1
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Weilbeer C, Jay D, Donnelly JC, Gentile F, Karimi-Busheri F, Yang X, Mani RS, Yu Y, Elmenoufy AH, Barakat KH, Tuszynski JA, Weinfeld M, West FG. Modulation of ERCC1-XPF Heterodimerization Inhibition via Structural Modification of Small Molecule Inhibitor Side-Chains. Front Oncol 2022; 12:819172. [PMID: 35372043 PMCID: PMC8968952 DOI: 10.3389/fonc.2022.819172] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2021] [Accepted: 01/28/2022] [Indexed: 12/02/2022] Open
Abstract
Inhibition of DNA repair enzymes is an attractive target for increasing the efficacy of DNA damaging chemotherapies. The ERCC1-XPF heterodimer is a key endonuclease in numerous single and double strand break repair processes, and inhibition of the heterodimerization has previously been shown to sensitize cancer cells to DNA damage. In this work, the previously reported ERCC1-XPF inhibitor 4 was used as the starting point for an in silico study of further modifications of the piperazine side-chain. A selection of the best scoring hits from the in silico screen were synthesized using a late stage functionalization strategy which should allow for further iterations of this class of inhibitors to be readily synthesized. Of the synthesized compounds, compound 6 performed the best in the in vitro fluorescence based endonuclease assay. The success of compound 6 in inhibiting ERCC1-XPF endonuclease activity in vitro translated well to cell-based assays investigating the inhibition of nucleotide excision repair and disruption of heterodimerization. Subsequently compound 6 was shown to sensitize HCT-116 cancer cells to treatment with UVC, cyclophosphamide, and ionizing radiation. This work serves as an important step towards the synergistic use of DNA repair inhibitors with chemotherapeutic drugs.
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Affiliation(s)
- Claudia Weilbeer
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | - David Jay
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
| | - James C. Donnelly
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
| | | | | | - Xiaoyan Yang
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
| | - Rajam S. Mani
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
| | - Yaping Yu
- Centre for Genome Engineering, University of Calgary, Calgary, AB, Canada
| | - Ahmed H. Elmenoufy
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Department of Pharmaceutical Chemistry, College of Pharmacy, Misr University for Science and Technology, 6th of October City, Egypt
| | - Khaled H. Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Jack A. Tuszynski
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
- Department of Physics, University of Alberta, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Michael Weinfeld
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Michael Weinfeld, ; Frederick G. West,
| | - Frederick G. West
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada
- Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
- *Correspondence: Michael Weinfeld, ; Frederick G. West,
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2
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D'Souza A, Blee AM, Chazin WJ. Mechanism of action of nucleotide excision repair machinery. Biochem Soc Trans 2022; 50:375-386. [PMID: 35076656 PMCID: PMC9275815 DOI: 10.1042/bst20210246] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 12/20/2021] [Accepted: 12/22/2021] [Indexed: 11/08/2023]
Abstract
Nucleotide excision repair (NER) is a versatile DNA repair pathway essential for the removal of a broad spectrum of structurally diverse DNA lesions arising from a variety of sources, including UV irradiation and environmental toxins. Although the core factors and basic stages involved in NER have been identified, the mechanisms of the NER machinery are not well understood. This review summarizes our current understanding of the mechanisms and order of assembly in the core global genome (GG-NER) pathway.
