1
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Geraud M, Cristini A, Salimbeni S, Bery N, Jouffret V, Russo M, Ajello AC, Fernandez Martinez L, Marinello J, Cordelier P, Trouche D, Favre G, Nicolas E, Capranico G, Sordet O. TDP1 mutation causing SCAN1 neurodegenerative syndrome hampers the repair of transcriptional DNA double-strand breaks. Cell Rep 2024; 43:114214. [PMID: 38761375 DOI: 10.1016/j.celrep.2024.114214] [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: 03/02/2023] [Revised: 03/05/2024] [Accepted: 04/24/2024] [Indexed: 05/20/2024] Open
Abstract
TDP1 removes transcription-blocking topoisomerase I cleavage complexes (TOP1ccs), and its inactivating H493R mutation causes the neurodegenerative syndrome SCAN1. However, the molecular mechanism underlying the SCAN1 phenotype is unclear. Here, we generate human SCAN1 cell models using CRISPR-Cas9 and show that they accumulate TOP1ccs along with changes in gene expression and genomic distribution of R-loops. SCAN1 cells also accumulate transcriptional DNA double-strand breaks (DSBs) specifically in the G1 cell population due to increased DSB formation and lack of repair, both resulting from abortive removal of transcription-blocking TOP1ccs. Deficient TDP1 activity causes increased DSB production, and the presence of mutated TDP1 protein hampers DSB repair by a TDP2-dependent backup pathway. This study provides powerful models to study TDP1 functions under physiological and pathological conditions and unravels that a gain of function of the mutated TDP1 protein, which prevents DSB repair, rather than a loss of TDP1 activity itself, could contribute to SCAN1 pathogenesis.
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Affiliation(s)
- Mathéa Geraud
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Agnese Cristini
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Simona Salimbeni
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France; Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Nicolas Bery
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Virginie Jouffret
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France; BigA Core Facility, Centre de Biologie Intégrative (CBI), Université de Toulouse, 31062 Toulouse, France
| | - Marco Russo
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Andrea Carla Ajello
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Lara Fernandez Martinez
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Jessica Marinello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy
| | - Pierre Cordelier
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Didier Trouche
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France
| | - Estelle Nicolas
- MCD, Centre de Biologie Intégrative (CBI), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum, University of Bologna, 40126 Bologna, Italy.
| | - Olivier Sordet
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, 31037 Toulouse, France.
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2
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Palani S, Machida Y, Alvey JR, Mishra V, Welter AL, Cui G, Bragantini B, Botuyan MV, Cong ATQ, Mer G, Schellenberg MJ, Machida YJ. Dimerization-dependent serine protease activity of FAM111A prevents replication fork stalling at topoisomerase 1 cleavage complexes. Nat Commun 2024; 15:2064. [PMID: 38453899 PMCID: PMC10920703 DOI: 10.1038/s41467-024-46207-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Accepted: 02/16/2024] [Indexed: 03/09/2024] Open
Abstract
FAM111A, a serine protease, plays roles in DNA replication and antiviral defense. Missense mutations in the catalytic domain cause hyper-autocleavage and are associated with genetic disorders with developmental defects. Despite the enzyme's biological significance, the molecular architecture of the FAM111A serine protease domain (SPD) is unknown. Here, we show that FAM111A is a dimerization-dependent protease containing a narrow, recessed active site that cleaves substrates with a chymotrypsin-like specificity. X-ray crystal structures and mutagenesis studies reveal that FAM111A dimerizes via the N-terminal helix within the SPD. This dimerization induces an activation cascade from the dimerization sensor loop to the oxyanion hole through disorder-to-order transitions. Dimerization is essential for proteolytic activity in vitro and for facilitating DNA replication at DNA-protein crosslink obstacles in cells, while it is dispensable for autocleavage. These findings underscore the role of dimerization in FAM111A's function and highlight the distinction in its dimerization dependency between substrate cleavage and autocleavage.
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Affiliation(s)
- Sowmiya Palani
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA
| | - Yuka Machida
- Department of Oncology, Division of Oncology Research, Mayo Clinic, Rochester, MN, USA
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Julia R Alvey
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Vandana Mishra
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Allison L Welter
- Mayo Clinic Graduate School of Biomedical Sciences, Mayo Clinic, Rochester, MN, USA
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA
| | - Gaofeng Cui
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Benoît Bragantini
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - Anh T Q Cong
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | - Georges Mer
- Department of Biochemistry and Molecular Biology, Mayo Clinic, Rochester, MN, USA
| | | | - Yuichi J Machida
- Department of Oncology, Division of Oncology Research, Mayo Clinic, Rochester, MN, USA.
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD, USA.
- Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, Rochester, MN, USA.
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3
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Torrecilla I, Ruggiano A, Kiianitsa K, Aljarbou F, Lascaux P, Hoslett G, Song W, Maizels N, Ramadan K. Isolation and detection of DNA-protein crosslinks in mammalian cells. Nucleic Acids Res 2024; 52:525-547. [PMID: 38084926 PMCID: PMC10810220 DOI: 10.1093/nar/gkad1178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2023] [Revised: 11/21/2023] [Accepted: 11/23/2023] [Indexed: 01/26/2024] Open
Abstract
DNA-protein crosslinks (DPCs) are toxic DNA lesions wherein a protein is covalently attached to DNA. If not rapidly repaired, DPCs create obstacles that disturb DNA replication, transcription and DNA damage repair, ultimately leading to genome instability. The persistence of DPCs is associated with premature ageing, cancer and neurodegeneration. In mammalian cells, the repair of DPCs mainly relies on the proteolytic activities of SPRTN and the 26S proteasome, complemented by other enzymes including TDP1/2 and the MRN complex, and many of the activities involved are essential, restricting genetic approaches. For many years, the study of DPC repair in mammalian cells was hindered by the lack of standardised assays, most notably assays that reliably quantified the proteins or proteolytic fragments covalently bound to DNA. Recent interest in the field has spurred the development of several biochemical methods for DPC analysis. Here, we critically analyse the latest techniques for DPC isolation and the benefits and drawbacks of each. We aim to assist researchers in selecting the most suitable isolation method for their experimental requirements and questions, and to facilitate the comparison of results across different laboratories using different approaches.
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Affiliation(s)
- Ignacio Torrecilla
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Annamaria Ruggiano
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Kostantin Kiianitsa
- Department of Immunology, University of Washington, Seattle, WA 98195-7350, USA
| | - Ftoon Aljarbou
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Pauline Lascaux
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Gwendoline Hoslett
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Wei Song
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
| | - Nancy Maizels
- Department of Immunology, University of Washington, Seattle, WA 98195-7350, USA
- Department of Biochemistry, University of Washington, Seattle, WA 98195-7350, USA
| | - Kristijan Ramadan
- The MRC Weatherall Institute of Molecular Medicine, Department of Oncology, John Radcliffe Hospital, University of Oxford, Oxford, OX3 9DS, UK
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4
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Rubio-Contreras D, Gómez-Herreros F. TDP1 suppresses chromosomal translocations and cell death induced by abortive TOP1 activity during gene transcription. Nat Commun 2023; 14:6940. [PMID: 37945566 PMCID: PMC10636166 DOI: 10.1038/s41467-023-42622-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 10/17/2023] [Indexed: 11/12/2023] Open
Abstract
DNA topoisomerase I (TOP1) removes torsional stress by transiently cutting one DNA strand. Such cuts are rejoined by TOP1 but can occasionally become abortive generating permanent protein-linked single strand breaks (SSBs). The repair of these breaks is initiated by tyrosyl-DNA phosphodiesterase 1 (TDP1), a conserved enzyme that unlinks the TOP1 peptide from the DNA break. Additionally, some of these SSBs can result in double strand breaks (DSBs) either during replication or by a poorly understood transcription-associated process. In this study, we identify these DSBs as a source of genome rearrangements, which are suppressed by TDP1. Intriguingly, we also provide a mechanistic explanation for the formation of chromosomal translocations unveiling an error-prone pathway that relies on the MRN complex and canonical non-homologous end-joining. Collectively, these data highlight the threat posed by TOP1-induced DSBs during transcription and demonstrate the importance of TDP1-dependent end-joining in protecting both gene transcription and genome stability.
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Affiliation(s)
- Diana Rubio-Contreras
- Instituto de Biomedicina de Sevilla, IBiS, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain
- Departamento de Genética, Universidad de Sevilla, 41012, Seville, Spain
| | - Fernando Gómez-Herreros
- Instituto de Biomedicina de Sevilla, IBiS, Hospital Universitario Virgen del Rocío/CSIC/Universidad de Sevilla, 41013, Seville, Spain.
- Departamento de Genética, Universidad de Sevilla, 41012, Seville, Spain.
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5
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Rose AM, Goncalves T, Cunniffe S, Geiller HEB, Kent T, Shepherd S, Ratnaweera M, O’Sullivan R, Gibbons R, Clynes D. Induction of the alternative lengthening of telomeres pathway by trapping of proteins on DNA. Nucleic Acids Res 2023; 51:6509-6527. [PMID: 36940725 PMCID: PMC10359465 DOI: 10.1093/nar/gkad150] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2022] [Revised: 02/06/2023] [Accepted: 02/21/2023] [Indexed: 03/23/2023] Open
Abstract
Telomere maintenance is a hallmark of malignant cells and allows cancers to divide indefinitely. In some cancers, this is achieved through the alternative lengthening of telomeres (ALT) pathway. Whilst loss of ATRX is a near universal feature of ALT-cancers, it is insufficient in isolation. As such, other cellular events must be necessary - but the exact nature of the secondary events has remained elusive. Here, we report that trapping of proteins (such as TOP1, TOP2A and PARP1) on DNA leads to ALT induction in cells lacking ATRX. We demonstrate that protein-trapping chemotherapeutic agents, such as etoposide, camptothecin and talazoparib, induce ALT markers specifically in ATRX-null cells. Further, we show that treatment with G4-stabilising drugs cause an increase in trapped TOP2A levels which leads to ALT induction in ATRX-null cells. This process is MUS81-endonuclease and break-induced replication dependent, suggesting that protein trapping leads to replication fork stalling, with these forks being aberrantly processed in the absence of ATRX. Finally, we show ALT-positive cells harbour a higher load of genome-wide trapped proteins, such as TOP1, and knockdown of TOP1 reduced ALT activity. Taken together, these findings suggest that protein trapping is a fundamental driving force behind ALT-biology in ATRX-deficient malignancies.
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Affiliation(s)
- Anna M Rose
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
- Department of Paediatrics, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Tomas Goncalves
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Siobhan Cunniffe
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Thomas Kent
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - Sam Shepherd
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | | | - Roderick J O’Sullivan
- Department of Pharmacology and Chemical Biology, UPMC Hillman Cancer Center, University of Pittsburgh, Pittsburgh, PA, USA
| | - Richard J Gibbons
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Oxford OX3 9DS, UK
| | - David Clynes
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
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6
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Guha Majumdar A, Shree S, Das A, Kumar BK, Dey P, Subramanian M, Patro BS. Design, synthesis and development of a dual inhibitor of Topoisomerase 1 and poly (ADP-ribose) polymerase 1 for efficient killing of cancer cells. Eur J Med Chem 2023; 258:115598. [PMID: 37406384 DOI: 10.1016/j.ejmech.2023.115598] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/07/2023]
Abstract
Combinatorial inhibition of Topoisomerase 1 (TOP1) and Poly (ADP-ribose) polymerase 1 (PARP1) is an attractive therapeutic strategy which is under active investigation to address chemoresistance to TOP1 inhibitors. However, this combinatorial regimen suffers from severe dose limiting toxicities. Dual inhibitors often offer significant advantages over combinatorial therapies involving individual agents by minimizing toxicity and providing conducive pharmacokinetic profiles. In this study, we have designed, synthesized and evaluated a library of 11 candidate conjugated dual inhibitors for PARP1 and TOP1, named as DiPT-1 to DiPT-11. Our extensive screening showed that one of the hits i.e.DiPT-4 has promising cytotoxicity profile against multiple cancers with limited toxicities towards normal cells. DiPT-4 induces extensive DNA double stand breaks (DSBs), cell cycle arrest and apoptosis in cancer cells. Mechanistically, DiPT-4 has the propensity to bind catalytic pockets of TOP1 and PARP1, leading to significant inhibition of both TOP1 and PARP1 at in vitro and cellular level. Interestingly, DiPT-4 causes extensive stabilization of TOP1-DNA covalent complex (TOP1cc), a key lethal intermediate associated with induction of DSBs and cell death. Moreover, DiPT-4 inhibited poly (ADP-ribosylation) i.e. PARylation of TOP1cc, leading to long lived TOP1cc with a slower kinetics of degradation. This is one of the important molecular processes which helps in overcoming resistance in cancer in response to TOP1 inhibitors. Together, our investigation showed DiPT-4 as a promising dual inhibitor of TOP1 and PARP1, which may have the potential to offer significant advantages over combinatorial therapy in clinical settings.
