jurynec M, Zhou Y, Adelman K, Calo E, Zon LI. RNA helicase DDX21 mediates nucleotide stress responses in neural crest and melanoma cells. Nat Cell Biol 2020; 22:372-379. [PMID: 32231306 PMCID: PMC7185069 DOI: 10.1038/s41556-020-0493-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Accepted: 02/24/2020] [Indexed: 12/25/2022]
Abstract
The availability of nucleotides has a direct impact on transcription. The inhibition of dihydroorotate dehydrogenase (DHODH) with leflunomide impacts nucleotide pools by reducing pyrimidine levels. Leflunomide abrogates the effective transcription elongation of genes required for neural crest development and melanoma growth in vivo1. To define the mechanism of action, we undertook an in vivo chemical suppressor screen for restoration of neural crest after leflunomide treatment. Surprisingly, we found that alterations in progesterone and progesterone receptor (Pgr) signalling strongly suppressed leflunomide-mediated neural crest effects in zebrafish. In addition, progesterone bypasses the transcriptional elongation block resulting from Paf complex deficiency, rescuing neural crest defects in ctr9 morphant and paf1(alnz24) mutant embryos. Using proteomics, we found that Pgr binds the RNA helicase protein Ddx21. ddx21-deficient zebrafish show resistance to leflunomide-induced stress. At a molecular level, nucleotide depletion reduced the chromatin occupancy of DDX21 in human A375 melanoma cells. Nucleotide supplementation reversed the gene expression signature and DDX21 occupancy changes prompted by leflunomide. Together, our results show that DDX21 acts as a sensor and mediator of transcription during nucleotide stress.
Collapse
Affiliation(s)
- Cristina Santoriello
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Audrey Sporrij
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Song Yang
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Ryan A Flynn
- Department of Chemistry, Stanford University, Stanford, CA, USA
| | - Telmo Henriques
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Bilguujin Dorjsuren
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Eugenia Custo Greig
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Wyatt McCall
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Meredith E Stanhope
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Maurizio Fazio
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Michael Superdock
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Asher Lichtig
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Isaac Adatto
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA
| | - Brian J Abraham
- Whitehead Institute for Biomedical Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Marian Kalocsay
- Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Michael Jurynec
- Department of Orthopedics, University of Utah, Salt Lake City, UT, USA
| | - Yi Zhou
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA.,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA
| | - Karen Adelman
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, MA, USA
| | - Eliezer Calo
- Department of Biology and Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA
| | - Leonard I Zon
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA, USA. .,Stem Cell Program and Division of Hematology/Oncology, Boston Children's Hospital, Harvard Stem Cell Institute, Howard Hughes Medical Institute and Harvard Medical School, Boston, MA, USA.
| |
Collapse
|
18
|
MUC1 oncoprotein mitigates ER stress via CDA-mediated reprogramming of pyrimidine metabolism. Oncogene 2020; 39:3381-3395. [PMID: 32103170 PMCID: PMC7165067 DOI: 10.1038/s41388-020-1225-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2019] [Revised: 02/12/2020] [Accepted: 02/14/2020] [Indexed: 12/12/2022]
Abstract
The Mucin 1 (MUC1) protein is overexpressed in various cancers and mediates chemotherapy resistance. However, the mechanism is not fully understood. Given that most chemotherapeutic drugs disrupt ER homeostasis as part of their toxicity, and MUC1 expression is regulated by proteins involved in ER homeostasis, we investigated the link between MUC1 and ER homeostasis. MUC1 knockdown in pancreatic cancer cells enhanced unfolded protein response (UPR) signaling and cell death upon ER stress induction. Transcriptomic analysis revealed alterations in the pyrimidine metabolic pathway and cytidine deaminase (CDA). ChIP and CDA activity assays showed that MUC1 occupied CDA gene promoter upon ER stress induction correlating with increased CDA expression and activity in MUC1-expressing cells as compared to MUC1 knockdown cells. Inhibition of either the CDA or pyrimidine metabolic pathway diminished survival in MUC1-expressing cancer cells upon ER stress induction. Metabolomic analysis demonstrated that MUC1-mediated CDA activity corresponded to deoxycytidine to deoxyuridine metabolic reprogramming upon ER stress induction. The resulting increase in deoxyuridine mitigated ER stress-induced cytotoxicity. Additionally, given 1) the established roles of MUC1 in protecting cells against reactive oxygen species (ROS) insults, 2) ER stress-generated ROS further promote ER stress and 3) the emerging anti-oxidant property of deoxyuridine, we further investigated if MUC1 regulated ER stress by a deoxyuridine-mediated modulation of ROS levels. We observed that deoxyuridine could abrogate ROS-induced ER stress to promote cancer cell survival. Taken together, our findings demonstrate a novel MUC1-CDA axis of the adaptive UPR that provides survival advantage upon ER stress induction.
Collapse
|
19
|
Furusho K, Shibata T, Sato R, Fukui R, Motoi Y, Zhang Y, Saitoh SI, Ichinohe T, Moriyama M, Nakamura S, Miyake K. Cytidine deaminase enables Toll-like receptor 8 activation by cytidine or its analogs. Int Immunol 2020; 31:167-173. [PMID: 30535046 DOI: 10.1093/intimm/dxy075] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Accepted: 11/16/2018] [Indexed: 12/25/2022] Open
Abstract
Toll-like receptor 8 (TLR8), a sensor for pathogen-derived single-stranded RNA (ssRNA), binds to uridine (Uri) and ssRNA to induce defense responses. We here show that cytidine (Cyd) with ssRNA also activated TLR8 in peripheral blood leukocytes (PBLs) and a myeloid cell line U937, but not in an embryonic kidney cell line 293T. Cyd deaminase (CDA), an enzyme highly expressed in leukocytes, deaminates Cyd to Uri. CDA expression enabled TLR8 response to Cyd and ssRNA in 293T cells. CDA deficiency and a CDA inhibitor both reduced TLR8 responses to Cyd and ssRNA in U937. The CDA inhibitor also reduced PBL response to Cyd and ssRNA. A Cyd analogue, azacytidine, is used for the therapy of myelodysplastic syndrome and acute myeloid leukemia. Azacytidine with ssRNA induced tumor necrosis factor-α expression in U937 and PBLs in a manner dependent on CDA and TLR8. These results suggest that CDA enables TLR8 activation by Cyd or its analogues with ssRNA through deaminating activity. Nucleoside metabolism might impact TLR8 responses in a variety of situations such as the treatment with nucleoside analogues.
Collapse
Affiliation(s)
- Katsuhiro Furusho
- Division of Innate Immunity, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan.,Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Takuma Shibata
- Division of Innate Immunity, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan.,Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology Agency (JST), Saitama, Japan
| | - Ryota Sato
- Division of Innate Immunity, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Ryutaro Fukui
- Division of Innate Immunity, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yuji Motoi
- Division of Innate Immunity, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Yun Zhang
- Division of Innate Immunity, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Shin-Ichiroh Saitoh
- Division of Innate Immunity, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Takeshi Ichinohe
- Division of Viral Infection, Department of Infectious Disease Control, International Research Center for Infectious Diseases, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| | - Masafumi Moriyama
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Seiji Nakamura
- Section of Oral and Maxillofacial Oncology, Division of Maxillofacial Diagnostic and Surgical Sciences, Faculty of Dental Science, Kyushu University, Fukuoka, Japan
| | - Kensuke Miyake
- Division of Innate Immunity, Department of Microbiology and Immunology, Institute of Medical Science, University of Tokyo, Minato-ku, Tokyo, Japan
| |
Collapse
|
20
|
Huang CY, Yagüe-Capilla M, González-Pacanowska D, Chang ZF. Quantitation of deoxynucleoside triphosphates by click reactions. Sci Rep 2020; 10:611. [PMID: 31953472 PMCID: PMC6969045 DOI: 10.1038/s41598-020-57463-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Accepted: 11/26/2019] [Indexed: 12/11/2022] Open
Abstract
The levels of the four deoxynucleoside triphosphates (dNTPs) are under strict control in the cell, as improper or imbalanced dNTP pools may lead to growth defects and oncogenesis. Upon treatment of cancer cells with therapeutic agents, changes in the canonical dNTPs levels may provide critical information for evaluating drug response and mode of action. The radioisotope-labeling enzymatic assay has been commonly used for quantitation of cellular dNTP levels. However, the disadvantage of this method is the handling of biohazard materials. Here, we described the use of click chemistry to replace radioisotope-labeling in template-dependent DNA polymerization for quantitation of the four canonical dNTPs. Specific oligomers were designed for dCTP, dTTP, dATP and dGTP measurement, and the incorporation of 5-ethynyl-dUTP or C8-alkyne-dCTP during the polymerization reaction allowed for fluorophore conjugation on immobilized oligonucleotides. The four reactions gave a linear correlation coefficient >0.99 in the range of the concentration of dNTPs present in 106 cells, with little interference of cellular rNTPs. We present evidence indicating that data generated by this methodology is comparable to radioisotope-labeling data. Furthermore, the design and utilization of a robust microplate assay based on this technology evidenced the modulation of dNTPs in response to different chemotherapeutic agents in cancer cells.