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Affiliation(s)
- Areetha D'Souza
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240-7917, U.S.A
| | - Alexandra M Blee
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240-7917, U.S.A
| | - Walter J Chazin
- Departments of Biochemistry and Chemistry, Center for Structural Biology, Vanderbilt University, Nashville, TN 37240-7917, U.S.A
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3
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Apelt K, White SM, Kim HS, Yeo JE, Kragten A, Wondergem AP, Rooimans MA, González-Prieto R, Wiegant WW, Lunke S, Flanagan D, Pantaleo S, Quinlan C, Hardikar W, van Attikum H, Vertegaal AC, Wilson BT, Wolthuis RM, Schärer OD, Luijsterburg MS. ERCC1 mutations impede DNA damage repair and cause liver and kidney dysfunction in patients. J Exp Med 2021; 218:e20200622. [PMID: 33315086 PMCID: PMC7927433 DOI: 10.1084/jem.20200622] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Revised: 09/25/2020] [Accepted: 10/15/2020] [Indexed: 12/12/2022] Open
Abstract
ERCC1-XPF is a multifunctional endonuclease involved in nucleotide excision repair (NER), interstrand cross-link (ICL) repair, and DNA double-strand break (DSB) repair. Only two patients with bi-allelic ERCC1 mutations have been reported, both of whom had features of Cockayne syndrome and died in infancy. Here, we describe two siblings with bi-allelic ERCC1 mutations in their teenage years. Genomic sequencing identified a deletion and a missense variant (R156W) within ERCC1 that disrupts a salt bridge below the XPA-binding pocket. Patient-derived fibroblasts and knock-in epithelial cells carrying the R156W substitution show dramatically reduced protein levels of ERCC1 and XPF. Moreover, mutant ERCC1 weakly interacts with NER and ICL repair proteins, resulting in diminished recruitment to DNA damage. Consequently, patient cells show strongly reduced NER activity and increased chromosome breakage induced by DNA cross-linkers, while DSB repair was relatively normal. We report a new case of ERCC1 deficiency that severely affects NER and considerably impacts ICL repair, which together result in a unique phenotype combining short stature, photosensitivity, and progressive liver and kidney dysfunction.
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Affiliation(s)
- Katja Apelt
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Susan M. White
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Australia
- Department of Paediatrics, University of Melbourne, Parkville, Australia
| | - Hyun Suk Kim
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Jung-Eun Yeo
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
| | - Angela Kragten
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | | | - Martin A. Rooimans
- Section of Oncogenetics, Department of Clinical Genetics, Vrije Universiteit Medical Center and Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Román González-Prieto
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Wouter W. Wiegant
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Sebastian Lunke
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Australia
- Department of Pathology, University of Melbourne, Parkville, Australia
| | - Daniel Flanagan
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Australia
| | - Sarah Pantaleo
- Victorian Clinical Genetics Services, Murdoch Children’s Research Institute, Parkville, Australia
| | - Catherine Quinlan
- Department of Paediatrics, University of Melbourne, Parkville, Australia
- Department of Nephrology, Royal Children’s Hospital, Melbourne, Australia
- Department of Kidney Regeneration, Murdoch Children’s Research Institute, Melbourne, Australia
| | - Winita Hardikar
- Department of Paediatrics, University of Melbourne, Parkville, Australia
- Department of Gastroenterology, Royal Children's Hospital, Melbourne, Victoria, Australia
- Murdoch Children’s Research Institute, Parkville, Australia
| | - Haico van Attikum
- Department of Human Genetics, Leiden University Medical Center, Leiden, Netherlands
| | - Alfred C.O. Vertegaal
- Department of Cell and Chemical Biology, Leiden University Medical Center, Leiden, Netherlands
| | - Brian T. Wilson
- Institute of Genetic Medicine, Newcastle University, International Centre for Life, Newcastle upon Tyne, UK
- Northern Genetics Service, Newcastle upon Tyne Hospitals National Health Service Foundation Trust, International Centre for Life, Newcastle upon Tyne, UK
- Department of Clinical Genetics, Great Ormond Street Hospital, London, UK
| | - Rob M.F. Wolthuis
- Section of Oncogenetics, Department of Clinical Genetics, Vrije Universiteit Medical Center and Cancer Center Amsterdam, Amsterdam, Netherlands
| | - Orlando D. Schärer
- Center for Genomic Integrity, Institute for Basic Science, Ulsan, Republic of Korea
- Department of Biological Sciences, School of Life Sciences, Ulsan National Institute of Science and Technology, Ulsan, Republic of Korea