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Affiliation(s)
- Ananda Guha Majumdar
- Bio-Organic Division, India; Homi Bhabha National Institute, Mumbai, Maharashtra, 400094, India
| | - Shikha Shree
- Bio-Organic Division, India; Homi Bhabha National Institute, Mumbai, Maharashtra, 400094, India
| | - Amit Das
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, 400085, India; Homi Bhabha National Institute, Mumbai, Maharashtra, 400094, India
| | - Binita K Kumar
- Radiation Biology & Health Sciences Division, Bhabha Atomic Research Centre, Mumbai, Maharashtra, 400085, India
| | | | - Mahesh Subramanian
- Bio-Organic Division, India; Homi Bhabha National Institute, Mumbai, Maharashtra, 400094, India
| | - Birija Sankar Patro
- Bio-Organic Division, India; Homi Bhabha National Institute, Mumbai, Maharashtra, 400094, India.
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7
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Sun Y, Baechler SA, Zhang X, Kumar S, Factor VM, Arakawa Y, Chau CH, Okamoto K, Parikh A, Walker B, Su YP, Chen J, Ting T, Huang SYN, Beck E, Itkin Z, McKnight C, Xie C, Roper N, Nijhawan D, Figg WD, Meltzer PS, Yang JC, Thomas CJ, Pommier Y. Targeting neddylation sensitizes colorectal cancer to topoisomerase I inhibitors by inactivating the DCAF13-CRL4 ubiquitin ligase complex. Nat Commun 2023; 14:3762. [PMID: 37353483 PMCID: PMC10290057 DOI: 10.1038/s41467-023-39374-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Accepted: 06/09/2023] [Indexed: 06/25/2023] Open
Abstract
Colorectal cancers (CRCs) are prevalent worldwide, yet current treatments remain inadequate. Using chemical genetic screens, we identify that co-inhibition of topoisomerase I (TOP1) and NEDD8 is synergistically cytotoxic in human CRC cells. Combination of the TOP1 inhibitor irinotecan or its bioactive metabolite SN38 with the NEDD8-activating enzyme inhibitor pevonedistat exhibits synergy in CRC patient-derived organoids and xenografts. Mechanistically, we show that pevonedistat blocks the ubiquitin/proteasome-dependent repair of TOP1 DNA-protein crosslinks (TOP1-DPCs) induced by TOP1 inhibitors and that the CUL4-RBX1 complex (CRL4) is a prominent ubiquitin ligase acting on TOP1-DPCs for proteasomal degradation upon auto-NEDD8 modification during replication. We identify DCAF13, a DDB1 and Cullin Associated Factor, as the receptor of TOP1-DPCs for CRL4. Our study not only uncovers a replication-coupled ubiquitin-proteasome pathway for the repair of TOP1-DPCs but also provides molecular and translational rationale for combining TOP1 inhibitors and pevonedistat for CRC and other types of cancers.
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Affiliation(s)
- Yilun Sun
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
| | - Simone A Baechler
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Xiaohu Zhang
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Suresh Kumar
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Valentina M Factor
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yasuhiro Arakawa
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Cindy H Chau
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Kanako Okamoto
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Anup Parikh
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Bob Walker
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Yijun P Su
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Jiji Chen
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Tabitha Ting
- Department of Internal Medicine, University of Texas Southwestern Medical Center, Dallas, TX, 75390, USA
| | - Shar-Yin N Huang
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Erin Beck
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Zina Itkin
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Crystal McKnight
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Changqing Xie
- Thoracic and GI Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Nitin Roper
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Deepak Nijhawan
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, National Institutes of Health, Bethesda, MD, 20892, USA
| | - William Douglas Figg
- Genitourinary Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Paul S Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - James C Yang
- Surgery Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Craig J Thomas
- Division of Preclinical Innovation, National Center for Advancing Translational Sciences, National Institutes of Health, Rockville, MD, 20850, USA
| | - Yves Pommier
- Developmental Therapeutics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, 20892, USA.
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8
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A CRISPR-Cas9 screen identifies EXO1 as a formaldehyde resistance gene. Nat Commun 2023; 14:381. [PMID: 36693839 PMCID: PMC9873647 DOI: 10.1038/s41467-023-35802-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2022] [Accepted: 12/28/2022] [Indexed: 01/25/2023] Open
Abstract
Fanconi Anemia (FA) is a rare, genome instability-associated disease characterized by a deficiency in repairing DNA crosslinks, which are known to perturb several cellular processes, including DNA transcription, replication, and repair. Formaldehyde, a by-product of metabolism, is thought to drive FA by generating DNA interstrand crosslinks (ICLs) and DNA-protein crosslinks (DPCs). However, the impact of formaldehyde on global cellular pathways has not been investigated thoroughly. Herein, using a pangenomic CRISPR-Cas9 screen, we identify EXO1 as a critical regulator of formaldehyde-induced DNA lesions. We show that EXO1 knockout cell lines exhibit formaldehyde sensitivity leading to the accumulation of replicative stress, DNA double-strand breaks, and quadriradial chromosomes, a typical feature of FA. After formaldehyde exposure, EXO1 is recruited to chromatin, protects DNA replication forks from degradation, and functions in parallel with the FA pathway to promote cell survival. In vitro, EXO1-mediated exonuclease activity is proficient in removing DPCs. Collectively, we show that EXO1 limits replication stress and DNA damage to counteract formaldehyde-induced genome instability.
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9
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Perry M, Ghosal G. Isolation and Immunodetection of Enzymatic DNA-Protein Crosslinks by RADAR Assay. Methods Mol Biol 2023; 2701:135-148. [PMID: 37574479 DOI: 10.1007/978-1-0716-3373-1_8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/15/2023]
Abstract
DNA-protein crosslinks (DPCs) are steric hindrances to DNA metabolic processes and the removal and repair of DPCs is a rapidly evolving area of research. A critical component of deciphering this repair pathway is developing techniques that detect and quantify specific types of DPCs in cells. Here we describe a protocol for direct detection of enzymatic DPCs from mammalian cells-the RADAR assay. The method involves isolating genomic DNA and DPCs from cells and binding them to nitrocellulose membrane with a vacuum slot blot manifold. DPCs are detected using antibodies raised against the protein of interest and quantified by normalizing to a DNA loading control. The RADAR assay allows for the detection of specific types of DPCs and the sensitive analysis of the DNA-protein crosslinking activity of various drugs, is adaptable across different cell types and conditions, and requires little specialized equipment.
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Affiliation(s)
- Megan Perry
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA
| | - Gargi Ghosal
- Department of Genetics, Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE, USA.
- Fred and Pamela Buffett Cancer Center, Omaha, NE, USA.
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10
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TDP1-independent pathways in the process and repair of TOP1-induced DNA damage. Nat Commun 2022; 13:4240. [PMID: 35869071 PMCID: PMC9307636 DOI: 10.1038/s41467-022-31801-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2021] [Accepted: 06/29/2022] [Indexed: 11/15/2022] Open
Abstract
Anticancer drugs, such as camptothecin (CPT), trap topoisomerase I (TOP1) on DNA and form TOP1 cleavage complexes (TOP1cc). Alternative repair pathways have been suggested in the repair of TOP1cc. However, how these pathways work with TDP1, a key repair enzyme that specifically hydrolyze the covalent bond between TOP1 catalytic tyrosine and the 3’-end of DNA and contribute to the repair of TOP1cc is poorly understood. Here, using unbiased whole-genome CRISPR screens and generation of co-deficient cells with TDP1 and other genes, we demonstrate that MUS81 is an important factor that mediates the generation of excess double-strand breaks (DSBs) in TDP1 KO cells. APEX1/2 are synthetic lethal with TDP1. However, deficiency of APEX1/2 does not reduce DSB formation in TDP1 KO cells. Together, our data suggest that TOP1cc can be either resolved directly by TDP1 or be converted into DSBs and repaired further by the Homologous Recombination (HR) pathway. Here the authors find that MUS81 mediates excess DNA double strand break (DSB) generation in TDP1 KO cells after camptothecin treatment. They show that TOP1 cleavage complexes can be either resolved directly by TDP1 or be converted into DSBs and repaired further by the Homologous Recombination pathway.
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11
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Dang X, Cao D, Zhao J, Schank M, Khanal S, Nguyen LNT, Wu XY, Zhang Y, Zhang J, Jiang Y, Ning S, Wang L, El Gazzar M, Moorman JP, Yao ZQ. Mitochondrial topoisomerase 1 inhibition induces topological DNA damage and T cell dysfunction in patients with chronic viral infection. Front Cell Infect Microbiol 2022; 12:1026293. [PMID: 36405960 PMCID: PMC9669385 DOI: 10.3389/fcimb.2022.1026293] [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: 08/23/2022] [Accepted: 10/18/2022] [Indexed: 11/06/2022] Open
Abstract
T cells are crucial for controlling viral infections; however, the mechanisms that dampen their responses during viral infections remain incompletely understood. Here, we studied the role and mechanisms of mitochondrial topoisomerase 1 (Top1mt) inhibition in mitochondrial dysfunction and T cell dysregulation using CD4 T cells from patients infected with HCV or HIV and compared it with CD4 T cells from healthy individuals following treatment with Top1 inhibitor - camptothecin (CPT). We found that Top1mt protein levels and enzymatic activity are significantly decreased, along with Top1 cleavage complex (Top1cc) formation, in mitochondria of CD4 T cells from HCV- and HIV-infected patients. Notably, treatment of healthy CD4 T cells with CPT caused similar changes, including inhibition of Top1mt, accumulation of Top1cc in mitochondria, increase in PARP1 cleavage, and decrease in mtDNA copy numbers. These molecular changes resulted in mitochondrial dysfunction, T cell dysregulation, and programmed cell death through multiple signaling pathways, recapitulating the phenotype we detected in CD4 T cells from HCV- and HIV-infected patients. Moreover, treatment of CD4 T cells from HCV or HIV patients with CPT further increased cellular and mitochondrial reactive oxygen species (ROS) production and cell apoptosis, demonstrating a critical role for Top1 in preventing mtDNA damage and cell death. These results provide new insights into the molecular mechanisms underlying immune dysregulation during viral infection and indicate that Top1 inhibition during chronic HCV or HIV infection can induce mtDNA damage and T cell dysfunction. Thus, reconstituting Top1mt protein may restore the mtDNA topology and T cell functions in humans with chronic viral infection.