Collapse
Affiliation(s)
- Chang-Yu Huang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No.155, Sec. 2, Linong Street, Taipei, 112, Taiwan.,Institute of Molecular Medicine, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 100, Taiwan, ROC
| | - Miriam Yagüe-Capilla
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas. Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Dolores González-Pacanowska
- Instituto de Parasitología y Biomedicina "López-Neyra" (IPBLN), Consejo Superior de Investigaciones Científicas. Parque Tecnológico de Ciencias de la Salud, Avenida del Conocimiento, 17, 18016, Armilla, Granada, Spain
| | - Zee-Fen Chang
- Institute of Biochemistry and Molecular Biology, National Yang-Ming University, No.155, Sec. 2, Linong Street, Taipei, 112, Taiwan. .,Institute of Molecular Medicine, College of Medicine, National Taiwan University, No. 1, Section 1, Jen-Ai Road, Taipei, 100, Taiwan, ROC. .,Center of Precision Medicine, College of Medicine, National Taiwan University, Taipei, Taiwan.
| |
Collapse
|
21
|
Tsegay PS, Lai Y, Liu Y. Replication Stress and Consequential Instability of the Genome and Epigenome. Molecules 2019; 24:molecules24213870. [PMID: 31717862 PMCID: PMC6864812 DOI: 10.3390/molecules24213870] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2019] [Revised: 10/25/2019] [Accepted: 10/25/2019] [Indexed: 12/12/2022] Open
Abstract
Cells must faithfully duplicate their DNA in the genome to pass their genetic information to the daughter cells. To maintain genomic stability and integrity, double-strand DNA has to be replicated in a strictly regulated manner, ensuring the accuracy of its copy number, integrity and epigenetic modifications. However, DNA is constantly under the attack of DNA damage, among which oxidative DNA damage is the one that most frequently occurs, and can alter the accuracy of DNA replication, integrity and epigenetic features, resulting in DNA replication stress and subsequent genome and epigenome instability. In this review, we summarize DNA damage-induced replication stress, the formation of DNA secondary structures, peculiar epigenetic modifications and cellular responses to the stress and their impact on the instability of the genome and epigenome mainly in eukaryotic cells.
Collapse
Affiliation(s)
- Pawlos S. Tsegay
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA;
| | - Yanhao Lai
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA;
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
| | - Yuan Liu
- Biochemistry Ph.D. Program, Florida International University, Miami, FL 33199, USA;
- Department of Chemistry and Biochemistry, Florida International University, 11200 SW 8th Street, Miami, FL 33199, USA;
- Biomolecular Sciences Institute, Florida International University, Miami, FL 33199, USA
- Correspondence:
| |
Collapse
|
22
|
Gratia M, Rodero MP, Conrad C, Bou Samra E, Maurin M, Rice GI, Duffy D, Revy P, Petit F, Dale RC, Crow YJ, Amor-Gueret M, Manel N. Bloom syndrome protein restrains innate immune sensing of micronuclei by cGAS. J Exp Med 2019; 216:1199-1213. [PMID: 30936263 PMCID: PMC6504208 DOI: 10.1084/jem.20181329] [Citation(s) in RCA: 76] [Impact Index Per Article: 15.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2018] [Revised: 01/25/2019] [Accepted: 03/12/2019] [Indexed: 12/16/2022] Open
Abstract
Cellular innate immune sensors of DNA are essential for host defense against invading pathogens. However, the presence of self-DNA inside cells poses a risk of triggering unchecked immune responses. The mechanisms limiting induction of inflammation by self-DNA are poorly understood. BLM RecQ-like helicase is essential for genome integrity and is deficient in Bloom syndrome (BS), a rare genetic disease characterized by genome instability, accumulation of micronuclei, susceptibility to cancer, and immunodeficiency. Here, we show that BLM-deficient fibroblasts show constitutive up-regulation of inflammatory interferon-stimulated gene (ISG) expression, which is mediated by the cGAS-STING-IRF3 cytosolic DNA-sensing pathway. Increased DNA damage or down-regulation of the cytoplasmic exonuclease TREX1 enhances ISG expression in BLM-deficient fibroblasts. cGAS-containing cytoplasmic micronuclei are increased in BS cells. Finally, BS patients demonstrate elevated ISG expression in peripheral blood. These results reveal that BLM limits ISG induction, thus connecting DNA damage to cellular innate immune response, which may contribute to human pathogenesis.
Collapse
Affiliation(s)
- Matthieu Gratia
- Immunity and Cancer Department, Institut Curie, Paris-Sciences-et-Lettres Research University, Institut National de la Santé et de la Recherche Medicale U932, Paris, France,Institut Curie, Paris-Sciences-et-Lettres Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3348, Orsay, France,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3348, Centre Universitaire, Orsay, France
| | - Mathieu P. Rodero
- Institut National de la Santé et de la Recherche Médicale U1163, Paris Descartes University, Sorbonne-Paris-Cité, Institut Imagine, Paris, France,Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine, Paris, France
| | - Cécile Conrad
- Immunity and Cancer Department, Institut Curie, Paris-Sciences-et-Lettres Research University, Institut National de la Santé et de la Recherche Medicale U932, Paris, France
| | - Elias Bou Samra
- Institut Curie, Paris-Sciences-et-Lettres Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3348, Orsay, France,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3348, Centre Universitaire, Orsay, France
| | - Mathieu Maurin
- Immunity and Cancer Department, Institut Curie, Paris-Sciences-et-Lettres Research University, Institut National de la Santé et de la Recherche Medicale U932, Paris, France
| | - Gillian I. Rice
- Manchester Centre for Genomic Medicine, University of Manchester, Manchester, UK
| | - Darragh Duffy
- Immunobiology of Dendritic Cells, Institut National de la Santé et de la Recherche Médicale U1223, Institut Pasteur, Paris, France
| | - Patrick Revy
- Institut National de la Santé et de la Recherche Médicale U1163, Paris Descartes University, Sorbonne-Paris-Cité, Institut Imagine, Paris, France
| | - Florence Petit
- Clinique de Génétique, Centre Hospitalier Universitaire Lille, Hôpital Jeanne de Flandre, Lille, France
| | - Russell C. Dale
- Kids Neuroscience Centre, The Children’s Hospital at Westmead, Faculty of Medicine and Health, University of Sydney, Sydney, Australia
| | - Yanick J. Crow
- Institut National de la Santé et de la Recherche Médicale U1163, Paris Descartes University, Sorbonne-Paris-Cité, Institut Imagine, Paris, France,Laboratory of Neurogenetics and Neuroinflammation, Institut Imagine, Paris, France,Centre for Genomic and Experimental Medicine, Medical Research Council Institute of Genetics and Molecular Medicine, University of Edinburgh, Edinburgh, UK,Yanick J. Crow:
| | - Mounira Amor-Gueret
- Institut Curie, Paris-Sciences-et-Lettres Research University, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3348, Orsay, France .,Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3348, Centre Universitaire, Orsay, France.,Université Paris Sud, Université Paris-Saclay, Centre National de la Recherche Scientifique, Unité Mixte de Recherche 3348, Orsay, France
| | - Nicolas Manel
- Immunity and Cancer Department, Institut Curie, Paris-Sciences-et-Lettres Research University, Institut National de la Santé et de la Recherche Medicale U932, Paris, France
| |
Collapse
|
23
|
Du L, Yang F, Fang H, Sun H, Chen Y, Xu Y, Li H, Zheng L, Zhou BBS. AICAr suppresses cell proliferation by inducing NTP and dNTP pool imbalances in acute lymphoblastic leukemia cells. FASEB J 2019; 33:4525-4537. [PMID: 30702927 DOI: 10.1096/fj.201801559rr] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
It has been shown that 5-amino-4-imidazolecarboxamide riboside (AICAr) can inhibit cell proliferation and induce apoptosis in childhood acute lymphoblastic leukemia (ALL) cells. Although AICAr could regulate cellular energy metabolism by activating AMPK, the cytotoxic mechanisms of AICAr are still unclear. Here, we knocked out TP53 or PRKAA1 gene (encoding AMPKα1) in NALM-6 and Reh cells by using the clustered regularly interspaced short palindromic repeats/Cas9 system and found that AICAr-induced proliferation inhibition was independent of AMPK activation but dependent on p53. Liquid chromatography-mass spectrometry analysis of nucleotide metabolites indicated that AICAr caused an increase in adenosine triphosphate, deoxyadenosine triphosphate, and deoxyguanosine triphosphate levels by up-regulating purine biosynthesis, while AICAr led to a decrease in cytidine triphosphate, uridine triphosphate, deoxycytidine triphosphate, and deoxythymidine triphosphate levels because of reduced phosphoribosyl pyrophosphate production, which consequently impaired the pyrimidine biosynthesis. Ribonucleoside triphosphate (NTP) pool imbalances suppressed the rRNA transcription efficiency. Furthermore, deoxy-ribonucleoside triphosphate (dNTP) pool imbalances induced DNA replication stress and DNA double-strand breaks, followed by cell cycle arrest and apoptosis in ALL cells. Exogenous uridine could rebalance the NTP and dNTP pools by supplementing pyrimidine and then attenuate AICAr-induced cytotoxicity. Our data indicate that RNA transcription inhibition and DNA replication stress induced by NTP and dNTP pool imbalances might play a key role in AICAr-mediated cytotoxic effects on ALL cells, suggesting a potential clinical application of AICAr in future ALL therapy.-Du, L., Yang, F., Fang, H., Sun, H., Chen, Y., Xu, Y., Li, H., Zheng, L., Zhou, B.-B. S. AICAr suppresses cell proliferation by inducing NTP and dNTP pool imbalances in acute lymphoblastic leukemia cells.