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4
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Puerta-García E, Urbano-Pérez D, Carrasco-Campos MI, Pérez-Ramírez C, Segura-Pérez A, Calleja-Hernández, Cañadas-Garre M. Effect of DPYD, MTHFR, ABCB1, XRCC1, ERCC1 and GSTP1 on chemotherapy related toxicity in colorectal carcinoma. Surg Oncol 2020; 35:388-398. [PMID: 33035787 DOI: 10.1016/j.suronc.2020.09.016] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 09/09/2020] [Accepted: 09/13/2020] [Indexed: 12/13/2022]
Abstract
ABCB1, DPYD, MHTFR, XRCC1, ERCC1, GSTP1 and UGT1A1 genetic variants affect proteins related to CRC chemotherapy toxicity. A retrospective cohort study was conducted in 194 CRC patients. In first line treatment, DPYD rs17376848 AG genotype was associated with hematological toxicity (OR = 4.85; p = 0.03); GSTP1 G-allele (OR = 3.01; p = 0.005) and MTHFR rs1801133 T allele (OR = 2.51; p = 0.03) with respiratory toxicity; GSTP1 G-allele with cardiovascular toxicity (OR = 4.05; p = 0.01); ERCC1 rs11615 GG genotype with neurological toxicity (OR = 3.98; p = 0.01) and with asthenia (OR = 2.91; p = 0.08); XRCC1 rs1799782 T allele (OR = 0.31; p = 0.03) and GSTP1 G-allele (OR = 1.81; p = 0.01) with cutaneous toxicity. In second line treatment, XRCC1 rs1799782 T-allele was associated with asthenia (OR = 0.17; p = 0.03) and XRCC1 rs25487 T-allele with gastrointestinal toxicity (OR = 3.03; p = 0.005). After stratifying by treatment, in the 5-Fluorouracil group, the DPYD rs17376848 AG genotype was associated with hematological toxicity (OR = 2.76; p = 0.003), ABCB1 rs1045642 T-allele with the need of treatment adjustment due to toxicity (OR = 3.06; p = 0.01), and rs1045642 CC genotype with gastrointestinal toxicity (OR = 5.80; p = 0.03). In the capecitabine group, the MTHFR rs1801131 CC genotype was associated with asthenia (OR = 3.48; p = 0.009). In the oxaliplatin group, rs1045642 TT genotype was associated with the need to adjust treatment (OR = 0.32; p = 0.02), ERCC1 rs11615 GG genotype with asthenia (OR = 3.01; p = 0.01) and rs1615 GSTP1 GG genotype with respiratory toxicity (OR = 5.07; p = 0.009). ABCB1 rs1045642 T-allele reduces the need for treatment modification with both 5FU and oxaliplatin. Although several biomarkers predicted different toxic effects, they cannot be considered as risk factors for severe toxicity.
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Affiliation(s)
- E Puerta-García
- Pharmacy Service, Pharmacogenetics Unit. University, Hospital Virgen de las Nieves, Granada, Av. de las Fuerzas Armadas, 2, 18014 Granada, Spain.
| | - D Urbano-Pérez
- Pharmacy Service, Pharmacogenetics Unit. University, Hospital Virgen de las Nieves, Granada, Av. de las Fuerzas Armadas, 2, 18014 Granada, Spain.
| | - M I Carrasco-Campos
- Pharmacy Service, Pharmacogenetics Unit. University, Hospital Virgen de las Nieves, Granada, Av. de las Fuerzas Armadas, 2, 18014 Granada, Spain.
| | - C Pérez-Ramírez
- Department of Social Pharmacy, Faculty of Pharmacy. University of Lisbon, Av. Prof. Gama. Pinto, 1600-083, Lisbon, Lisboa e Vale do Tejo, Portugal.
| | - A Segura-Pérez
- Pathology Department, Universitary Hospital Campus de la, Salud, Granada, Av. de la Investigación, s/n, 18016, Granada, Spain.
| | - Calleja-Hernández
- Department of Pharmacy, Unidad de Gestion Clinica (UGC), University Hospital Virgen Macarena, Sevilla, Calle Dr. Fedriani, 3, 41009, Sevilla, Spain.
| | - M Cañadas-Garre
- Epidemiology and Public Health Research Group Centre for Public Health, Queen's University of Belfast, Belfast, Northern Ireland, United Kingdom.
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5
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Liu W, Palovcak A, Li F, Zafar A, Yuan F, Zhang Y. Fanconi anemia pathway as a prospective target for cancer intervention. Cell Biosci 2020; 10:39. [PMID: 32190289 PMCID: PMC7075017 DOI: 10.1186/s13578-020-00401-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Accepted: 03/06/2020] [Indexed: 12/13/2022] Open
Abstract
Fanconi anemia (FA) is a recessive genetic disorder caused by biallelic mutations in at least one of 22 FA genes. Beyond its pathological presentation of bone marrow failure and congenital abnormalities, FA is associated with chromosomal abnormality and genomic instability, and thus represents a genetic vulnerability for cancer predisposition. The cancer relevance of the FA pathway is further established with the pervasive occurrence of FA gene alterations in somatic cancers and observations of FA pathway activation-associated chemotherapy resistance. In this article we describe the role of the FA pathway in canonical interstrand crosslink (ICL) repair and possible contributions of FA gene alterations to cancer development. We also discuss the perspectives and potential of targeting the FA pathway for cancer intervention.