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Affiliation(s)
- Xindi Dang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Dechao Cao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Juan Zhao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Madison Schank
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Sushant Khanal
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Lam Ngoc Thao Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Xiao Y Wu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Yi Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Jinyu Zhang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Yong Jiang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Shunbin Ning
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Ling Wang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Mohamed El Gazzar
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
| | - Jonathan P Moorman
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
- Hepatitis (HBV/HCV) and HIV Programs, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson, TN, United States
| | - Zhi Q Yao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson, TN, United States
- Hepatitis (HBV/HCV) and HIV Programs, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson, TN, United States
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12
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Pommier Y, Nussenzweig A, Takeda S, Austin C. Human topoisomerases and their roles in genome stability and organization. Nat Rev Mol Cell Biol 2022; 23:407-427. [PMID: 35228717 PMCID: PMC8883456 DOI: 10.1038/s41580-022-00452-3] [Citation(s) in RCA: 136] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/06/2022] [Indexed: 12/15/2022]
Abstract
Human topoisomerases comprise a family of six enzymes: two type IB (TOP1 and mitochondrial TOP1 (TOP1MT), two type IIA (TOP2A and TOP2B) and two type IA (TOP3A and TOP3B) topoisomerases. In this Review, we discuss their biochemistry and their roles in transcription, DNA replication and chromatin remodelling, and highlight the recent progress made in understanding TOP3A and TOP3B. Because of recent advances in elucidating the high-order organization of the genome through chromatin loops and topologically associating domains (TADs), we integrate the functions of topoisomerases with genome organization. We also discuss the physiological and pathological formation of irreversible topoisomerase cleavage complexes (TOPccs) as they generate topoisomerase DNA–protein crosslinks (TOP-DPCs) coupled with DNA breaks. We discuss the expanding number of redundant pathways that repair TOP-DPCs, and the defects in those pathways, which are increasingly recognized as source of genomic damage leading to neurological diseases and cancer. Topoisomerases have essential roles in transcription, DNA replication, chromatin remodelling and, as recently revealed, 3D genome organization. However, topoisomerases also generate DNA–protein crosslinks coupled with DNA breaks, which are increasingly recognized as a source of disease-causing genomic damage.
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13
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Marinello J, Capranico G. Highly Purified Top1-Bound DNA Fragments. Methods Mol Biol 2022; 2528:203-213. [PMID: 35704193 DOI: 10.1007/978-1-0716-2477-7_13] [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] [Indexed: 06/15/2023]
Abstract
Topoisomerase 1-DNA cleavage complexes (Top1ccs) form at DNA sites of Top1 activity and are increased by a highly specific anticancer drug (camptothecin, CPT) in living cells. Various methods are available to detect Top1ccs in cultured cells, including protocols based on the use of specific antibodies. Here, we describe a protocol to isolate Top1ccs at high purity, which does not depend on antibodies.
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Affiliation(s)
- Jessica Marinello
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Bologna, Italy
| | - Giovanni Capranico
- Department of Pharmacy and Biotechnology, Alma Mater Studiorum - University of Bologna, Bologna, Italy.
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14
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Wahner Hendrickson AE, Visscher DW, Hou X, Goergen KM, Atkinson HJ, Beito TG, Negron V, Lingle WL, Bruzek AK, Hurley RM, Wagner JM, Flatten KS, Peterson KL, Schneider PA, Larson MC, Maurer MJ, Kalli KR, Oberg AL, Weroha SJ, Kaufmann SH. CHFR and Paclitaxel Sensitivity of Ovarian Cancer. Cancers (Basel) 2021; 13:cancers13236043. [PMID: 34885153 PMCID: PMC8657201 DOI: 10.3390/cancers13236043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2021] [Revised: 11/17/2021] [Accepted: 11/27/2021] [Indexed: 12/14/2022] Open
Abstract
The poly(ADP-ribose) binding protein CHFR regulates cellular responses to mitotic stress. The deubiquitinase UBC13, which regulates CHFR levels, has been associated with better overall survival in paclitaxel-treated ovarian cancer. Despite the extensive use of taxanes in the treatment of ovarian cancer, little is known about expression of CHFR itself in this disease. In the present study, tissue microarrays containing ovarian carcinoma samples from 417 women who underwent initial surgical debulking were stained with anti-CHFR antibody and scored in a blinded fashion. CHFR levels, expressed as a modified H-score, were examined for association with histology, grade, time to progression (TTP) and overall survival (OS). In addition, patient-derived xenografts from 69 ovarian carcinoma patients were examined for CHFR expression and sensitivity to paclitaxel monotherapy. In clinical ovarian cancer specimens, CHFR expression was positively associated with serous histology (p = 0.0048), higher grade (p = 0.000014) and higher stage (p = 0.016). After correction for stage and debulking, there was no significant association between CHFR staining and overall survival (p = 0.62) or time to progression (p = 0.91) in patients with high grade serous cancers treated with platinum/taxane chemotherapy (N = 249). Likewise, no association between CHFR expression and paclitaxel sensitivity was observed in ovarian cancer PDXs treated with paclitaxel monotherapy. Accordingly, differences in CHFR expression are unlikely to play a major role in paclitaxel sensitivity of high grade serous ovarian cancer.
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Affiliation(s)
- Andrea E. Wahner Hendrickson
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA; (X.H.); (J.M.W.); (S.J.W.)
- Correspondence: (A.E.W.H.); (S.H.K.); Tel.: +1-507-284-3731 (A.E.W.H.); +1-507-284-8950 (S.H.K.); Fax: +1-507-293-0107 (A.E.W.H. & S.H.K.)
| | - Daniel W. Visscher
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN 55905, USA;
| | - Xiaonan Hou
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA; (X.H.); (J.M.W.); (S.J.W.)
| | - Krista M. Goergen
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (K.M.G.); (H.J.A.); (M.C.L.); (M.J.M.); (A.L.O.)
| | - Hunter J. Atkinson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (K.M.G.); (H.J.A.); (M.C.L.); (M.J.M.); (A.L.O.)
| | | | - Vivian Negron
- Pathology Research Core, Mayo Clinic, Rochester, MN 55905, USA; (V.N.); (W.L.L.); (A.K.B.)
| | - Wilma L. Lingle
- Pathology Research Core, Mayo Clinic, Rochester, MN 55905, USA; (V.N.); (W.L.L.); (A.K.B.)
| | - Amy K. Bruzek
- Pathology Research Core, Mayo Clinic, Rochester, MN 55905, USA; (V.N.); (W.L.L.); (A.K.B.)
| | - Rachel M. Hurley
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA;
| | - Jill M. Wagner
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA; (X.H.); (J.M.W.); (S.J.W.)
| | - Karen S. Flatten
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA; (K.S.F.); (K.L.P.); (P.A.S.)
| | - Kevin L. Peterson
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA; (K.S.F.); (K.L.P.); (P.A.S.)
| | - Paula A. Schneider
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA; (K.S.F.); (K.L.P.); (P.A.S.)
| | - Melissa C. Larson
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (K.M.G.); (H.J.A.); (M.C.L.); (M.J.M.); (A.L.O.)
| | - Matthew J. Maurer
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (K.M.G.); (H.J.A.); (M.C.L.); (M.J.M.); (A.L.O.)
| | | | - Ann L. Oberg
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, MN 55905, USA; (K.M.G.); (H.J.A.); (M.C.L.); (M.J.M.); (A.L.O.)
| | - S. John Weroha
- Division of Medical Oncology, Mayo Clinic, Rochester, MN 55905, USA; (X.H.); (J.M.W.); (S.J.W.)
| | - Scott H. Kaufmann
- Department of Molecular Pharmacology & Experimental Therapeutics, Mayo Clinic, Rochester, MN 55905, USA;
- Division of Oncology Research, Mayo Clinic, Rochester, MN 55905, USA; (K.S.F.); (K.L.P.); (P.A.S.)
- Correspondence: (A.E.W.H.); (S.H.K.); Tel.: +1-507-284-3731 (A.E.W.H.); +1-507-284-8950 (S.H.K.); Fax: +1-507-293-0107 (A.E.W.H. & S.H.K.)
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15
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Downing SM, Schreiner PA, Kwak YD, Li Y, Shaw TI, Russell HR, McKinnon PJ. Genome instability independent of type I interferon signaling drives neuropathology caused by impaired ribonucleotide excision repair. Neuron 2021; 109:3962-3979.e6. [PMID: 34655526 DOI: 10.1016/j.neuron.2021.09.040] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Revised: 08/22/2021] [Accepted: 09/20/2021] [Indexed: 12/25/2022]
Abstract
Aicardi-Goutières syndrome (AGS) is a monogenic type I interferonopathy characterized by neurodevelopmental defects and upregulation of type I interferon signaling and neuroinflammation. Mutations in genes that function in nucleic acid metabolism, including RNASEH2, are linked to AGS. Ribonuclease H2 (RNASEH2) is a genome surveillance factor critical for DNA integrity by removing ribonucleotides incorporated into replicating DNA. Here we show that RNASEH2 is necessary for neurogenesis and to avoid activation of interferon-responsive genes and neuroinflammation. Cerebellar defects after RNASEH2B inactivation are rescued by p53 but not cGAS deletion, suggesting that DNA damage signaling, not neuroinflammation, accounts for neuropathology. Coincident inactivation of Atm and Rnaseh2 further affected cerebellar development causing ataxia, which was dependent upon aberrant activation of non-homologous end-joining (NHEJ). The loss of ATM also markedly exacerbates cGAS-dependent type I interferon signaling. Thus, DNA damage-dependent signaling rather than type I interferon signaling underlies neurodegeneration in this class of neurodevelopmental/neuroinflammatory disease.
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Affiliation(s)
- Susanna M Downing
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Patrick A Schreiner
- Center for Applied Bioinformatics, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Young Don Kwak
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Yang Li
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | | | - Helen R Russell
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA
| | - Peter J McKinnon
- Center for Pediatric Neurological Disease Research, St. Jude Pediatric Translational Neuroscience Initiative, Department of Cell and Molecular Biology, St. Jude Children's Research Hospital, Memphis, TN, USA; St. Jude Graduate School of Biomedical Sciences, St. Jude Children's Research Hospital, Memphis, TN, USA.
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16
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Flor A, Wolfgeher D, Li J, Hanakahi LA, Kron SJ. Lipid-derived electrophiles mediate the effects of chemotherapeutic topoisomerase I poisons. Cell Chem Biol 2021; 28:776-787.e8. [PMID: 33352117 PMCID: PMC8206239 DOI: 10.1016/j.chembiol.2020.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2020] [Revised: 10/13/2020] [Accepted: 11/25/2020] [Indexed: 12/19/2022]
Abstract
Topoisomerase 1 (Top1) reversibly nicks chromosomal DNA to relax strain accumulated during transcription, replication, chromatin assembly, and chromosome condensation. The Top1 poison camptothecin targets cancer cells by trapping the enzyme in the covalent complex Top1cc, tethered to cleaved DNA by a tyrosine-3'-phosphate bond. In vitro mechanistic studies point to interfacial inhibition, where camptothecin binding to the Top1-DNA interface stabilizes Top1cc. Here we present a complementary covalent mechanism that is critical in vivo. We observed that camptothecins induce oxidative stress, leading to lipid peroxidation, lipid-derived electrophile accumulation, and Top1 poisoning via covalent modification. The electrophile 4-hydroxy-2-nonenal can induce Top1cc on its own and forms a Michael adduct to a cysteine thiol in the Top1 active site, potentially blocking tyrosine dephosphorylation and 3' DNA phosphate release. Thereby, camptothecins may leverage a physiological cysteine-based redox switch in Top1 to mediate their selective toxicity to rapidly proliferating cancer cells.