Collapse
Affiliation(s)
- Lijuan Du
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Fan Yang
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Houshun Fang
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Huiying Sun
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yao Chen
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Yan Xu
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Hui Li
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pharmacology and Chemical Biology, School of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Liang Zheng
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| | - Bin-Bing S Zhou
- Key Laboratory of Pediatric Hematology and Oncology, Ministry of Health, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Pediatric Translational Medicine Institute, Shanghai Children's Medical Center, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Department of Pharmacology and Chemical Biology, School of Basic Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China.,Collaborative Innovation Center for Translational Medicine, Shanghai Jiao Tong University School of Medicine, Shanghai, China
| |
Collapse
|
24
|
Courtot L, Hoffmann JS, Bergoglio V. The Protective Role of Dormant Origins in Response to Replicative Stress. Int J Mol Sci 2018; 19:ijms19113569. [PMID: 30424570 PMCID: PMC6274952 DOI: 10.3390/ijms19113569] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 11/05/2018] [Accepted: 11/07/2018] [Indexed: 02/07/2023] Open
Abstract
Genome stability requires tight regulation of DNA replication to ensure that the entire genome of the cell is duplicated once and only once per cell cycle. In mammalian cells, origin activation is controlled in space and time by a cell-specific and robust program called replication timing. About 100,000 potential replication origins form on the chromatin in the gap 1 (G1) phase but only 20⁻30% of them are active during the DNA replication of a given cell in the synthesis (S) phase. When the progress of replication forks is slowed by exogenous or endogenous impediments, the cell must activate some of the inactive or "dormant" origins to complete replication on time. Thus, the many origins that may be activated are probably key to protect the genome against replication stress. This review aims to discuss the role of these dormant origins as safeguards of the human genome during replicative stress.
Collapse
Affiliation(s)
- Lilas Courtot
- CRCT, Université de Toulouse, Inserm, CNRS, UPS; Equipe labellisée Ligue Contre le Cancer, Laboratoire d'excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France.
| | - Jean-Sébastien Hoffmann
- CRCT, Université de Toulouse, Inserm, CNRS, UPS; Equipe labellisée Ligue Contre le Cancer, Laboratoire d'excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France.
| | - Valérie Bergoglio
- CRCT, Université de Toulouse, Inserm, CNRS, UPS; Equipe labellisée Ligue Contre le Cancer, Laboratoire d'excellence Toulouse Cancer, 2 Avenue Hubert Curien, 31037 Toulouse, France.
| |
Collapse
|
25
|
Label-free fluorescent and electrochemical biosensors based on defective G-quadruplexes. Biosens Bioelectron 2018; 118:1-8. [DOI: 10.1016/j.bios.2018.07.033] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2018] [Revised: 07/13/2018] [Accepted: 07/16/2018] [Indexed: 12/14/2022]
|
26
|
Mauney CH, Hollis T. SAMHD1: Recurring roles in cell cycle, viral restriction, cancer, and innate immunity. Autoimmunity 2018; 51:96-110. [PMID: 29583030 PMCID: PMC6117824 DOI: 10.1080/08916934.2018.1454912] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/16/2018] [Indexed: 12/24/2022]
Abstract
Sterile alpha motif and histidine-aspartic acid domain-containing protein 1 (SAMHD1) is a deoxynucleotide triphosphate (dNTP) hydrolase that plays an important role in the homeostatic balance of cellular dNTPs. Its emerging role as an effector of innate immunity is affirmed by mutations in the SAMHD1 gene that cause the severe autoimmune disease, Aicardi-Goutieres syndrome (AGS) and that are linked to cancer. Additionally, SAMHD1 functions as a restriction factor for retroviruses, such as HIV. Here, we review the current biochemical and biological properties of the enzyme including its structure, activity, and regulation by post-translational modifications in the context of its cellular function. We outline open questions regarding the biology of SAMHD1 whose answers will be important for understanding its function as a regulator of cell cycle progression, genomic integrity, and in autoimmunity.
Collapse
Affiliation(s)
- Christopher H Mauney
- a Department of Biochemistry , Center for Structural Biology, Wake Forest School of Medicine , Winston Salem , NC , USA
| | - Thomas Hollis
- a Department of Biochemistry , Center for Structural Biology, Wake Forest School of Medicine , Winston Salem , NC , USA
| |
Collapse
|
27
|
Brosh RM, Matson SW. Replication checkpoint-mediated symmetric DNA synthesis: beginning to understand mechanism. Cell Cycle 2017; 17:271-272. [PMID: 29169274 DOI: 10.1080/15384101.2017.1408234] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022] Open
Affiliation(s)
- Robert M Brosh
- a Laboratory of Molecular Gerontology , National Institute on Aging , NIH , Baltimore , Maryland
| | - Steven W Matson
- b Department of Biology , Curriculum in Genetics and Molecular Biology , University of North Carolina at Chapel Hill , Chapel Hill , North Carolina
| |
Collapse
|
28
|
A role for Tau protein in maintaining ribosomal DNA stability and cytidine deaminase-deficient cell survival. Nat Commun 2017; 8:693. [PMID: 28947735 PMCID: PMC5612969 DOI: 10.1038/s41467-017-00633-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 07/14/2017] [Indexed: 12/20/2022] Open
Abstract
Cells from Bloom’s syndrome patients display genome instability due to a defective BLM and the downregulation of cytidine deaminase. Here, we use a genome-wide RNAi-synthetic lethal screen and transcriptomic profiling to identify genes enabling BLM-deficient and/or cytidine deaminase-deficient cells to tolerate constitutive DNA damage and replication stress. We found a synthetic lethal interaction between cytidine deaminase and microtubule-associated protein Tau deficiencies. Tau is overexpressed in cytidine deaminase-deficient cells, and its depletion worsens genome instability, compromising cell survival. Tau is recruited, along with upstream-binding factor, to ribosomal DNA loci. Tau downregulation decreases upstream binding factor recruitment, ribosomal RNA synthesis, ribonucleotide levels, and affects ribosomal DNA stability, leading to the formation of a new subclass of human ribosomal ultrafine anaphase bridges. We describe here Tau functions in maintaining survival of cytidine deaminase-deficient cells, and ribosomal DNA transcription and stability. Moreover, our findings for cancer tissues presenting concomitant cytidine deaminase underexpression and Tau upregulation open up new possibilities for anti-cancer treatment. Cytidine deaminase (CDA) deficiency leads to genome instability. Here the authors find a synthetic lethal interaction between CDA and the microtubule-associated protein Tau deficiencies, and report that Tau depletion affects rRNA synthesis, ribonucleotide pool balance, and rDNA stability.
Collapse
|
29
|
The impact of replication stress on replication dynamics and DNA damage in vertebrate cells. Nat Rev Genet 2017; 18:535-550. [DOI: 10.1038/nrg.2017.46] [Citation(s) in RCA: 170] [Impact Index Per Article: 24.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
|
30
|
Herold N, Rudd SG, Sanjiv K, Kutzner J, Myrberg IH, Paulin CBJ, Olsen TK, Helleday T, Henter JI, Schaller T. With me or against me: Tumor suppressor and drug resistance activities of SAMHD1. Exp Hematol 2017; 52:32-39. [PMID: 28502830 DOI: 10.1016/j.exphem.2017.05.001] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Revised: 04/29/2017] [Accepted: 05/02/2017] [Indexed: 01/04/2023]
Abstract
Sterile alpha motif and histidine/aspartic acid domain-containing protein 1 (SAMHD1) is a (deoxy)guanosine triphosphate (dGTP/GTP)-activated deoxyribonucleoside triphosphate (dNTP) triphosphohydrolase involved in cellular dNTP homoeostasis. Mutations in SAMHD1 have been associated with the hyperinflammatory disease Aicardi-Goutières syndrome (AGS). SAMHD1 also limits cells' permissiveness to infection with diverse viruses, including human immunodeficiency virus (HIV-1), and controls endogenous retroviruses. Increasing evidence supports the role of SAMHD1 as a tumor suppressor. However, SAMHD1 also can act as a resistance factor to nucleoside-based chemotherapies by hydrolyzing their active triphosphate metabolites, thereby reducing response of various malignancies to these anticancer drugs. Hence, informed cancer therapies must take into account the ambiguous properties of SAMHD1 as both an inhibitor of uncontrolled proliferation and a resistance factor limiting the efficacy of anticancer treatments. Here, we provide evidence that SAMHD1 is a double-edged sword for patients with acute myelogenous leukemia (AML). Our time-dependent analyses of The Cancer Genome Atlas (TCGA) AML cohort indicate that high expression of SAMHD1, even though it critically limits the efficacy of high-dose ara-C therapy, might be associated with more favorable disease progression.
Collapse
Affiliation(s)
- Nikolas Herold
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, and Karolinska University Hospital, Stockholm, Sweden; Theme of Children's and Women's Health, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden.
| | - Sean G Rudd
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Kumar Sanjiv
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Juliane Kutzner
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany
| | - Ida Hed Myrberg
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, and Karolinska University Hospital, Stockholm, Sweden
| | - Cynthia B J Paulin
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Thale Kristin Olsen
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, and Karolinska University Hospital, Stockholm, Sweden
| | - Thomas Helleday
- Science for Life Laboratory, Division of Translational Medicine and Chemical Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden
| | - Jan-Inge Henter
- Childhood Cancer Research Unit, Department of Women's and Children's Health, Karolinska Institutet, and Karolinska University Hospital, Stockholm, Sweden; Theme of Children's and Women's Health, Astrid Lindgren Children's Hospital, Karolinska University Hospital, Stockholm, Sweden
| | - Torsten Schaller
- Department of Infectious Diseases, Virology, University Hospital Heidelberg, Heidelberg, Germany.
| |
Collapse
|
31
|
Gemble S, Buhagiar-Labarchède G, Onclercq-Delic R, Jaulin C, Amor-Guéret M. Cytidine deaminase deficiency impairs sister chromatid disjunction by decreasing PARP-1 activity. Cell Cycle 2017; 16:1128-1135. [PMID: 28463527 DOI: 10.1080/15384101.2017.1317413] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Bloom Syndrome (BS) is a rare genetic disease characterized by high levels of chromosomal instability and an increase in cancer risk. Cytidine deaminase (CDA) expression is downregulated in BS cells, leading to an excess of cellular dC and dCTP that reduces basal PARP-1 activity, compromising optimal Chk1 activation and reducing the efficiency of downstream checkpoints. This process leads to the accumulation of unreplicated DNA during mitosis and, ultimately, ultrafine anaphase bridge (UFB) formation. BS cells also display incomplete sister chromatid disjunction when depleted of cohesin. Using a combination of fluorescence in situ hybridization and chromosome spreads, we investigated the possible role of CDA deficiency in the incomplete sister chromatid disjunction in cohesin-depleted BS cells. The decrease in basal PARP-1 activity in CDA-deficient cells compromised sister chromatid disjunction in cohesin-depleted cells, regardless of BLM expression status. The observed incomplete sister chromatid disjunction may be due to the accumulation of unreplicated DNA during mitosis in CDA-deficient cells, as reflected in the changes in centromeric DNA structure associated with the decrease in basal PARP-1 activity. Our findings reveal a new function of PARP-1 in sister chromatid disjunction during mitosis.