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Affiliation(s)
- Amy Flor
- University of Chicago, Department of Molecular Genetics and Cell Biology, Chicago IL 60637, USA,Further information and requests for resources and reagents should be directed to and will be fulfilled by the Lead Contact, Amy Flor ()
| | - Donald Wolfgeher
- University of Chicago, Department of Molecular Genetics and Cell Biology, Chicago IL 60637, USA
| | - Jing Li
- University of Illinois Chicago, College of Pharmacy, Department of Pharmaceutical Sciences, Rockford IL 61107, USA
| | - Leslyn A. Hanakahi
- University of Illinois Chicago, College of Pharmacy, Department of Pharmaceutical Sciences, Rockford IL 61107, USA
| | - Stephen J. Kron
- University of Chicago, Department of Molecular Genetics and Cell Biology, Chicago IL 60637, USA,Corresponding author: 929 E. 57th St. W522A, Chicago IL 60637, USA;
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17
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Haber AO, Jain A, Mani C, Nevler A, Agostini LC, Golan T, Palle K, Yeo CJ, Gmeiner WH, Brody JR. AraC-FdUMP[10] Is a Next-Generation Fluoropyrimidine with Potent Antitumor Activity in PDAC and Synergy with PARG Inhibition. Mol Cancer Res 2021; 19:565-572. [PMID: 33593942 DOI: 10.1158/1541-7786.mcr-20-0985] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/16/2020] [Accepted: 02/10/2021] [Indexed: 11/16/2022]
Abstract
AraC-FdUMP[10] (CF10) is a second-generation polymeric fluoropyrimidine that targets both thymidylate synthase (TS), the target of 5-fluorouracil (5-FU), and DNA topoisomerase 1 (Top1), the target of irinotecan, two drugs that are key components of FOLFIRNOX, a standard-of-care regimen for pancreatic ductal adenocarcinoma (PDAC). We demonstrated that F10 and CF10 are potent inhibitors of PDAC cell survival (in multiple cell lines including patient-derived lines) with IC50s in the nanomolar range and are nearly 1,000-fold more potent than 5-FU. The increased potency of CF10 relative to 5-FU correlated with enhanced TS inhibition and strong Top1 cleavage complex formation. Furthermore, CF10 displayed single-agent activity in PDAC murine xenografts without inducing weight loss. Through a focused drug synergy screen, we identified that combining CF10 with targeting the DNA repair enzyme, poly (ADP-ribose) glycohydrolase, induces substantial DNA damage and apoptosis. This work moves CF10 closer to a clinical trial for the treatment of PDAC. IMPLICATIONS: CF10 is a promising polymeric fluoropyrimidine with dual mechanisms of action (i.e., TS and Top1 inhibition) for the treatment of PDAC and synergizes with targeting of DNA repair. VISUAL OVERVIEW: http://mcr.aacrjournals.org/content/molcanres/19/4/565/F1.large.jpg.
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Affiliation(s)
- Alex O Haber
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Aditi Jain
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | | | - Avinoam Nevler
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Lebaron C Agostini
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Talia Golan
- Oncology Institute, Chaim Sheba Medical Center, Tel Aviv, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Komaraiah Palle
- Texas Tech University Health Sciences Center, Lubbock, Texas
| | - Charles J Yeo
- The Jefferson Pancreas, Biliary and Related Cancer Center, Department of Surgery, Thomas Jefferson University, Philadelphia, Pennsylvania.,Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - William H Gmeiner
- Deparment of Cancer Biology, Wake Forest School of Medicine, Wake Forest University, Winston-Salem, North Carolina.
| | - Jonathan R Brody
- Department of Surgery and Cell, Developmental and Cancer Biology, Knight Cancer Institute, Oregon Health & Science University, Portland, Oregon.
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18
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Gmeiner WH, Dominijanni A, Haber AO, Ghiraldeli LP, Caudell DL, D'Agostino R, Pasche BC, Smith TL, Deng Z, Kiren S, Mani C, Palle K, Brody JR. Improved Antitumor Activity of the Fluoropyrimidine Polymer CF10 in Preclinical Colorectal Cancer Models through Distinct Mechanistic and Pharmacologic Properties. Mol Cancer Ther 2020; 20:553-563. [PMID: 33361273 DOI: 10.1158/1535-7163.mct-20-0516] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 10/26/2020] [Accepted: 12/16/2020] [Indexed: 12/11/2022]
Abstract
Chemotherapy regimens that include 5-fluorouracil (5-FU) are central to colorectal cancer treatment; however, risk/benefit concerns limit 5-FU's use, necessitating development of improved fluoropyrimidine (FP) drugs. In our study, we evaluated a second-generation nanoscale FP polymer, CF10, for improved antitumor activity. CF10 was more potent than the prototype FP polymer F10 and much more potent than 5-FU in multiple colorectal cancer cell lines including HCT-116, LS174T, SW480, and T84D. CF10 displayed improved stability to exonuclease degradation relative to F10 and reduced susceptibility to thymidine antagonism due to extension of the polymer with arabinosyl cytidine. In colorectal cancer cells, CF10 strongly inhibited thymidylate synthase (TS), induced Top1 cleavage complex formation and caused replication stress, while similar concentrations of 5-FU were ineffective. CF10 was well tolerated in vivo and invoked a reduced inflammatory response relative to 5-FU. Blood chemistry parameters in CF10-treated mice were within normal limits. In vivo, CF10 displayed antitumor activity in several colorectal cancer flank tumor models including HCT-116, HT-29, and CT-26. CF10's antitumor activity was associated with increased plasma levels of FP deoxynucleotide metabolites relative to 5-FU. CF10 significantly reduced tumor growth and improved survival (84.5 days vs. 32 days; P < 0.0001) relative to 5-FU in an orthotopic HCT-116-luc colorectal cancer model that spontaneously metastasized to liver. Improved survival in the orthotopic model correlated with localization of a fluorescent CF10 conjugate to tumor. Together, our preclinical data support an early-phase clinical trial of CF10 for treatment of colorectal cancer.
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Affiliation(s)
- William H Gmeiner
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina.
- Comprehensive Cancer Center Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Anthony Dominijanni
- Wake Forest Institute for Regenerative Medicine, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Alex O Haber
- Department of Surgery, Jefferson Pancreas, Biliary and Related Cancer Center, Thomas Jefferson University, Philadelphia, Pennsylvania
| | - Lais P Ghiraldeli
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - David L Caudell
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Ralph D'Agostino
- Department of Public Health Sciences, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Boris C Pasche
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
- Comprehensive Cancer Center Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Thomas L Smith
- Department of Orthopedic Surgery, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Zhiyong Deng
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, North Carolina
| | - Sezgin Kiren
- Department of Chemistry, Winston-Salem State University, Winston-Salem, North Carolina
| | - Chinnadurai Mani
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Centre, Lubbock, Texas
| | - Komaraiah Palle
- Department of Cell Biology and Biochemistry, Texas Tech University Health Sciences Centre, Lubbock, Texas
| | - Jonathan R Brody
- Brenden Colson Center for Pancreatic Care, Departments of Surgery and Cell, Developmental & Cancer Biology, Knight Cancer Institute, Oregon Health and Science University, Portland, Oregon
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19
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Sun Y, Miller Jenkins LM, Su YP, Nitiss KC, Nitiss JL, Pommier Y. A conserved SUMO pathway repairs topoisomerase DNA-protein cross-links by engaging ubiquitin-mediated proteasomal degradation. SCIENCE ADVANCES 2020; 6:6/46/eaba6290. [PMID: 33188014 PMCID: PMC7673754 DOI: 10.1126/sciadv.aba6290] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2020] [Accepted: 09/24/2020] [Indexed: 05/04/2023]
Abstract
Topoisomerases form transient covalent DNA cleavage complexes to perform their reactions. Topoisomerase I cleavage complexes (TOP1ccs) are trapped by camptothecin and TOP2ccs by etoposide. Proteolysis of the trapped topoisomerase DNA-protein cross-links (TOP-DPCs) is a key step for some pathways to repair these lesions. We describe a pathway that features a prominent role of the small ubiquitin-like modifier (SUMO) modification for both TOP1- and TOP2-DPC repair. Both undergo rapid and sequential SUMO-2/3 and SUMO-1 modifications in human cells. The SUMO ligase PIAS4 is required for these modifications. RNF4, a SUMO-targeted ubiquitin ligase (STUbL), then ubiquitylates the TOP-DPCs for their subsequent degradation by the proteasome. This pathway is conserved in yeast with Siz1 and Slx5-Slx8, the orthologs of human PIAS4 and RNF4.
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Affiliation(s)
- Yilun Sun
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Rockford, IL 61107, USA
| | - Lisa M Miller Jenkins
- Collaborative Protein Technology Resource, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Yijun P Su
- Advanced Imaging and Microscopy Resource, National Institute of Biomedical Imaging and Bioengineering, NIH, MD 20892, USA
| | - Karin C Nitiss
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Rockford, IL 61107, USA
| | - John L Nitiss
- Department of Biopharmaceutical Sciences, College of Pharmacy, University of Illinois, Rockford, IL 61107, USA.
| | - Yves Pommier
- Developmental Therapeutics Branch and Laboratory of Molecular Pharmacology, Center for Cancer Research, NCI, NIH, Bethesda, MD 20892, USA.
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20
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Huang J, Zhou Q, Gao M, Nowsheen S, Zhao F, Kim W, Zhu Q, Kojima Y, Yin P, Zhang Y, Guo G, Tu X, Deng M, Luo K, Qin B, Machida Y, Lou Z. Tandem Deubiquitination and Acetylation of SPRTN Promotes DNA-Protein Crosslink Repair and Protects against Aging. Mol Cell 2020; 79:824-835.e5. [PMID: 32649882 DOI: 10.1016/j.molcel.2020.06.027] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2020] [Revised: 05/20/2020] [Accepted: 06/17/2020] [Indexed: 12/14/2022]
Abstract
DNA-protein crosslinks (DPCs) are highly toxic DNA lesions that threaten genomic integrity. Recent findings highlight that SPRTN, a specialized DNA-dependent metalloprotease, is a central player in proteolytic cleavage of DPCs. Previous studies suggest that SPRTN deubiquitination is important for its chromatin association and activation. However, the regulation and consequences of SPRTN deubiquitination remain unclear. Here we report that, in response to DPC induction, the deubiquitinase VCPIP1/VCIP135 is phosphorylated and activated by ATM/ATR. VCPIP1, in turn, deubiquitinates SPRTN and promotes its chromatin relocalization. Deubiquitination of SPRTN is required for its subsequent acetylation, which promotes SPRTN relocation to the site of chromatin damage. Furthermore, Vcpip1 knockout mice are prone to genomic instability and premature aging. We propose a model where two sequential post-translational modifications (PTMs) regulate SPRTN chromatin accessibility to repair DPCs and maintain genomic stability and a healthy lifespan.
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Affiliation(s)
- Jinzhou Huang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qin Zhou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ming Gao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | | | - Fei Zhao
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Wootae Kim
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Qian Zhu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yusuke Kojima
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Ping Yin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yong Zhang
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Guijie Guo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Xinyi Tu
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Min Deng
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Kuntian Luo
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Bo Qin
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Yuichi Machida
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA
| | - Zhenkun Lou
- Department of Oncology, Mayo Clinic, Rochester, MN 55905, USA.
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21
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Tsuda M, Kitamasu K, Kumagai C, Sugiyama K, Nakano T, Ide H. Tyrosyl-DNA phosphodiesterase 2 (TDP2) repairs topoisomerase 1 DNA-protein crosslinks and 3'-blocking lesions in the absence of tyrosyl-DNA phosphodiesterase 1 (TDP1). DNA Repair (Amst) 2020; 91-92:102849. [PMID: 32460231 DOI: 10.1016/j.dnarep.2020.102849] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 03/19/2020] [Accepted: 03/23/2020] [Indexed: 01/29/2023]
Abstract
Topoisomerase I (TOP1) resolves DNA topology during replication and transcription. The enzyme forms an intermediate TOP1 cleavage complex (TOP1cc) through transient TOP1-DNA-protein crosslinks. Camptothecin is a frontline anticancer agent that freezes this reaction intermediate, leading to the generation of irreversible TOP1ccs that act as 3'-blocking lesions. It is widely accepted that TOP1cc is repaired via a two-step pathway involving proteasomal degradation of TOP1cc to the crosslinked peptide, followed by removal of the TOP1cc-derived peptide from DNA by tyrosyl-DNA phosphodiesterase 1 (TDP1). In the present study, we developed an assay system to estimate repair kinetics of TOP1cc separately in the first and second steps, using monoclonal antibodies against the TOP1 protein and the TOP1 catalytic site peptide-DNA complex, respectively. Although TDP1-deficient (TDP1-/-) TK6 cells had normal kinetics of the first step, a delay in the kinetics of the second step was observed relative to that in wild-type cells. Tyrosyl-DNA phosphodiesterase 2 (TDP2) reportedly promotes the repair of TOP1-induced DNA damage in the absence of TDP1. The present assays additionally demonstrated that TDP2 promotes the second, but not the first, step of TOP1cc repair in the absence of TDP1. We also analyzed sensitivities of TK6 cells with deficiencies in TDP1 and/or TDP2 to agents that produce 3' -blocking lesions. These experiments showed that TDP1-/-TDP2-/- cells were more sensitive to the agents Azidothymidine (zidovudine), Cytarabine, Abacavir, Gemcitabine, and Trifluridine than TDP1-/- or TDP2-/- cells. Taken together, our findings confirm the roles of TDP2 in the repair of 3'-blocking lesions.
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Affiliation(s)
- Masataka Tsuda
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
| | - Kaito Kitamasu
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Chiho Kumagai
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Kazuya Sugiyama
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan
| | - Toshiaki Nakano
- DNA Damage Chemistry Research Group, Institute for Quantum Life Science, National Institutes of Quantum and Radiological Science and Technology, 8-1-7 Umemidai, Kizugawa-shi, Kyoto 619-0215, Japan
| | - Hiroshi Ide
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima 739-8526, Japan.
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22
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Aichinger G, Lichtenberger FB, Steinhauer TN, Flörkemeier I, Del Favero G, Clement B, Marko D. The Aza-Analogous Benzo[ c]phenanthridine P8-D6 Acts as a Dual Topoisomerase I and II Poison, thus Exhibiting Potent Genotoxic Properties. Molecules 2020; 25:molecules25071524. [PMID: 32230817 PMCID: PMC7180443 DOI: 10.3390/molecules25071524] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 03/21/2020] [Accepted: 03/25/2020] [Indexed: 11/16/2022] Open
Abstract
The benzo[c]phenanthridine P8-D6 was recently found to suppress the catalytic activity of both human topoisomerase (Topo) I and II. Concomitantly, potent cytotoxic activity was observed in different human tumor cell lines, raising questions about the underlying mechanisms in vitro. In the present study, we addressed the question of whether P8-D6 acts as a so-called Topo poison, stabilizing the covalent Topo-DNA intermediate, thus inducing fatal DNA strand breaks in proliferating cells. In HT-29 colon carcinoma cells, fluorescence imaging revealed P8-D6 to be taken up by the cells and to accumulate in the perinuclear region. Confocal microscopy demonstrated that the compound is partially located inside the nuclei, thus reaching the potential target. In the "in vivo complex of enzyme" (ICE) bioassay, treatment of HT-29 cells with P8-D6 for 1 h significantly enhanced the proportion of Topo I and II covalently linked to the DNA in concentrations ≥1 µM, indicating effective dual Topo poisoning. Potentially resulting DNA damage was analyzed by single-cell gel electrophoresis ("comet assay"). Already at 1 h of incubation, significant genotoxic effects were observed in the comet assay in concentrations as low as 1 nM. Taken together, the present study demonstrates the high Topo-poisoning and genotoxic potential of P8-D6 in human tumor cells.
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Affiliation(s)
- Georg Aichinger
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Waehringerstr. 38, A-1090 Vienna, Austria; (G.A.); (F.-B.L.); (G.D.F.)
| | - Falk-Bach Lichtenberger
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Waehringerstr. 38, A-1090 Vienna, Austria; (G.A.); (F.-B.L.); (G.D.F.)
- Christian-Albrechts-University Kiel, Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Gutenbergstraße 76, D-24118 Kiel, Germany; (T.N.S.); (I.F.); (B.C.)
| | - Tamara N. Steinhauer
- Christian-Albrechts-University Kiel, Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Gutenbergstraße 76, D-24118 Kiel, Germany; (T.N.S.); (I.F.); (B.C.)
| | - Inken Flörkemeier
- Christian-Albrechts-University Kiel, Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Gutenbergstraße 76, D-24118 Kiel, Germany; (T.N.S.); (I.F.); (B.C.)
| | - Giorgia Del Favero
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Waehringerstr. 38, A-1090 Vienna, Austria; (G.A.); (F.-B.L.); (G.D.F.)
| | - Bernd Clement
- Christian-Albrechts-University Kiel, Pharmaceutical Institute, Department of Pharmaceutical and Medicinal Chemistry, Gutenbergstraße 76, D-24118 Kiel, Germany; (T.N.S.); (I.F.); (B.C.)
| | - Doris Marko
- University of Vienna, Faculty of Chemistry, Department of Food Chemistry and Toxicology, Waehringerstr. 38, A-1090 Vienna, Austria; (G.A.); (F.-B.L.); (G.D.F.)
- Correspondence:
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23
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FAM111A protects replication forks from protein obstacles via its trypsin-like domain. Nat Commun 2020; 11:1318. [PMID: 32165630 PMCID: PMC7067828 DOI: 10.1038/s41467-020-15170-7] [Citation(s) in RCA: 62] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2019] [Accepted: 02/24/2020] [Indexed: 12/25/2022] Open
Abstract
Persistent protein obstacles on genomic DNA, such as DNA-protein crosslinks (DPCs) and tight nucleoprotein complexes, can block replication forks. DPCs can be removed by the proteolytic activities of the metalloprotease SPRTN or the proteasome in a replication-coupled manner; however, additional proteolytic mechanisms may exist to cope with the diversity of protein obstacles. Here, we show that FAM111A, a PCNA-interacting protein, plays an important role in mitigating the effect of protein obstacles on replication forks. This function of FAM111A requires an intact trypsin-like protease domain, the PCNA interaction, and the DNA-binding domain that is necessary for protease activity in vivo. FAM111A, but not SPRTN, protects replication forks from stalling at poly(ADP-ribose) polymerase 1 (PARP1)-DNA complexes trapped by PARP inhibitors, thereby promoting cell survival after drug treatment. Altogether, our findings reveal a role of FAM111A in overcoming protein obstacles to replication forks, shedding light on cellular responses to anti-cancer therapies.
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24
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Fielden J, Wiseman K, Torrecilla I, Li S, Hume S, Chiang SC, Ruggiano A, Narayan Singh A, Freire R, Hassanieh S, Domingo E, Vendrell I, Fischer R, Kessler BM, Maughan TS, El-Khamisy SF, Ramadan K. TEX264 coordinates p97- and SPRTN-mediated resolution of topoisomerase 1-DNA adducts. Nat Commun 2020; 11:1274. [PMID: 32152270 PMCID: PMC7062751 DOI: 10.1038/s41467-020-15000-w] [Citation(s) in RCA: 58] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Accepted: 02/16/2020] [Indexed: 12/03/2022] Open
Abstract
Eukaryotic topoisomerase 1 (TOP1) regulates DNA topology to ensure efficient DNA replication and transcription. TOP1 is also a major driver of endogenous genome instability, particularly when its catalytic intermediate-a covalent TOP1-DNA adduct known as a TOP1 cleavage complex (TOP1cc)-is stabilised. TOP1ccs are highly cytotoxic and a failure to resolve them underlies the pathology of neurological disorders but is also exploited in cancer therapy where TOP1ccs are the target of widely used frontline anti-cancer drugs. A critical enzyme for TOP1cc resolution is the tyrosyl-DNA phosphodiesterase (TDP1), which hydrolyses the bond that links a tyrosine in the active site of TOP1 to a 3' phosphate group on a single-stranded (ss)DNA break. However, TDP1 can only process small peptide fragments from ssDNA ends, raising the question of how the ~90 kDa TOP1 protein is processed upstream of TDP1. Here we find that TEX264 fulfils this role by forming a complex with the p97 ATPase and the SPRTN metalloprotease. We show that TEX264 recognises both unmodified and SUMO1-modifed TOP1 and initiates TOP1cc repair by recruiting p97 and SPRTN. TEX264 localises to the nuclear periphery, associates with DNA replication forks, and counteracts TOP1ccs during DNA replication. Altogether, our study elucidates the existence of a specialised repair complex required for upstream proteolysis of TOP1ccs and their subsequent resolution.
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Affiliation(s)
- John Fielden
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Katherine Wiseman
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Ignacio Torrecilla
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Shudong Li
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Samuel Hume
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Shih-Chieh Chiang
- The University of Sheffield Neuroscience Institute and the Healthy Lifespan Institute, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
| | - Annamaria Ruggiano
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Abhay Narayan Singh
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Raimundo Freire
- Unidad de Investigación, Hospital Universitario de Canarias, Ofra s/n, La Cuesta, 38320, La Laguna, Tenerife, Spain
- Instituto de Tecnologías Biomédicas, Universidad de La Laguna, 38200, La Laguna, Tenerife, Spain
- Universidad Fernando Pessoa Canarias, 35450, Las Palmas de Gran Canaria, Spain
| | - Sylvana Hassanieh
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Enric Domingo
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Iolanda Vendrell
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Roman Fischer
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Benedikt M Kessler
- TDI Mass Spectrometry Laboratory, Target Discovery Institute, Nuffield Department of Medicine, University of Oxford, Oxford, UK
| | - Timothy S Maughan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK
| | - Sherif F El-Khamisy
- The University of Sheffield Neuroscience Institute and the Healthy Lifespan Institute, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN, Sheffield, UK
| | - Kristijan Ramadan
- Cancer Research UK and Medical Research Council Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, OX3 7DQ, UK.
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25
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Gmeiner WH. Entrapment of DNA topoisomerase-DNA complexes by nucleotide/nucleoside analogs. CANCER DRUG RESISTANCE (ALHAMBRA, CALIF.) 2019; 2:994-1001. [PMID: 31930190 PMCID: PMC6953902 DOI: 10.20517/cdr.2019.95] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/12/2019] [Revised: 11/22/2019] [Accepted: 11/29/2019] [Indexed: 06/10/2023]
Abstract
Topoisomerases are well-validated targets for cancer chemotherapy and DNA topoisomerase 1 (Top1) is the sole target of the camptothecin (CPT) class of anticancer drugs. Over the last 20 years, multiple studies have shown Top1 activity is modulated by non-native DNA structures and this can lead to trapping of Top1 cleavage complexes (Top1cc) and conversion to DNA double strand breaks. Among the perturbations to DNA structure that generate Top1cc are nucleoside analogs that are incorporated into genomic DNA during replication including cytarabine, gemcitabine, and 5-fluoro-2'-deoxyuridine (FdU). We review the literature summarizing the role of Top1cc in mediating the DNA damaging and cytotoxic activities of nucleoside analogs. We also summarize studies demonstrating distinct differences between Top1cc induced by nucleoside analogs and CPTs, particularly with regard to DNA repair. Collectively, these studies demonstrate that, while Top1 is a common target for both Top1 poisons such as CPT and nucleoside analogs such as FdU, these agents are not redundant. In recent years, studies have shown that Top1 poisons and nucleoside analogs together with other anti-cancer drugs such as cisplatin cause replication stress and the DNA repair pathways that modulate the cytotoxic activities of these compounds are being elucidated. We present an overview of this evolving literature, which has implications for how targeting of Top1 with nucleoside analogs can be used more effectively for cancer treatment.