Collapse
Affiliation(s)
- Simon Gemble
- a Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche , Orsay , France.,b CNRS UMR 3348, Centre Universitaire , Orsay , France.,c Université Paris Sud , Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay , France
| | - Géraldine Buhagiar-Labarchède
- a Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche , Orsay , France.,b CNRS UMR 3348, Centre Universitaire , Orsay , France.,c Université Paris Sud , Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay , France
| | - Rosine Onclercq-Delic
- a Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche , Orsay , France.,b CNRS UMR 3348, Centre Universitaire , Orsay , France.,c Université Paris Sud , Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay , France
| | - Christian Jaulin
- d Institut de Génétique et Développement de Rennes, Equipe Epigénétique et Cancer, UMR 6290 CNRS, Université Rennes 1 , Rennes Cedex , France
| | - Mounira Amor-Guéret
- a Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche , Orsay , France.,b CNRS UMR 3348, Centre Universitaire , Orsay , France.,c Université Paris Sud , Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay , France
| |
Collapse
|
32
|
So A, Le Guen T, Lopez BS, Guirouilh-Barbat J. Genomic rearrangements induced by unscheduled DNA double strand breaks in somatic mammalian cells. FEBS J 2017; 284:2324-2344. [PMID: 28244221 DOI: 10.1111/febs.14053] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Revised: 02/02/2017] [Accepted: 02/24/2017] [Indexed: 12/13/2022]
Abstract
DNA double-strand breaks (DSBs) are highly toxic lesions that can lead to profound genome rearrangements and/or cell death. They routinely occur in genomes due to endogenous or exogenous stresses. Efficient repair systems, canonical non-homologous end-joining and homologous recombination exist in the cell and not only ensure the maintenance of genome integrity but also, via specific programmed DNA double-strand breaks, permit its diversity and plasticity. However, these repair systems need to be tightly controlled because they can also generate genomic rearrangements. Thus, when DSB repair is not properly regulated, genome integrity is no longer guaranteed. In this review, we will focus on non-programmed genome rearrangements generated by DSB repair, in somatic cells. We first discuss genome rearrangements induced by homologous recombination and end-joining. We then discuss recently described rearrangement mechanisms, driven by microhomologies, that do not involve the joining of DNA ends but rather initiate DNA synthesis (microhomology-mediated break-induced replication, fork stalling and template switching and microhomology-mediated template switching). Finally, we discuss chromothripsis, which is the shattering of a localized region of the genome followed by erratic rejoining.
Collapse
Affiliation(s)
- Ayeong So
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
| | - Tangui Le Guen
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
| | - Bernard S Lopez
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
| | - Josée Guirouilh-Barbat
- CNRS UMR 8200, Institut de Cancérologie Gustave-Roussy, Université Paris-Saclay, Equipe Labellisée Ligue Contre le Cancer, Villejuif, France
| |
Collapse
|
33
|
Pai CC, Kearsey SE. A Critical Balance: dNTPs and the Maintenance of Genome Stability. Genes (Basel) 2017; 8:genes8020057. [PMID: 28146119 PMCID: PMC5333046 DOI: 10.3390/genes8020057] [Citation(s) in RCA: 98] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Accepted: 01/24/2017] [Indexed: 01/14/2023] Open
Abstract
A crucial factor in maintaining genome stability is establishing deoxynucleoside triphosphate (dNTP) levels within a range that is optimal for chromosomal replication. Since DNA replication is relevant to a wide range of other chromosomal activities, these may all be directly or indirectly affected when dNTP concentrations deviate from a physiologically normal range. The importance of understanding these consequences is relevant to genetic disorders that disturb dNTP levels, and strategies that inhibit dNTP synthesis in cancer chemotherapy and for treatment of other disorders. We review here how abnormal dNTP levels affect DNA replication and discuss the consequences for genome stability.
Collapse
Affiliation(s)
- Chen-Chun Pai
- CRUK-MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, ORCRB, Roosevelt Drive, Oxford OX3 7DQ, UK.
| | - Stephen E Kearsey
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK.
| |
Collapse
|
34
|
Karras JR, Schrock MS, Batar B, Zhang J, La Perle K, Druck T, Huebner K. Fhit loss-associated initiation and progression of neoplasia in vitro. Cancer Sci 2016; 107:1590-1598. [PMID: 27513973 PMCID: PMC5132276 DOI: 10.1111/cas.13032] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2016] [Revised: 08/05/2016] [Accepted: 08/09/2016] [Indexed: 12/28/2022] Open
Abstract
The FHIT gene, encompassing an active common fragile site, FRA3B, is frequently silenced in preneoplasia and cancer, through gene rearrangement or methylation of regulatory sequences. Silencing of Fhit protein expression causes thymidine kinase 1 downregulation, resulting in dNTP imbalance, and spontaneous replication stress that leads to chromosomal aberrations, allele copy number variations, insertions/deletions, and single-base substitutions. Thus, Fhit, which is reduced in expression in the majority of human cancers, is a genome "caretaker" whose loss initiates genome instability in preneoplastic lesions. To follow the early genetic alterations and functional changes induced by Fhit loss that may recapitulate the neoplastic process in vitro, we established epithelial cell lines from kidney tissues of Fhit-/- and +/+ mouse pups early after weaning, and subjected cell cultures to nutritional and carcinogen stress, which +/+ cells did not survive. Through transcriptome profiling and protein expression analysis, we observed changes in the Trp53/p21 and survivin apoptotic pathways in -/- cells, and in expression of proteins involved in epithelial-mesenchymal transition. Some Fhit-deficient cell lines showed anchorage-independent colony formation and increased invasive capacity in vitro. Furthermore, cells of stressed Fhit-/- cell lines formed s.c. and metastatic tumors in nude mice. Collectively, we show that Fhit loss and subsequent thymidine kinase 1 inactivation, combined with selective pressures, leads to neoplasia-associated alterations in genes and gene expression patterns in vitro and in vivo.
Collapse
Affiliation(s)
- Jenna R. Karras
- Department of Cancer Biology and GeneticsOhio State University Wexner Medical CenterColumbusOhioUSA
| | - Morgan S. Schrock
- Department of Cancer Biology and GeneticsOhio State University Wexner Medical CenterColumbusOhioUSA
| | - Bahadir Batar
- Department of Cancer Biology and GeneticsOhio State University Wexner Medical CenterColumbusOhioUSA
| | - Jie Zhang
- Department of Biomedical InformaticsOhio State University Wexner Medical CenterColumbusOhioUSA
| | - Krista La Perle
- Department of Veterinary BiosciencesCollege of Veterinary MedicineOhio State UniversityColumbusOhioUSA
| | - Teresa Druck
- Department of Cancer Biology and GeneticsOhio State University Wexner Medical CenterColumbusOhioUSA
| | - Kay Huebner
- Department of Cancer Biology and GeneticsOhio State University Wexner Medical CenterColumbusOhioUSA
| |
Collapse
|
35
|
Mameri H, Bièche I, Meseure D, Marangoni E, Buhagiar-Labarchède G, Nicolas A, Vacher S, Onclercq-Delic R, Rajapakse V, Varma S, Reinhold WC, Pommier Y, Amor-Guéret M. Cytidine Deaminase Deficiency Reveals New Therapeutic Opportunities against Cancer. Clin Cancer Res 2016; 23:2116-2126. [PMID: 27601591 DOI: 10.1158/1078-0432.ccr-16-0626] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2016] [Revised: 07/25/2016] [Accepted: 08/25/2016] [Indexed: 12/21/2022]
Abstract
Purpose: One of the main challenges in cancer therapy is the identification of molecular mechanisms mediating resistance or sensitivity to treatment. Cytidine deaminase (CDA) was reported to be downregulated in cells derived from patients with Bloom syndrome, a genetic disease associated with a strong predisposition to a wide range of cancers. The purpose of this study was to determine whether CDA deficiency could be associated with tumors from the general population and could constitute a predictive marker of susceptibility to antitumor drugs.Experimental Design: We analyzed CDA expression in silico, in large datasets for cancer cell lines and tumors and in various cancer cell lines and primary tumor tissues using IHC, PDXs, qRT-PCR, and Western blotting. We also studied the mechanism underlying CDA silencing and searched for molecules that might target specifically CDA-deficient tumor cells using in silico analysis coupled to classical cellular experimental approaches.Results: We found that CDA expression is downregulated in about 60% of cancer cells and tissues. We demonstrate that DNA methylation is a prevalent mechanism of CDA silencing in tumors. Finally, we show that CDA-deficient tumor cells can be specifically targeted with epigenetic treatments and with the anticancer drug aminoflavone.Conclusions: CDA expression status identifies new subgroups of cancers, and CDA deficiency appears to be a novel and relevant predictive marker of susceptibility to antitumor drugs, opening up new possibilities for treating cancer. Clin Cancer Res; 23(8); 2116-26. ©2016 AACR.