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Affiliation(s)
- William H. Gmeiner
- Department of Cancer Biology, Wake Forest School of Medicine, Winston-Salem, NC 27157, USA
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26
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Srivastava M, Chen Z, Zhang H, Tang M, Wang C, Jung SY, Chen J. Replisome Dynamics and Their Functional Relevance upon DNA Damage through the PCNA Interactome. Cell Rep 2019; 25:3869-3883.e4. [PMID: 30590055 PMCID: PMC6364303 DOI: 10.1016/j.celrep.2018.11.099] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 10/09/2018] [Accepted: 11/28/2018] [Indexed: 12/19/2022] Open
Abstract
Eukaryotic cells use copious measures to ensure accurate duplication of the genome. Various genotoxic agents pose threats to the ongoing replication fork that, if not efficiently dealt with, can result in replication fork collapse. It is unknown how replication fork is precisely controlled and regulated under different conditions. Here, we examined the complexity of replication fork composition upon DNA damage by using a PCNA-based proteomic screen to uncover known and unexplored players involved in replication and replication stress response. We used camptothecin or UV radiation, which lead to fork-blocking lesions, to establish a comprehensive proteomics map of the replisome under such replication stress conditions. We identified and examined two potential candidate proteins WIZ and SALL1 for their roles in DNA replication and replication stress response. In addition, our unbiased screen uncovered many prospective candidate proteins that help fill the knowledge gap in understanding chromosomal DNA replication and DNA repair.
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Affiliation(s)
- Mrinal Srivastava
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Zhen Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Huimin Zhang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Mengfan Tang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Chao Wang
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Sung Yun Jung
- Department of Molecular and Cellular Biology, Baylor College of Medicine, Houston, TX 77030, USA
| | - Junjie Chen
- Department of Experimental Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA.
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27
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Abstract
DNA topoisomerases are enzymes that catalyze changes in the torsional and flexural strain of DNA molecules. Earlier studies implicated these enzymes in a variety of processes in both prokaryotes and eukaryotes, including DNA replication, transcription, recombination, and chromosome segregation. Studies performed over the past 3 years have provided new insight into the roles of various topoisomerases in maintaining eukaryotic chromosome structure and facilitating the decatenation of daughter chromosomes at cell division. In addition, recent studies have demonstrated that the incorporation of ribonucleotides into DNA results in trapping of topoisomerase I (TOP1)–DNA covalent complexes during aborted ribonucleotide removal. Importantly, such trapped TOP1–DNA covalent complexes, formed either during ribonucleotide removal or as a consequence of drug action, activate several repair processes, including processes involving the recently described nuclear proteases SPARTAN and GCNA-1. A variety of new TOP1 inhibitors and formulations, including antibody–drug conjugates and PEGylated complexes, exert their anticancer effects by also trapping these TOP1–DNA covalent complexes. Here we review recent developments and identify further questions raised by these new findings.
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Affiliation(s)
- Mary-Ann Bjornsti
- Department of Pharmacology and Toxicology, University of Alabama at Birmingham, Birmingham, AL, 35294-0019, USA
| | - Scott H Kaufmann
- Departments of Oncology and Molecular Pharmacolgy & Experimental Therapeutics, Mayo Clinic, Rochester, MN, 55905, USA
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28
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Gutiérrez-Corbo C, Álvarez-Velilla R, Reguera RM, García-Estrada C, Cushman M, Balaña-Fouce R, Pérez-Pertejo Y. Topoisomerase IB poisons induce histone H2A phosphorylation as a response to DNA damage in Leishmania infantum. INTERNATIONAL JOURNAL FOR PARASITOLOGY-DRUGS AND DRUG RESISTANCE 2019; 11:39-48. [PMID: 31563118 PMCID: PMC6796659 DOI: 10.1016/j.ijpddr.2019.09.005] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/28/2019] [Revised: 09/16/2019] [Accepted: 09/17/2019] [Indexed: 02/07/2023]
Abstract
DNA topoisomerases are considered consolidated druggable targets against diseases produced by trypanosomatids. Several reports indicated that indenoisoquinolines, a family of non-camptothecinic based topoisomerase poisons, have a strong leishmanicidal effect both in vitro and in vivo in murine models of visceral leishmaniasis. The antileishmanial effect of the indenoisoquinolines implies several mechanisms that include the stabilization of the cleavage complex, histone H2A phosphorylation and DNA fragmentation. A series of 20 compounds with the indenoisoquinoline scaffold and several substituents at positions N6, C3, C8 and C9, were tested both in promastigotes and in intramacrophage splenic amastigotes obtained from an experimental murine infection. The antileishmanial effect of most of these compounds was within the micromolar or submicromolar range. In addition, the introduction of an N atom in the indenoisoquinoline ring (7-azaindenoisoquinolines) produced the highest selectivity index along with strong DNA topoisomerase IB inhibition, histone H2A phosphorylation and DNA-topoisomerase IB complex stabilization. This report shows for the first time the effect of a series of synthetic indenoisoquinolines on histone H2A phosphorylation, which represents a primary signal of double stranded DNA break in genus Leishmania. N-6 indenoisoquinoline derivatives show strong antileishmanial activity. Indenoisoquinolines arrest Leishmania cell-cycle in S phase. Inhibition of leishmanial TopIB by indenoisoquinolines induces DNA fragmentation. Leishmanial H2A histone is phosphorylated at the Thr128 in response to DNA damage.
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Affiliation(s)
- Camino Gutiérrez-Corbo
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana S/n, 24071, León, Spain
| | - Raquel Álvarez-Velilla
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana S/n, 24071, León, Spain
| | - Rosa M Reguera
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana S/n, 24071, León, Spain
| | - Carlos García-Estrada
- INBIOTEC (Instituto de Biotecnología de León), Avda. Real 1 - Parque Científico de León, 24006, León, Spain
| | - Mark Cushman
- Department of Medicinal Chemistry, and Molecular Pharmacology, College of Pharmacy, The Purdue Center for Cancer Research, Purdue University, Lafayette, IN, USA
| | - Rafael Balaña-Fouce
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana S/n, 24071, León, Spain
| | - Yolanda Pérez-Pertejo
- Departamento de Ciencias Biomédicas, Universidad de León, Campus de Vegazana S/n, 24071, León, Spain.
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Riedlinger T, Bartkuhn M, Zimmermann T, Hake SB, Nist A, Stiewe T, Kracht M, Schmitz ML. Chemotherapeutic Drugs Inhibiting Topoisomerase 1 Activity Impede Cytokine-Induced and NF-κB p65-Regulated Gene Expression. Cancers (Basel) 2019; 11:cancers11060883. [PMID: 31242600 PMCID: PMC6627772 DOI: 10.3390/cancers11060883] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 06/18/2019] [Accepted: 06/20/2019] [Indexed: 02/03/2023] Open
Abstract
Inhibitors of DNA topoisomerase I (TOP1), an enzyme relieving torsional stress of DNA by generating transient single-strand breaks, are clinically used to treat ovarian, small cell lung and cervical cancer. As torsional stress is generated during transcription by progression of RNA polymerase II through the transcribed gene, we tested the effects of camptothecin and of the approved TOP1 inhibitors Topotecan and SN-38 on TNFα-induced gene expression. RNA-seq experiments showed that inhibition of TOP1 but not of TOP2 activity suppressed the vast majority of TNFα-triggered genes. The TOP1 effects were fully reversible and preferentially affected long genes. TNFα stimulation led to inducible recruitment of TOP1 to the gene body of IL8, where its inhibition by camptothecin reduced transcription elongation and also led to altered histone H3 acetylation. Together, these data show that TOP1 inhibitors potently suppress expression of proinflammatory cytokines, a feature that may contribute to the increased infection risk occurring in tumor patients treated with these agents. On the other hand, TOP1 inhibitors could also be considered as a therapeutic option in order to interfere with exaggerated cytokine expression seen in several inflammatory diseases.
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Affiliation(s)
- Tabea Riedlinger
- Institute of Biochemistry, Justus Liebig University, D-35392 Giessen, Germany.
| | - Marek Bartkuhn
- Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany.
| | - Tobias Zimmermann
- Bioinformatics and Systems Biology, University of Giessen, Heinrich-Buff-Ring 58-62, 35392 Giessen, Germany.
| | - Sandra B Hake
- Institute for Genetics, Justus-Liebig University Giessen, 35392 Giessen, Germany.
| | - Andrea Nist
- Genomics Core Facility and Institute of Molecular Oncology, Philipps University Marburg, D-35043 Marburg, Germany.
| | - Thorsten Stiewe
- Genomics Core Facility and Institute of Molecular Oncology, Philipps University Marburg, D-35043 Marburg, Germany.
| | - Michael Kracht
- Rudolf-Buchheim-Institute of Pharmacology, Justus Liebig University, D-35392 Giessen, Germany.
| | - M Lienhard Schmitz
- Institute of Biochemistry, Justus Liebig University, D-35392 Giessen, Germany.
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30
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Ji Y, Dang X, Nguyen LNT, Nguyen LN, Zhao J, Cao D, Khanal S, Schank M, Wu XY, Morrison ZD, Zou Y, El Gazzar M, Ning S, Wang L, Moorman JP, Yao ZQ. Topological DNA damage, telomere attrition and T cell senescence during chronic viral infections. Immun Ageing 2019; 16:12. [PMID: 31285747 PMCID: PMC6591813 DOI: 10.1186/s12979-019-0153-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2019] [Accepted: 06/18/2019] [Indexed: 12/24/2022]
Abstract
BACKGROUND T cells play a key role in controlling viral infections; however, the underlying mechanisms regulating their functions during human viral infections remain incompletely understood. Here, we used CD4 T cells derived from individuals with chronic viral infections or healthy T cells treated with camptothecin (CPT) - a topoisomerase I (Top 1) inhibitor - as a model to investigate the role of DNA topology in reprogramming telomeric DNA damage responses (DDR) and remodeling T cell functions. RESULTS We demonstrated that Top 1 protein expression and enzyme activity were significantly inhibited, while the Top 1 cleavage complex (TOP1cc) was trapped in genomic DNA, in T cells derived from individuals with chronic viral (HCV, HBV, or HIV) infections. Top 1 inhibition by CPT treatment of healthy CD4 T cells caused topological DNA damage, telomere attrition, and T cell apoptosis or dysfunction via inducing Top1cc accumulation, PARP1 cleavage, and failure in DNA repair, thus recapitulating T cell dysregulation in the setting of chronic viral infections. Moreover, T cells from virally infected subjects with inhibited Top 1 activity were more vulnerable to CPT-induced topological DNA damage and cell apoptosis, indicating an important role for Top 1 in securing DNA integrity and cell survival. CONCLUSION These findings provide novel insights into the molecular mechanisms for immunomodulation by chronic viral infections via disrupting DNA topology to induce telomeric DNA damage, T cell senescence, apoptosis and dysfunction. As such, restoring the impaired DNA topologic machinery may offer a new strategy for maintaining T cell function against human viral diseases.
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Affiliation(s)
- Yingjie Ji
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Center of Cadre Health Care, The Fifth Medical Center of PLA General Hospital, Being, 100000 China
| | - Xindi Dang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
| | - Lam Ngoc Thao Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
| | - Lam Nhat Nguyen
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
| | - Juan Zhao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
| | - Dechao Cao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
| | - Sushant Khanal
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
| | - Madison Schank
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
| | - Xiao Y. Wu
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
| | - Zheng D. Morrison
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
| | - Yue Zou
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
| | - Mohamed El Gazzar
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
| | - Shunbin Ning
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
| | - Ling Wang
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
| | - Jonathan P. Moorman
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614 USA
| | - Zhi Q. Yao
- Center of Excellence in Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson City, TN 37614 USA
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, ETSU, Johnson City, TN 37614 USA
- Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Department of Veterans Affairs, Johnson City, TN 37614 USA
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31
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Cao D, Zhao J, Nguyan LN, Nguyen LNT, Khanal S, Dang X, Schank M, Chand Thakuri BK, Wu XY, Morrison ZD, El Gazzar M, Zou Y, Ning S, Wang L, Moorman JP, Yao ZQ. Disruption of Telomere Integrity and DNA Repair Machineries by KML001 Induces T Cell Senescence, Apoptosis, and Cellular Dysfunctions. Front Immunol 2019; 10:1152. [PMID: 31191531 PMCID: PMC6540964 DOI: 10.3389/fimmu.2019.01152] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2019] [Accepted: 05/07/2019] [Indexed: 12/27/2022] Open
Abstract
T cells in chronic viral infections are featured by premature aging with accelerated telomere erosion, but the mechanisms underlying telomere attrition remain unclear. Here, we employed human CD4 T cells treated with KML001 (a telomere-targeting drug) as a model to investigate the role of telomere integrity in remodeling T cell senescence. We demonstrated that KML001 could inhibit cell proliferation, cytokine production, and promote apoptosis via disrupting telomere integrity and DNA repair machineries. Specifically, KML001-treated T cells increased dysfunctional telomere-induced foci (TIF), DNA damage marker γH2AX, and topoisomerase cleavage complex (TOPcc) accumulation, leading to telomere attrition. Mechanistically, KML001 compromised telomere integrity by inhibiting telomeric repeat binding factor 2 (TRF2), telomerase, topoisomerase I and II alpha (Top1/2a), and ataxia telangiectasia mutated (ATM) kinase activities. Importantly, these KML001-induced telomeric DNA damage and T cell senescent phenotype and machineries recapitulated our findings in patients with clinical HCV or HIV infection in that their T cells were also senescent with short telomeres and thus more vulnerable to KML001-induced apoptosis. These results shed new insights on the T cell aging network that is critical and essential in protecting chromosomal telomeres from unwanted DNA damage and securing T cell survival during cell crisis upon genomic insult.
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Affiliation(s)
- Dechao Cao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Juan Zhao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Lam N. Nguyan
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Lam N. T. Nguyen
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Sushant Khanal
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Xindi Dang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Madison Schank
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Bal K. Chand Thakuri
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Xiao Y. Wu
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Zheng D. Morrison
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Mohamed El Gazzar
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Yue Zou
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Shunbin Ning
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Ling Wang
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
| | - Jonathan P. Moorman
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Department of Veterans Affairs, Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Johnson, TN, United States
| | - Zhi Q. Yao
- Center of Excellence for Inflammation, Infectious Disease and Immunity, James H. Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Division of Infectious, Inflammatory and Immunologic Diseases, Department of Internal Medicine, Quillen College of Medicine, East Tennessee State University, Johnson, TN, United States
- Department of Veterans Affairs, Hepatitis (HCV/HBV/HIV) Program, James H. Quillen VA Medical Center, Johnson, TN, United States
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32
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Ahmed SM, Ramani PD, Wong SQR, Zhao X, Ivanyi-Nagy R, Leong TC, Chua C, Li Z, Hentze H, Tan IB, Yan J, DasGupta R, Dröge P. The chromatin structuring protein HMGA2 influences human subtelomere stability and cancer chemosensitivity. PLoS One 2019; 14:e0215696. [PMID: 31067275 PMCID: PMC6505889 DOI: 10.1371/journal.pone.0215696] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/05/2019] [Indexed: 12/31/2022] Open
Abstract
The transient build-up of DNA supercoiling during the translocation of replication forks threatens genome stability and is controlled by DNA topoisomerases (TOPs). This crucial process has been exploited with TOP poisons for cancer chemotherapy. However, pinpointing cellular determinants of the best clinical response to TOP poisons still remains enigmatic. Here, we present an integrated approach and demonstrate that endogenous and exogenous expression of the oncofetal high-mobility group AT-hook 2 (HMGA2) protein exhibited broad protection against the formation of hydroxyurea-induced DNA breaks in various cancer cells, thus corroborating our previously proposed model in which HMGA2 functions as a replication fork chaperone that forms a protective DNA scaffold at or close to stalled replication forks. We now further demonstrate that high levels of HMGA2 also protected cancer cells against DNA breaks triggered by the clinically important TOP1 poison irinotecan. This protection is most likely due to the recently identified DNA supercoil constraining function of HMGA2 in combination with exclusion of TOP1 from binding to supercoiled substrate DNA. In contrast, low to moderate HMGA2 protein levels surprisingly potentiated the formation of irinotecan-induced genotoxic covalent TOP1-DNA cleavage complexes. Our data from cell-based and several in vitro assays indicate that, mechanistically, this potentiating role involves enhanced drug-target interactions mediated by HMGA2 in ternary complexes with supercoiled DNA. Subtelomeric regions were found to be extraordinarily vulnerable to these genotoxic challenges induced by TOP1 poisoning, pointing at strong DNA topological barriers located at human telomeres. These findings were corroborated by an increased irinotecan sensitivity of patient-derived xenografts of colorectal cancers exhibiting low to moderate HMGA2 levels. Collectively, we uncovered a therapeutically important control mechanism of transient changes in chromosomal DNA topology that ultimately leads to enhanced human subtelomere stability.
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Affiliation(s)
- Syed Moiz Ahmed
- School of Biological Sciences, Nanyang Technological University, Singapore
| | | | - Stephen Qi Rong Wong
- Biological Resource Centre, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Xiaodan Zhao
- Mechanobiology Institute, National University of Singapore, Singapore
| | - Roland Ivanyi-Nagy
- School of Biological Sciences, Nanyang Technological University, Singapore
| | - Tang Choong Leong
- Department of Colorectal Surgery, Singapore General Hospital, Singapore
| | - Clarinda Chua
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, Singapore
| | - Zhizhong Li
- Genomics Institute of the Novartis Research Foundation, San Diego, California, United States of America
| | - Hannes Hentze
- Biological Resource Centre, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Iain BeeHuat Tan
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
- National Cancer Centre Singapore, Cancer Therapeutics Research Laboratory, Singapore
| | - Jie Yan
- Mechanobiology Institute, National University of Singapore, Singapore
- Graduate School for Integrative Sciences and Engineering, National University of Singapore, Singapore
- Centre for Bioimaging Sciences, National University of Singapore, Singapore
- Department of Physics, National University of Singapore, Singapore
| | - Ramanuj DasGupta
- Genome Institute of Singapore, Agency for Science, Technology and Research (A*STAR), Singapore
| | - Peter Dröge
- School of Biological Sciences, Nanyang Technological University, Singapore
- Nanyang Institute of Structural Biology, Nanyang Technological University, Singapore
- * E-mail:
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33
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Mouly L, Mamouni K, Gence R, Cristini A, Cherier J, Castinel A, Legrand M, Favre G, Sordet O, Monferran S. PARP-1-dependent RND1 transcription induced by topoisomerase I cleavage complexes confers cellular resistance to camptothecin. Cell Death Dis 2018; 9:931. [PMID: 30209297 PMCID: PMC6135836 DOI: 10.1038/s41419-018-0981-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Revised: 08/02/2018] [Accepted: 08/20/2018] [Indexed: 02/02/2023]
Abstract
RHO GTPases regulate essential functions such as the organization of the actin cytoskeleton. The classic members cycle between an active GTP-bound and an inactive GDP-bound conformation whereas atypical members are predominantly GTP-bound. Besides their well-established role, the classic RHO GTPases RHOB and RAC1, are rapidly induced and/or activated by genotoxic stress and contribute to the DNA damage response. Here we used camptothecin, a selective topoisomerase I (TOP1) inhibitor that stabilizes TOP1 cleavage complexes (TOP1cc), to search for other potential early DNA damage-inducible RHO GTPase genes. We identified that an atypical RHO GTPase, RND1, is rapidly induced by camptothecin. RND1 induction is closely associated with the presence of TOP1cc induced by camptothecin or by DNA lesions that elevate TOP1cc levels such as UV and hydrogen peroxide. We further demonstrated that camptothecin increases RND1 gene transcription and mRNA stability. Camptothecin also increases poly(ADP-ribose) polymerase 1 (PARP-1) activity, whose inhibition reduces RND1 transcription. In addition, overexpression of RND1 increases PARP-1, suggesting a cross-talk between PARP-1 and RND1. Finally, RND1 protects cells against camptothecin-induced apoptosis, and hence favors cellular resistance to camptothecin. Together, these findings highlight RND1 as an atypical RHO GTPase early induced by TOP1cc, and show that the TOP1cc-PARP-1-RND1 pathway protects cells against apoptosis induced by camptothecin.
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Affiliation(s)
- Laetitia Mouly
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France.,Faculté des Sciences Pharmaceutiques, Université de Toulouse, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Kenza Mamouni
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France.,Faculté des Sciences Pharmaceutiques, Université de Toulouse, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Remi Gence
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France.,Faculté des Sciences Pharmaceutiques, Université de Toulouse, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Agnese Cristini
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France.,Faculté des Sciences Pharmaceutiques, Université de Toulouse, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Julia Cherier
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France
| | - Adrien Castinel
- Faculté des Sciences Pharmaceutiques, Université de Toulouse, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Morgane Legrand
- Faculté des Sciences Pharmaceutiques, Université de Toulouse, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Gilles Favre
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France.,Faculté des Sciences Pharmaceutiques, Université de Toulouse, Université Toulouse III Paul Sabatier, Toulouse, France
| | - Olivier Sordet
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France.
| | - Sylvie Monferran
- Cancer Research Center of Toulouse (CRCT), INSERM, Université de Toulouse, Université Toulouse III Paul Sabatier, CNRS, Toulouse, France. .,Faculté des Sciences Pharmaceutiques, Université de Toulouse, Université Toulouse III Paul Sabatier, Toulouse, France.
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34
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Perkins AL, Peterson KL, Beito TG, Flatten KS, Kaufmann SH, Harki DA. Synthesis of a peptide-universal nucleotide antigen: towards next-generation antibodies to detect topoisomerase I-DNA covalent complexes. Org Biomol Chem 2018; 14:4103-9. [PMID: 27113574 DOI: 10.1039/c5ob02049b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The topoisomerase (topo) I-DNA covalent complex represents an attractive target for developing diagnostic antibodies to measure responsiveness to drugs. We report a new antigen, peptide , and four murine monoclonal antibodies raised against that exhibit excellent specificity for recognition of in comparison to structurally similar peptides by enzyme-linked immunosorbent assays. Although topo I-DNA complex detection was not achieved in cellular samples by these new antibodies, a new strategy for antigen design is reported.
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Affiliation(s)
- Angela L Perkins
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th Street SE, Minneapolis, MN 55455, USA.
| | - Kevin L Peterson
- Division of Oncology Research, Mayo Clinic, 200 First St., S.W., Rochester, MN 55905, USA
| | - Thomas G Beito
- Monoclonal Antibody Core, Mayo Clinic, 200 First St., S.W., Rochester, MN 55905, USA
| | - Karen S Flatten
- Division of Oncology Research, Mayo Clinic, 200 First St., S.W., Rochester, MN 55905, USA
| | - Scott H Kaufmann
- Division of Oncology Research, Mayo Clinic, 200 First St., S.W., Rochester, MN 55905, USA
| | - Daniel A Harki
- Department of Medicinal Chemistry, University of Minnesota, 2231 6th Street SE, Minneapolis, MN 55455, USA.