Collapse
Affiliation(s)
- Hamza Mameri
- Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France.,CNRS UMR 3348, Centre Universitaire, Bât. 110, 91405 Orsay, France.,Université Paris Sud, Université Paris-Saclay, UMR 3348, 91405 Orsay, France
| | - Ivan Bièche
- Institut Curie, Genetic Department, 26, rue d'Ulm, 75005 Paris, France
| | - Didier Meseure
- Institut Curie, Platform of Investigative Pathology, 26, rue d'Ulm, 75005 Paris, France
| | - Elisabetta Marangoni
- Institut Curie, PSL Research University, Translational Research Department, 26, rue d'Ulm, 75005 Paris, France
| | - Géraldine Buhagiar-Labarchède
- Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France.,CNRS UMR 3348, Centre Universitaire, Bât. 110, 91405 Orsay, France.,Université Paris Sud, Université Paris-Saclay, UMR 3348, 91405 Orsay, France
| | - André Nicolas
- Institut Curie, Platform of Investigative Pathology, 26, rue d'Ulm, 75005 Paris, France.,Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Sophie Vacher
- Institut Curie, Genetic Department, 26, rue d'Ulm, 75005 Paris, France
| | - Rosine Onclercq-Delic
- Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France.,CNRS UMR 3348, Centre Universitaire, Bât. 110, 91405 Orsay, France.,Université Paris Sud, Université Paris-Saclay, UMR 3348, 91405 Orsay, France
| | - Vinodh Rajapakse
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Sudhir Varma
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - William C Reinhold
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, Maryland, 20892
| | - Mounira Amor-Guéret
- Institut Curie, PSL Research University, UMR 3348, 91405 Orsay, France. .,CNRS UMR 3348, Centre Universitaire, Bât. 110, 91405 Orsay, France.,Université Paris Sud, Université Paris-Saclay, UMR 3348, 91405 Orsay, France
| |
Collapse
|
36
|
Tan JL, Fogley RD, Flynn RA, Ablain J, Yang S, Saint-André V, Fan ZP, Do BT, Laga AC, Fujinaga K, Santoriello C, Greer CB, Kim YJ, Clohessy JG, Bothmer A, Pandell N, Avagyan S, Brogie JE, van Rooijen E, Hagedorn EJ, Shyh-Chang N, White RM, Price DH, Pandolfi PP, Peterlin BM, Zhou Y, Kim TH, Asara JM, Chang HY, Young RA, Zon LI. Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma. Mol Cell 2016; 62:34-46. [PMID: 27058786 DOI: 10.1016/j.molcel.2016.03.013] [Citation(s) in RCA: 58] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Revised: 02/02/2016] [Accepted: 03/10/2016] [Indexed: 12/29/2022]
Abstract
Studying cancer metabolism gives insight into tumorigenic survival mechanisms and susceptibilities. In melanoma, we identify HEXIM1, a transcription elongation regulator, as a melanoma tumor suppressor that responds to nucleotide stress. HEXIM1 expression is low in melanoma. Its overexpression in a zebrafish melanoma model suppresses cancer formation, while its inactivation accelerates tumor onset in vivo. Knockdown of HEXIM1 rescues zebrafish neural crest defects and human melanoma proliferation defects that arise from nucleotide depletion. Under nucleotide stress, HEXIM1 is induced to form an inhibitory complex with P-TEFb, the kinase that initiates transcription elongation, to inhibit elongation at tumorigenic genes. The resulting alteration in gene expression also causes anti-tumorigenic RNAs to bind to and be stabilized by HEXIM1. HEXIM1 plays an important role in inhibiting cancer cell-specific gene transcription while also facilitating anti-cancer gene expression. Our study reveals an important role for HEXIM1 in coupling nucleotide metabolism with transcriptional regulation in melanoma.
Collapse
Affiliation(s)
- Justin L Tan
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Rachel D Fogley
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Ryan A Flynn
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Julien Ablain
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Song Yang
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Violaine Saint-André
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Zi Peng Fan
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Brian T Do
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Alvaro C Laga
- Department of Pathology, Brigham & Women's Hospital, Boston, MA 02215, USA
| | - Koh Fujinaga
- Departments of Medicine, Microbiology, and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Cristina Santoriello
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Celeste B Greer
- Department of Pharmacology, School of Medicine, Yale University, New Haven, CT 06520, USA
| | - Yoon Jung Kim
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - John G Clohessy
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, and Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA; Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Anne Bothmer
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, and Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Nicole Pandell
- Preclinical Murine Pharmacogenetics Facility, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - Serine Avagyan
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - John E Brogie
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Ellen van Rooijen
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Elliott J Hagedorn
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Ng Shyh-Chang
- Genome Institute of Singapore, 60 Biopolis Street, Singapore 138672, Singapore
| | - Richard M White
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY 10065, USA
| | - David H Price
- Department of Biochemistry, University of Iowa, Iowa City, IA 52242, USA
| | - Pier Paolo Pandolfi
- Cancer Research Institute, Beth Israel Deaconess Cancer Center, and Department of Medicine and Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02115, USA
| | - B Matija Peterlin
- Departments of Medicine, Microbiology, and Immunology, University of California, San Francisco, San Francisco, CA 94143, USA
| | - Yi Zhou
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA
| | - Tae Hoon Kim
- Department of Biological Sciences, The University of Texas at Dallas, Richardson, TX 75080, USA
| | - John M Asara
- Division of Signal Transduction, Department of Medicine, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA 02215, USA
| | - Howard Y Chang
- Center for Personal Dynamic Regulomes, Stanford University School of Medicine, Stanford, CA 94305, USA
| | - Richard A Young
- Whitehead Institute for Biomedical Research and Department of Biology, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Leonard I Zon
- Howard Hughes Medical Institute, Stem Cell Program and Division of Pediatric Hematology/Oncology, Boston Children's Hospital, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA 02115, USA; Department of Stem Cell and Regenerative Biology, Harvard Stem Cell Institute, Cambridge, MA 02138, USA.
| |
Collapse
|
37
|
Chi C, Ronai D, Than MT, Walker CJ, Sewell AK, Han M. Nucleotide levels regulate germline proliferation through modulating GLP-1/Notch signaling in C. elegans. Genes Dev 2016; 30:307-20. [PMID: 26833730 PMCID: PMC4743060 DOI: 10.1101/gad.275107.115] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
In this study, Chi et al. researched the link between known nutrient-sensing systems and reproductive programs. Using a model system in C. elegans, they show that a Notch signaling pathway senses the level of uridine/thymidine and controls germline proliferation, delineating a previously unknown nucleotide-sensing mechanism for controlling reproductivity. Animals alter their reproductive programs to accommodate changes in nutrient availability, yet the connections between known nutrient-sensing systems and reproductive programs are underexplored, and whether there is a mechanism that senses nucleotide levels to coordinate germline proliferation is unknown. We established a model system in which nucleotide metabolism is perturbed in both the nematode Caenorhabditis elegans (cytidine deaminases) and its food (Escherichia coli); when fed food with a low uridine/thymidine (U/T) level, germline proliferation is arrested. We provide evidence that this impact of U/T level on the germline is critically mediated by GLP-1/Notch and MPK-1/MAPK, known to regulate germline mitotic proliferation. This germline defect is suppressed by hyperactivation of glp-1 or disruption of genes downstream from glp-1 to promote meiosis but not by activation of the IIS or TORC1 pathways. Moreover, GLP-1 expression is post-transcriptionally modulated by U/T levels. Our results reveal a previously unknown nucleotide-sensing mechanism for controlling reproductivity.
Collapse
Affiliation(s)
- Congwu Chi
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Diana Ronai
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Minh T Than
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Cierra J Walker
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Aileen K Sewell
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| | - Min Han
- Howard Hughes Medical Institute, Department of Molecular, Cellular, and Developmental Biology, University of Colorado at Boulder, Boulder, Colorado 80309, USA
| |
Collapse
|
38
|
Wilhelm T, Ragu S, Magdalou I, Machon C, Dardillac E, Técher H, Guitton J, Debatisse M, Lopez BS. Slow Replication Fork Velocity of Homologous Recombination-Defective Cells Results from Endogenous Oxidative Stress. PLoS Genet 2016; 12:e1006007. [PMID: 27135742 PMCID: PMC4852921 DOI: 10.1371/journal.pgen.1006007] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2015] [Accepted: 04/05/2016] [Indexed: 01/01/2023] Open
Abstract
Replications forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Homologous recombination-defective cells consistently exhibit a spontaneously reduced replication speed, leading to mitotic extra centrosomes. Here, we identify oxidative stress as a major endogenous source of replication speed deceleration in homologous recombination-defective cells. The treatment of homologous recombination-defective cells with the antioxidant N-acetyl-cysteine or the maintenance of the cells at low O2 levels (3%) rescues both the replication fork speed, as monitored by single-molecule analysis (molecular combing), and the associated mitotic extra centrosome frequency. Reciprocally, the exposure of wild-type cells to H2O2 reduces the replication fork speed and generates mitotic extra centrosomes. Supplying deoxynucleotide precursors to H2O2-exposed cells rescued the replication speed. Remarkably, treatment with N-acetyl-cysteine strongly expanded the nucleotide pool, accounting for the replication speed rescue. Remarkably, homologous recombination-defective cells exhibit a high level of endogenous reactive oxygen species. Consistently, homologous recombination-defective cells accumulate spontaneous γH2AX or XRCC1 foci that are abolished by treatment with N-acetyl-cysteine or maintenance at 3% O2. Finally, oxidative stress stimulated homologous recombination, which is suppressed by supplying deoxynucleotide precursors. Therefore, the cellular redox status strongly impacts genome duplication and transmission. Oxidative stress should generate replication stress through different mechanisms, including DNA damage and nucleotide pool imbalance. These data highlight the intricacy of endogenous replication and oxidative stresses, which are both evoked during tumorigenesis and senescence initiation, and emphasize the importance of homologous recombination as a barrier against spontaneous genetic instability triggered by the endogenous oxidative/replication stress axis. Endogenous stress is an important stress because it challenges cells daily. However, endogenous stress is difficult to apprehend. Replication forks are routinely hindered by different endogenous stresses. Because homologous recombination plays a pivotal role in the reactivation of arrested replication forks, defects in homologous recombination reveal the initial endogenous stress(es). Here we identify endogenous oxidative stress among the different potential endogenous stresses as being responsible for spontaneous replication defects in homologous recombination-defective cells. Therefore, oxidative and replication stresses, which are both evoked during tumorigenesis and senescence initiation, are linked, and homologous recombination acts as a barrier against spontaneous genetic instability triggered by endogenous oxidative/replication stress.