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35
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Maskey RS, Flatten KS, Sieben CJ, Peterson KL, Baker DJ, Nam HJ, Kim MS, Smyrk TC, Kojima Y, Machida Y, Santiago A, van Deursen JM, Kaufmann SH, Machida YJ. Spartan deficiency causes accumulation of Topoisomerase 1 cleavage complexes and tumorigenesis. Nucleic Acids Res 2017; 45:4564-4576. [PMID: 28199696 PMCID: PMC5416836 DOI: 10.1093/nar/gkx107] [Citation(s) in RCA: 79] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2016] [Accepted: 02/06/2017] [Indexed: 11/30/2022] Open
Abstract
Germline mutations in SPRTN cause Ruijs–Aalfs syndrome (RJALS), a disorder characterized by genome instability, progeria and early onset hepatocellular carcinoma. Spartan, the protein encoded by SPRTN, is a nuclear metalloprotease that is involved in the repair of DNA–protein crosslinks (DPCs). Although Sprtn hypomorphic mice recapitulate key progeroid phenotypes of RJALS, whether this model expressing low amounts of Spartan is prone to DPC repair defects and spontaneous tumors is unknown. Here, we showed that the livers of Sprtn hypomorphic mice accumulate DPCs containing Topoisomerase 1 covalently linked to DNA. Furthermore, these mice exhibited DNA damage, aneuploidy and spontaneous tumorigenesis in the liver. Collectively, these findings provide evidence that partial loss of Spartan impairs DPC repair and tumor suppression.
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Affiliation(s)
- Reeja S Maskey
- Department of Oncology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Karen S Flatten
- Department of Oncology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Cynthia J Sieben
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Kevin L Peterson
- Department of Oncology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Darren J Baker
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Hyun-Ja Nam
- Department of Pediatric and Adolescent Medicine, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Myoung Shin Kim
- Department of Oncology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Thomas C Smyrk
- Department of Laboratory Medicine and Pathology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Yusuke Kojima
- Department of Oncology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Yuka Machida
- Department of Oncology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Annyoceli Santiago
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Jan M van Deursen
- Department of Biochemistry and Molecular Biology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Scott H Kaufmann
- Department of Oncology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
| | - Yuichi J Machida
- Department of Oncology, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA.,Department of Molecular Pharmacology and Experimental Therapeutics, Mayo Clinic, 200 First St. SW, Rochester, MN 55905, USA
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36
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Chiang SC, Meagher M, Kassouf N, Hafezparast M, McKinnon PJ, Haywood R, El-Khamisy SF. Mitochondrial protein-linked DNA breaks perturb mitochondrial gene transcription and trigger free radical-induced DNA damage. SCIENCE ADVANCES 2017; 3:e1602506. [PMID: 28508041 PMCID: PMC5409496 DOI: 10.1126/sciadv.1602506] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 03/02/2017] [Indexed: 05/06/2023]
Abstract
Breakage of one strand of DNA is the most common form of DNA damage. Most damaged DNA termini require end-processing in preparation for ligation. The importance of this step is highlighted by the association of defects in the 3'-end processing enzyme tyrosyl DNA phosphodiesterase 1 (TDP1) and neurodegeneration and by the cytotoxic induction of protein-linked DNA breaks (PDBs) and oxidized nucleic acid intermediates during chemotherapy and radiotherapy. Although much is known about the repair of PDBs in the nucleus, little is known about this process in the mitochondria. We reveal that TDP1 resolves mitochondrial PDBs (mtPDBs), thereby promoting mitochondrial gene transcription. Overexpression of a toxic form of mitochondrial topoisomerase I (TOP1mt*), which generates excessive mtPDBs, results in a TDP1-dependent compensatory up-regulation of mitochondrial gene transcription. In the absence of TDP1, the imbalance in transcription of mitochondrial- and nuclear-encoded electron transport chain (ETC) subunits results in misassembly of ETC complex III. Bioenergetics profiling further reveals that TDP1 promotes oxidative phosphorylation under both basal and high energy demands. It is known that mitochondrial dysfunction results in free radical leakage and nuclear DNA damage; however, the detection of intermediates of radical damage to DNA is yet to be shown. Consequently, we report an increased accumulation of carbon-centered radicals in cells lacking TDP1, using electron spin resonance spectroscopy. Overexpression of the antioxidant enzyme superoxide dismutase 1 (SOD1) reduces carbon-centered adducts and protects TDP1-deficient cells from oxidative stress. Conversely, overexpression of the amyotrophic lateral sclerosis-associated mutant SOD1G93A leads to marked sensitivity. Whereas Tdp1 knockout mice develop normally, overexpression of SOD1G93A suggests early embryonic lethality. Together, our data show that TDP1 resolves mtPDBs, thereby regulating mitochondrial gene transcription and oxygen consumption by oxidative phosphorylation, thus conferring cellular protection against reactive oxygen species-induced damage.
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Affiliation(s)
- Shih-Chieh Chiang
- Krebs Institute and Sheffield Institute for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN Sheffield, U.K
| | - Martin Meagher
- Wellcome Trust Centre for Mitochondrial Research, Medical School, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, U.K
| | - Nick Kassouf
- RAFT Institute, Mount Vernon Hospital, Northwood, Middlesex HA6 2RN, U.K
| | - Majid Hafezparast
- School of Life Sciences, University of Sussex, Brighton BN1 9QG, U.K
| | - Peter J. McKinnon
- Department of Genetics, St. Jude Children’s Research Hospital, Memphis, TN 38105–3678, USA
| | - Rachel Haywood
- RAFT Institute, Mount Vernon Hospital, Northwood, Middlesex HA6 2RN, U.K
| | - Sherif F. El-Khamisy
- Krebs Institute and Sheffield Institute for Nucleic Acids, Department of Molecular Biology and Biotechnology, Firth Court, University of Sheffield, S10 2TN Sheffield, U.K
- Center for Genomics, Helmy Institute for Medical Sciences, Zewail City of Science and Technology, Giza 12588, Egypt
- Corresponding author.
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37
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Vindigni A, Lopes M. Combining electron microscopy with single molecule DNA fiber approaches to study DNA replication dynamics. Biophys Chem 2016; 225:3-9. [PMID: 27939387 DOI: 10.1016/j.bpc.2016.11.014] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2016] [Revised: 11/30/2016] [Accepted: 11/30/2016] [Indexed: 10/20/2022]
Abstract
Replication stress is a crucial driver of genomic instability. Understanding the mechanisms of replication stress response is instrumental to improve diagnosis and treatment of human disease. Electron microscopy (EM) is currently the technique of choice to directly visualize a high number of replication intermediates and to monitor their remodeling upon stress. At the same time, DNA fiber analysis is useful to gain mechanistic insight on how genotoxic agents perturb replication fork dynamics genome-wide at single-molecule resolution. Combining these techniques has proven invaluable to achieve a comprehensive view of the mechanisms that ensure error-free processing of damaged replication forks. Here, we review how EM and single-molecule DNA fiber approaches can be used together to shed light into the mechanisms of replication stress response and discuss important cautions to be taken into account when comparing results obtained by EM and DNA fiber.
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Affiliation(s)
- Alessandro Vindigni
- Department of Biochemistry and Molecular Biology, Saint Louis University School of Medicine, St. Louis, MO 63104, USA.
| | - Massimo Lopes
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland.
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38
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de Campos-Nebel M, Palmitelli M, González-Cid M. A flow cytometry-based method for a high-throughput analysis of drug-stabilized topoisomerase II cleavage complexes in human cells. Cytometry A 2016; 89:852-60. [PMID: 27517472 DOI: 10.1002/cyto.a.22919] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2016] [Revised: 06/27/2016] [Accepted: 07/15/2016] [Indexed: 11/08/2022]
Abstract
Topoisomerase II (Top2) is an important target for anticancer therapy. A variety of drugs that poison Top2, including several epipodophyllotoxins, anthracyclines, and anthracenediones, are widely used in the clinic for both hematologic and solid tumors. The poisoning of Top2 involves the formation of a reaction intermediate Top2-DNA, termed Top2 cleavage complex (Top2cc), which is persistent in the presence of the drug and involves a 5' end of DNA covalently bound to a tyrosine from the enzyme through a phosphodiester group. Drug-induced Top2cc leads to Top2 linked-DNA breaks which are the major responsible for their cytotoxicity. While biochemical detection is very laborious, quantification of drug-induced Top2cc by immunofluorescence-based microscopy techniques is time consuming and requires extensive image segmentation for the analysis of a small population of cells. Here, we developed a flow cytometry-based method for the analysis of drug-induced Top2cc. This method allows a rapid analysis of a high number of cells in their cell cycle phase context. Moreover, it can be applied to almost any human cell type, including clinical samples. The methodology is useful for a high-throughput analysis of drugs that poison Top2, allowing not just the discrimination of the Top2 isoform that is targeted but also to track its removal. © 2016 International Society for Advancement of Cytometry.
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Affiliation(s)
- Marcelo de Campos-Nebel
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET, Buenos Aires, Argentina.
| | - Micaela Palmitelli
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET, Buenos Aires, Argentina
| | - Marcela González-Cid
- Laboratorio de Mutagénesis, Instituto de Medicina Experimental (IMEX), Academia Nacional de Medicina, CONICET, Buenos Aires, Argentina
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39
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Mabb AM, Simon JM, King IF, Lee HM, An LK, Philpot BD, Zylka MJ. Topoisomerase 1 Regulates Gene Expression in Neurons through Cleavage Complex-Dependent and -Independent Mechanisms. PLoS One 2016; 11:e0156439. [PMID: 27231886 PMCID: PMC4883752 DOI: 10.1371/journal.pone.0156439] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2016] [Accepted: 05/14/2016] [Indexed: 11/19/2022] Open
Abstract
Topoisomerase 1 (TOP1) inhibitors, including camptothecin and topotecan, covalently trap TOP1 on DNA, creating cleavage complexes (cc's) that must be resolved before gene transcription and DNA replication can proceed. We previously found that topotecan reduces the expression of long (>100 kb) genes and unsilences the paternal allele of Ube3a in neurons. Here, we sought to evaluate overlap between TOP1cc-dependent and -independent gene regulation in neurons. To do this, we utilized Top1 conditional knockout mice, Top1 knockdown, the CRISPR-Cas9 system to delete Top1, TOP1 catalytic inhibitors that do not generate TOP1cc's, and a TOP1 mutation (T718A) that stabilizes TOP1cc's. We found that topotecan treatment significantly alters the expression of many more genes, including long neuronal genes, immediate early genes, and paternal Ube3a, when compared to Top1 deletion. Our data show that topotecan has a stronger effect on neuronal transcription than Top1 deletion, and identifies TOP1cc-dependent and -independent contributions to gene expression.
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Affiliation(s)
- Angela M. Mabb
- Department of Cell Biology and Physiology, UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, The University of North Carolina, Chapel Hill, North Carolina, United States of America
- Neuroscience Institute, Georgia State University, Atlanta, Georgia, United States of America
| | - Jeremy M. Simon
- Department of Cell Biology and Physiology, UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, The University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Ian F. King
- Department of Cell Biology and Physiology, UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, The University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Hyeong-Min Lee
- Department of Cell Biology and Physiology, UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, The University of North Carolina, Chapel Hill, North Carolina, United States of America
| | - Lin-Kun An
- School of Pharmaceutical Sciences, Sun Yat-sen University, Guangzhou, China
| | - Benjamin D. Philpot
- Department of Cell Biology and Physiology, UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, The University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail: (BDP); (MJK)
| | - Mark J. Zylka
- Department of Cell Biology and Physiology, UNC Neuroscience Center, Carolina Institute for Developmental Disabilities, The University of North Carolina, Chapel Hill, North Carolina, United States of America
- * E-mail: (BDP); (MJK)
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