Collapse
Affiliation(s)
- Therese Wilhelm
- CNRS UMR 8200, Gustave Roussy Cancer Institute, Université Paris-Saclay, Team labeled “Ligue 2014”, Villejuif, France
| | - Sandrine Ragu
- CNRS UMR 8200, Gustave Roussy Cancer Institute, Université Paris-Saclay, Team labeled “Ligue 2014”, Villejuif, France
| | - Indiana Magdalou
- CNRS UMR 8200, Gustave Roussy Cancer Institute, Université Paris-Saclay, Team labeled “Ligue 2014”, Villejuif, France
| | - Christelle Machon
- Laboratoire de Biochimie et Toxicologie, Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Pierre-Bénite, France
- Laboratoire de Chimie Analytique, Université de Lyon, Université Lyon 1, ISPB Faculté de Pharmacie, Lyon, France
| | - Elodie Dardillac
- CNRS UMR 8200, Gustave Roussy Cancer Institute, Université Paris-Saclay, Team labeled “Ligue 2014”, Villejuif, France
| | - Hervé Técher
- Institut Curie, Centre de Recherche, Paris, France, UPMC Université Paris 06, Paris, France, CNRS UMR 3244, Paris, France
| | - Jérôme Guitton
- Laboratoire de Biochimie et Toxicologie, Hospices Civils de Lyon, Centre Hospitalier Lyon-Sud, Pierre-Bénite, France
- Laboratoire de Toxicologie, Université Lyon 1, ISPB, Faculté de Pharmacie, Lyon, France
| | - Michelle Debatisse
- Institut Curie, Centre de Recherche, Paris, France, UPMC Université Paris 06, Paris, France, CNRS UMR 3244, Paris, France
| | - Bernard S. Lopez
- CNRS UMR 8200, Gustave Roussy Cancer Institute, Université Paris-Saclay, Team labeled “Ligue 2014”, Villejuif, France
- * E-mail:
| |
Collapse
|
39
|
Tang W, Robles AI, Beyer RP, Gray LT, Nguyen GH, Oshima J, Maizels N, Harris CC, Monnat RJ. The Werner syndrome RECQ helicase targets G4 DNA in human cells to modulate transcription. Hum Mol Genet 2016; 25:2060-2069. [PMID: 26984941 DOI: 10.1093/hmg/ddw079] [Citation(s) in RCA: 65] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Accepted: 03/07/2016] [Indexed: 11/12/2022] Open
Abstract
The Werner syndrome (WS) is a prototypic adult Mendelian progeroid syndrome in which signs of premature aging are associated with genomic instability and an elevated risk of cancer. The WRN RECQ helicase protein binds and unwinds G-quadruplex (G4) DNA substrates in vitro, and we identified significant enrichment in G4 sequence motifs at the transcription start site and 5' ends of first introns (false discovery rate < 0.001) of genes down-regulated in WS patient fibroblasts. This finding provides strong evidence that WRN binds G4 DNA structures at many chromosomal sites to modulate gene expression. WRN appears to bind a distinct subpopulation of G4 motifs in human cells, when compared with the related Bloom syndrome RECQ helicase protein. Functional annotation of the genes and miRNAs altered in WS provided new insight into WS disease pathogenesis. WS patient fibroblasts displayed altered expression of multiple, mechanistically distinct, senescence-associated gene expression programs, with altered expression of disease-associated miRNAs, and dysregulation of canonical pathways that regulate cell signaling, genome stability and tumorigenesis. WS fibroblasts also displayed a highly statistically significant and distinct gene expression signature, with coordinate overexpression of nearly all of the cytoplasmic tRNA synthetases and associated ARS-interacting multifunctional protein genes. The 'non-canonical' functions of many of these upregulated tRNA charging proteins may together promote WS disease pathogenesis. Our results identify the human WRN RECQ protein as a G4 helicase that modulates gene expression in G4-dependent fashion at many chromosomal sites and provide several new and unexpected mechanistic insights into WS disease pathogenesis.
Collapse
Affiliation(s)
| | - Ana I Robles
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA and
| | | | | | - Giang H Nguyen
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA and
| | - Junko Oshima
- Department of Pathology, Department of Medicine, Chiba University, Chiba, Japan
| | - Nancy Maizels
- Department of Pathology, Department of Immunology, Department of Biochemistry
| | - Curtis C Harris
- Laboratory of Human Carcinogenesis, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA and
| | - Raymond J Monnat
- Department of Pathology, Department of Genome Sciences, University of Washington, Seattle, WA, USA,
| |
Collapse
|
40
|
Técher H, Koundrioukoff S, Carignon S, Wilhelm T, Millot GA, Lopez BS, Brison O, Debatisse M. Signaling from Mus81-Eme2-Dependent DNA Damage Elicited by Chk1 Deficiency Modulates Replication Fork Speed and Origin Usage. Cell Rep 2016; 14:1114-1127. [PMID: 26804904 DOI: 10.1016/j.celrep.2015.12.093] [Citation(s) in RCA: 61] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2014] [Revised: 11/10/2015] [Accepted: 12/19/2015] [Indexed: 11/20/2022] Open
Abstract
Mammalian cells deficient in ATR or Chk1 display moderate replication fork slowing and increased initiation density, but the underlying mechanisms have remained unclear. We show that exogenous deoxyribonucleosides suppress both replication phenotypes in Chk1-deficient, but not ATR-deficient, cells. Thus, in the absence of exogenous stress, depletion of either protein impacts the replication dynamics through different mechanisms. In addition, Chk1 deficiency, but not ATR deficiency, triggers nuclease-dependent DNA damage. Avoiding damage formation through invalidation of Mus81-Eme2 and Mre11, or preventing damage signaling by turning off the ATM pathway, suppresses the replication phenotypes of Chk1-deficient cells. Damage and resulting DDR activation are therefore the cause, not the consequence, of replication dynamics modulation in these cells. Together, we identify moderate reduction of precursors available for replication as an additional outcome of DDR activation. We propose that resulting fork slowing, and subsequent firing of backup origins, helps replication to proceed along damaged templates.
Collapse
Affiliation(s)
- Hervé Técher
- Institut Curie, PSL Research University, CNRS UMR 3244, 75248 Paris Cedex 05, France; Sorbonne Universités, UPMC Univ Paris 06, 75252 Paris Cedex 05, France
| | - Stéphane Koundrioukoff
- Institut Curie, PSL Research University, CNRS UMR 3244, 75248 Paris Cedex 05, France; Sorbonne Universités, UPMC Univ Paris 06, 75252 Paris Cedex 05, France
| | - Sandra Carignon
- Institut Curie, PSL Research University, CNRS UMR 3244, 75248 Paris Cedex 05, France; Sorbonne Universités, UPMC Univ Paris 06, 75252 Paris Cedex 05, France
| | - Therese Wilhelm
- Institut Curie, PSL Research University, CNRS UMR 3244, 75248 Paris Cedex 05, France; Sorbonne Universités, UPMC Univ Paris 06, 75252 Paris Cedex 05, France
| | - Gaël A Millot
- Institut Curie, PSL Research University, CNRS UMR 3244, 75248 Paris Cedex 05, France; Sorbonne Universités, UPMC Univ Paris 06, 75252 Paris Cedex 05, France
| | - Bernard S Lopez
- Institut de Cancérologie Gustave Roussy, CNRS UMR 8200 and Université Paris Sud, 94805 Villejuif, France
| | - Olivier Brison
- Institut Curie, PSL Research University, CNRS UMR 3244, 75248 Paris Cedex 05, France; Sorbonne Universités, UPMC Univ Paris 06, 75252 Paris Cedex 05, France
| | - Michelle Debatisse
- Institut Curie, PSL Research University, CNRS UMR 3244, 75248 Paris Cedex 05, France; Sorbonne Universités, UPMC Univ Paris 06, 75252 Paris Cedex 05, France.
| |
Collapse
|
41
|
Gemble S, Buhagiar-Labarchède G, Onclercq-Delic R, Biard D, Lambert S, Amor-Guéret M. A balanced pyrimidine pool is required for optimal Chk1 activation to prevent ultrafine anaphase bridge formation. J Cell Sci 2016; 129:3167-77. [DOI: 10.1242/jcs.187781] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2016] [Accepted: 06/27/2016] [Indexed: 01/05/2023] Open
Abstract
Cytidine deaminase (CDA) deficiency induces an excess of cellular dCTP, which reduces basal PARP-1 activity, thereby compromising complete DNA replication, leading to ultrafine anaphase bridge (UFB) formation. CDA dysfunction has pathological implications, notably in cancer and in Bloom syndrome. It remains unknown how reduced levels of PARP-1 activity and pyrimidine pool imbalance lead to the accumulation of unreplicated DNA during mitosis. We report that a decrease in PARP-1 activity in CDA-deficient cells impairs DNA damage-induced Chk1 activation, and, thus, the downstream checkpoints. Chemical inhibition of the ATR-Chk1 pathway leads to UFB accumulation, and we found that this pathway was compromised in CDA-deficient cells. Our data demonstrate that ATR-Chk1 acts downstream from PARP-1, preventing the accumulation of unreplicated DNA in mitosis, and, thus, UFB formation. Finally, delaying entry into mitosis is sufficient to prevent UFB formation in both CDA-deficient and CDA-proficient cells, suggesting that both physiological and pathological UFBs are derived from unreplicated DNA. Our findings demonstrate an unsuspected requirement for a balanced nucleotide pool for optimal Chk1 activation both in unchallenged cells and in response to genotoxic stress.
Collapse
Affiliation(s)
- Simon Gemble
- Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France
- Université Paris Sud, Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay, France
| | - Géraldine Buhagiar-Labarchède
- Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France
- Université Paris Sud, Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay, France
| | - Rosine Onclercq-Delic
- Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France
- Université Paris Sud, Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay, France
| | - Denis Biard
- CEA, DSV, iMETI, SEPIA, 18, route du Panorama. Bât. 60, BP6, 92265 Fontenay-aux-Roses Cedex, France
| | - Sarah Lambert
- Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France
- Université Paris Sud, Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay, France
| | - Mounira Amor-Guéret
- Institut Curie, PSL Research University, UMR 3348, Unité Stress Génotoxiques et Cancer, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Centre Universitaire, Bât. 110. 91405, Orsay, France
- Université Paris Sud, Université Paris Saclay, UMR3348, Centre Universitaire d'Orsay, France
| |
Collapse
|
42
|
Graindorge D, Martineau S, Machon C, Arnoux P, Guitton J, Francesconi S, Frochot C, Sage E, Girard PM. Singlet Oxygen-Mediated Oxidation during UVA Radiation Alters the Dynamic of Genomic DNA Replication. PLoS One 2015; 10:e0140645. [PMID: 26485711 PMCID: PMC4618472 DOI: 10.1371/journal.pone.0140645] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Accepted: 09/29/2015] [Indexed: 02/07/2023] Open
Abstract
UVA radiation (320–400 nm) is a major environmental agent that can exert its deleterious action on living organisms through absorption of the UVA photons by endogenous or exogenous photosensitizers. This leads to the production of reactive oxygen species (ROS), such as singlet oxygen (1O2) and hydrogen peroxide (H2O2), which in turn can modify reversibly or irreversibly biomolecules, such as lipids, proteins and nucleic acids. We have previously reported that UVA-induced ROS strongly inhibit DNA replication in a dose-dependent manner, but independently of the cell cycle checkpoints activation. Here, we report that the production of 1O2 by UVA radiation leads to a transient inhibition of replication fork velocity, a transient decrease in the dNTP pool, a quickly reversible GSH-dependent oxidation of the RRM1 subunit of ribonucleotide reductase and sustained inhibition of origin firing. The time of recovery post irradiation for each of these events can last from few minutes (reduction of oxidized RRM1) to several hours (replication fork velocity and origin firing). The quenching of 1O2 by sodium azide prevents the delay of DNA replication, the decrease in the dNTP pool and the oxidation of RRM1, while inhibition of Chk1 does not prevent the inhibition of origin firing. Although the molecular mechanism remains elusive, our data demonstrate that the dynamic of replication is altered by UVA photosensitization of vitamins via the production of singlet oxygen.
Collapse
Affiliation(s)
- Dany Graindorge
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Sylvain Martineau
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Christelle Machon
- Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Laboratoire de biochimie-toxicologie, Pierre Bénite, France
- Laboratoire de chimie analytique, Université Lyon 1, ISPBL, Faculté de pharmacie, Lyon, France
| | - Philippe Arnoux
- Université de Lorraine, Laboratoire Réactions et Génie des Procédés (LRGP), Nancy, France
- CNRS, UMR7274, Nancy, France
| | - Jérôme Guitton
- Centre Hospitalier Lyon-Sud, Hospices Civils de Lyon, Laboratoire de biochimie-toxicologie, Pierre Bénite, France
- Laboratoire de Toxicologie, Université Lyon 1, ISPBL, Faculté de pharmacie, Lyon, France
| | - Stefania Francesconi
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Céline Frochot
- Université de Lorraine, Laboratoire Réactions et Génie des Procédés (LRGP), Nancy, France
- CNRS, UMR7274, Nancy, France
| | - Evelyne Sage
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
| | - Pierre-Marie Girard
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Orsay, France
- Curie Institute, PSL Research University, Orsay, France
- * E-mail:
| |
Collapse
|
43
|
Gemble S, Ahuja A, Buhagiar-Labarchède G, Onclercq-Delic R, Dairou J, Biard DSF, Lambert S, Lopes M, Amor-Guéret M. Pyrimidine Pool Disequilibrium Induced by a Cytidine Deaminase Deficiency Inhibits PARP-1 Activity, Leading to the Under Replication of DNA. PLoS Genet 2015; 11:e1005384. [PMID: 26181065 PMCID: PMC4504519 DOI: 10.1371/journal.pgen.1005384] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2015] [Accepted: 06/23/2015] [Indexed: 12/31/2022] Open
Abstract
Genome stability is jeopardized by imbalances of the dNTP pool; such imbalances affect the rate of fork progression. For example, cytidine deaminase (CDA) deficiency leads to an excess of dCTP, slowing the replication fork. We describe here a novel mechanism by which pyrimidine pool disequilibrium compromises the completion of replication and chromosome segregation: the intracellular accumulation of dCTP inhibits PARP-1 activity. CDA deficiency results in incomplete DNA replication when cells enter mitosis, leading to the formation of ultrafine anaphase bridges between sister-chromatids at "difficult-to-replicate" sites such as centromeres and fragile sites. Using molecular combing, electron microscopy and a sensitive assay involving cell imaging to quantify steady-state PAR levels, we found that DNA replication was unsuccessful due to the partial inhibition of basal PARP-1 activity, rather than slower fork speed. The stimulation of PARP-1 activity in CDA-deficient cells restores replication and, thus, chromosome segregation. Moreover, increasing intracellular dCTP levels generates under-replication-induced sister-chromatid bridges as efficiently as PARP-1 knockdown. These results have direct implications for Bloom syndrome (BS), a rare genetic disease combining susceptibility to cancer and genomic instability. BS results from mutation of the BLM gene, encoding BLM, a RecQ 3'-5' DNA helicase, a deficiency of which leads to CDA downregulation. BS cells thus have a CDA defect, resulting in a high frequency of ultrafine anaphase bridges due entirely to dCTP-dependent PARP-1 inhibition and independent of BLM status. Our study describes previously unknown pathological consequences of the distortion of dNTP pools and reveals an unexpected role for PARP-1 in preventing DNA under-replication and chromosome segregation defects.
Collapse
Affiliation(s)
- Simon Gemble
- Institut Curie, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Centre Universitaire, Orsay, France
| | - Akshay Ahuja
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Géraldine Buhagiar-Labarchède
- Institut Curie, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Centre Universitaire, Orsay, France
| | - Rosine Onclercq-Delic
- Institut Curie, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Centre Universitaire, Orsay, France
| | - Julien Dairou
- Université Paris Diderot, Sorbonne Paris Cité, Unité de Biologie Fonctionnelle et Adaptative (BFA) UMR 8251 CNRS, Plateforme Bioprofiler Bâtiment Buffon, 346A Case 7073, Paris, France
| | | | - Sarah Lambert
- Institut Curie, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Centre Universitaire, Orsay, France
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, Zurich, Switzerland
| | - Mounira Amor-Guéret
- Institut Curie, Centre de Recherche, Orsay, France
- CNRS UMR 3348, Stress Génotoxiques et Cancer, Centre Universitaire, Orsay, France
- * E-mail:
| |
Collapse
|
44
|
Relhan V, Sinha S, Bhatnagar T, Garg VK, Kochhar A. Bloom syndrome with extensive pulmonary involvement in a child. Indian J Dermatol 2015; 60:217. [PMID: 25814763 PMCID: PMC4372967 DOI: 10.4103/0019-5154.152593] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022] Open
Affiliation(s)
- Vineet Relhan
- Departments of Dermatology, Maulana Azad Medical College, New Delhi, India
| | - Surabhi Sinha
- Dr Ram Manohar Lohia Hospital and PGIMER, New Delhi, India. E-mail:
| | - Tarun Bhatnagar
- Department of Respiratory Diseases, Rajan Babu Institute of Pulmonary Medicine and Tuberculosis, New Delhi, India
| | - Vijay K Garg
- Departments of Dermatology, Maulana Azad Medical College, New Delhi, India
| | - Aditi Kochhar
- Department of Pediatrics, Al Shifa Hospital, New Delhi, India
| |
Collapse
|
45
|
Usdin K, Hayward BE, Kumari D, Lokanga RA, Sciascia N, Zhao XN. Repeat-mediated genetic and epigenetic changes at the FMR1 locus in the Fragile X-related disorders. Front Genet 2014; 5:226. [PMID: 25101111 PMCID: PMC4101883 DOI: 10.3389/fgene.2014.00226] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2014] [Accepted: 06/29/2014] [Indexed: 01/01/2023] Open
Abstract
The Fragile X-related disorders are a group of genetic conditions that include the neurodegenerative disorder, Fragile X-associated tremor/ataxia syndrome (FXTAS), the fertility disorder, Fragile X-associated primary ovarian insufficiency (FXPOI) and the intellectual disability, Fragile X syndrome (FXS). The pathology in all these diseases is related to the number of CGG/CCG-repeats in the 5′ UTR of the Fragile X mental retardation 1 (FMR1) gene. The repeats are prone to continuous expansion and the increase in repeat number has paradoxical effects on gene expression increasing transcription on mid-sized alleles and decreasing it on longer ones. In some cases the repeats can simultaneously both increase FMR1 mRNA production and decrease the levels of the FMR1 gene product, Fragile X mental retardation 1 protein (FMRP). Since FXTAS and FXPOI result from the deleterious consequences of the expression of elevated levels of FMR1 mRNA and FXS is caused by an FMRP deficiency, the clinical picture is turning out to be more complex than once appreciated. Added complications result from the fact that increasing repeat numbers make the alleles somatically unstable. Thus many individuals have a complex mixture of different sized alleles in different cells. Furthermore, it has become apparent that the eponymous fragile site, once thought to be no more than a useful diagnostic criterion, may have clinical consequences for females who inherit chromosomes that express this site. This review will cover what is currently known about the mechanisms responsible for repeat instability, for the repeat-mediated epigenetic changes that affect expression of the FMR1 gene, and for chromosome fragility. It will also touch on what current and future options are for ameliorating some of these effects.
Collapse
Affiliation(s)
- Karen Usdin
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Bruce E Hayward
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Daman Kumari
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Rachel A Lokanga
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Nicholas Sciascia
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| | - Xiao-Nan Zhao
- Section on Gene Structure and Disease, Laboratory of Cell and Molecular Biology, National Institute of Diabetes, Digestive and Kidney Diseases, National Institutes of Health, Bethesda MD, USA
| |
Collapse
|
46
|
Regulation of gene expression by the BLM helicase correlates with the presence of G-quadruplex DNA motifs. Proc Natl Acad Sci U S A 2014; 111:9905-10. [PMID: 24958861 DOI: 10.1073/pnas.1404807111] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022] Open
Abstract
Bloom syndrome is a rare autosomal recessive disorder characterized by genetic instability and cancer predisposition, and caused by mutations in the gene encoding the Bloom syndrome, RecQ helicase-like (BLM) protein. To determine whether altered gene expression might be responsible for pathological features of Bloom syndrome, we analyzed mRNA and microRNA (miRNA) expression in fibroblasts from individuals with Bloom syndrome and in BLM-depleted control fibroblasts. We identified mRNA and miRNA expression differences in Bloom syndrome patient and BLM-depleted cells. Differentially expressed mRNAs are connected with cell proliferation, survival, and molecular mechanisms of cancer, and differentially expressed miRNAs target genes involved in cancer and in immune function. These and additional altered functions or pathways may contribute to the proportional dwarfism, elevated cancer risk, immune dysfunction, and other features observed in Bloom syndrome individuals. BLM binds to G-quadruplex (G4) DNA, and G4 motifs were enriched at transcription start sites (TSS) and especially within first introns (false discovery rate ≤ 0.001) of differentially expressed mRNAs in Bloom syndrome compared with normal cells, suggesting that G-quadruplex structures formed at these motifs are physiologic targets for BLM. These results identify a network of mRNAs and miRNAs that may drive the pathogenesis of Bloom syndrome.
Collapse
|
47
|
Magdalou I, Lopez BS, Pasero P, Lambert SAE. The causes of replication stress and their consequences on genome stability and cell fate. Semin Cell Dev Biol 2014; 30:154-64. [PMID: 24818779 DOI: 10.1016/j.semcdb.2014.04.035] [Citation(s) in RCA: 101] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2014] [Accepted: 04/29/2014] [Indexed: 01/28/2023]
Abstract
Alterations of the dynamics of DNA replication cause genome instability. These alterations known as "replication stress" have emerged as a major source of genomic instability in pre-neoplasic lesions, contributing to cancer development. The concept of replication stress covers a wide variety of events that distort the temporal and spatial DNA replication program. These events have endogenous or exogenous origins and impact globally or locally on the dynamics of DNA replication. They may arise within a short window of time (acute stress) or during each S phase (chronic stress). Here, we review the known situations in which the dynamics of DNA replication is distorted. We have united them in four main categories: (i) inadequate firing of replication origins (deficiency or excess), (ii) obstacles to fork progression, (iii) conflicts between replication and transcription and (iv) DNA replication under inappropriate metabolic conditions (unbalanced DNA replication). Because the DNA replication program is a process tightly regulated by many factors, replication stress often appears as a cascade of events. A local stress may prevent the completion of DNA replication at a single locus and subsequently compromise chromosome segregation in mitosis and therefore have a global effect on genome integrity. Finally, we discuss how replication stress drives genome instability and to what extent it is relevant to cancer biology.
Collapse
Affiliation(s)
- Indiana Magdalou
- Université Paris Sud, CNRS, UMR 8200 and Institut de Cancérologie Gustave Roussy, équipe labélisée «LIGUE 2014», Villejuif, France
| | - Bernard S Lopez
- Université Paris Sud, CNRS, UMR 8200 and Institut de Cancérologie Gustave Roussy, équipe labélisée «LIGUE 2014», Villejuif, France
| | - Philippe Pasero
- Institute of Human Genetics, CNRS UPR 1142, équipe labélisée LIGUE contre le Cancer, 141 rue de la Cardonille, 34396 Montpellier, France
| | - Sarah A E Lambert
- Institut Curie, centre de recherche, CNRS UMR338, Bat 110, centre universitaire, 91405 Orsay, France.
| |
Collapse
|
48
|
Abstract
Replication stress is a complex phenomenon that has serious implications for genome stability, cell survival and human disease. Generation of aberrant replication fork structures containing single-stranded DNA activates the replication stress response, primarily mediated by the kinase ATR (ATM- and Rad3-related). Along with its downstream effectors, ATR stabilizes and helps to restart stalled replication forks, avoiding the generation of DNA damage and genome instability. Understanding this response may be key to diagnosing and treating human diseases caused by defective responses to replication stress.
Collapse
Affiliation(s)
- Michelle K Zeman
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Karlene A Cimprich
- Department of Chemical and Systems Biology, Stanford University School of Medicine, Stanford, California 94305, USA
| |
Collapse
|
49
|
Aird KM, Zhang R. Nucleotide metabolism, oncogene-induced senescence and cancer. Cancer Lett 2014; 356:204-10. [PMID: 24486217 DOI: 10.1016/j.canlet.2014.01.017] [Citation(s) in RCA: 98] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2013] [Revised: 01/06/2014] [Accepted: 01/22/2014] [Indexed: 01/28/2023]
Abstract
Senescence is defined as a stable cell growth arrest. Oncogene-induced senescence (OIS) occurs when an activated oncogene is expressed in a normal cell. OIS acts as a bona fide tumor suppressor mechanism by driving stable growth arrest of cancer progenitor cells harboring the initial oncogenic hit. OIS is often characterized by aberrant DNA replication and the associated DNA damage response. Nucleotides, in particular deoxyribonucleotide triphosphates (dNTPs), are necessary for both DNA replication and repair. Imbalanced dNTP pools play a role in a number of human diseases, including during the early stages of cancer development. This review will highlight what is currently known about the role of decreased nucleotide metabolism in OIS, how nucleotide metabolism leads to transformation and tumor progression, and how this pathway can be targeted as a cancer therapeutic by inducing senescence of cancer cells.
Collapse
Affiliation(s)
- Katherine M Aird
- Gene Expression and Regulation Program, The Wistar Institute Cancer Center, The Wistar Institute, Philadelphia, PA 19104, United States
| | - Rugang Zhang
- Gene Expression and Regulation Program, The Wistar Institute Cancer Center, The Wistar Institute, Philadelphia, PA 19104, United States.
| |
Collapse
|
50
|
Spontaneous slow replication fork progression elicits mitosis alterations in homologous recombination-deficient mammalian cells. Proc Natl Acad Sci U S A 2013; 111:763-8. [PMID: 24347643 DOI: 10.1073/pnas.1311520111] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Homologous recombination deficient (HR(-)) mammalian cells spontaneously display reduced replication fork (RF) movement and mitotic extra centrosomes. We show here that these cells present a complex mitotic phenotype, including prolonged metaphase arrest, anaphase bridges, and multipolar segregations. We then asked whether the replication and the mitotic phenotypes are interdependent. First, we determined low doses of hydroxyurea that did not affect the cell cycle distribution or activate CHK1 phosphorylation but did slow the replication fork movement of wild-type cells to the same level than in HR(-) cells. Remarkably, these low hydroxyurea doses generated the same mitotic defects (and to the same extent) in wild-type cells as observed in unchallenged HR(-) cells. Reciprocally, supplying nucleotide precursors to HR(-) cells suppressed both their replication deceleration and mitotic extra centrosome phenotypes. Therefore, subtle replication stress that escapes to surveillance pathways and, thus, fails to prevent cells from entering mitosis alters metaphase progression and centrosome number, resulting in multipolar mitosis. Importantly, multipolar mitosis results in global unbalanced chromosome segregation involving the whole genome, even fully replicated chromosomes. These data highlight the cross-talk between chromosome replication and segregation, and the importance of HR at the interface of these two processes for protection against general genome instability.
Collapse
|