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Affiliation(s)
- Wenjun Liu
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Anna Palovcak
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Fang Li
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Alyan Zafar
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Fenghua Yuan
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
| | - Yanbin Zhang
- Department of Biochemistry and Molecular Biology, University of Miami Miller School of Medicine, Gautier Building Room 311, 1011 NW 15th Street, Miami, FL 33136 USA
- Sylvester Comprehensive Cancer Center, University of Miami Miller School of Medicine, Miami, FL 33136 USA
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6
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Zhou X, Wang Z, Ni Y, Yu Y, Wang G, Chen L. Suppression effect of N-acetylcysteine on bone loss in ovariectomized mice. Am J Transl Res 2020; 12:731-742. [PMID: 32269708 PMCID: PMC7137068] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2019] [Accepted: 01/22/2020] [Indexed: 06/11/2023]
Abstract
Oxidative stress can trigger DNA damage response and activation of cellular senescence. Accumulating studies have demonstrated that senescent cells can produce senescence-associated secretory phenotype that leads to increased bone resorption and decreased bone formation. And elimination of senescent cells or inhibition of SASP secretion has been shown to prevent bone loss in mice. N-acetylcysteine (NAC) is a strong antioxidant. However, it is unclear whether reversed estrogen deficiency-induced bone loss by antioxidant NAC was associated with the inhibition of oxidative stress, DNA damage, osteocyte senescence and SASP. In this study, OVX mice were supplemented with/without E2 or NAC, and were compared with each other. Our results showed that oxidative stress, DNA damage, osteocyte senescence and the secretion of senescence-associated inflammatory cytokines were increased in OVX mice compared with sham-operated mice. However, these parameters were obviously rescued in OVX mice supplemented with E2 or NAC. Data from this study suggest that NAC can prevent OVX-induced bone loss by inhibiting oxidative stress, DNA damage, cell senescence and the secretion of the senescence-associated secretory phenotype.
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Affiliation(s)
- Xun Zhou
- Department of Basic Medical Sciences, Jiangsu College of NursingHuai’an 223005, Jiangsu, People’s Republic of China
| | - Zhengbo Wang
- Department of Anatomy, Histology and Embryology, The Research Center for Bone and Stem Cells, Nanjing Medical UniversityNanjing 210006, Jiangsu, People’s Republic of China
| | - Yihong Ni
- Department of Anatomy, Histology and Embryology, The Research Center for Bone and Stem Cells, Nanjing Medical UniversityNanjing 210006, Jiangsu, People’s Republic of China
| | - Yue Yu
- Suqian First HospitalSuqian 223800, Jiangsu, People’s Republic of China
| | - Guantong Wang
- Department of Orthopedics, Nanjing First Hospital, Nanjing Medical UniversityNanjing 210006, Jiangsu, People’s Republic of China
| | - Lulu Chen
- Department of Anatomy, Histology and Embryology, The Research Center for Bone and Stem Cells, Nanjing Medical UniversityNanjing 210006, Jiangsu, People’s Republic of China
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7
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Zheng H, Jarvis IWH, Bottai M, Dreij K, Stenius U. TGF beta promotes repair of bulky DNA damage through increased ERCC1/XPF and ERCC1/XPA interaction. Carcinogenesis 2020; 40:580-591. [PMID: 30418489 DOI: 10.1093/carcin/bgy156] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2018] [Revised: 10/30/2018] [Accepted: 11/07/2018] [Indexed: 12/15/2022] Open
Abstract
Transforming growth factor beta (TGFβ) is multifunctional cytokine that is involved in the coordination and regulation of many cellular homeostatic processes. Compromised TGFβ activity has been attributed to promotion of human cancers. Recent studies have identified a role for TGFβ in response to radiation-induced DNA damage, suggesting a link between TGFβ and the DNA damage response with implications for cancer development. In this study, the effects of TGFβ on promoting the repair of bulky DNA damage, through modulation of nucleotide excision repair (NER), were investigated. We show that treatment of cells with exogenous TGFβ leads to enhanced repair of DNA damage formed by polycyclic aromatic hydrocarbons and ultraviolet-C radiation; similarly, cells with constitutively activated endogenous TGFβ signaling show comparable responses. This effect of TGFβ is independent of the cell cycle. The response to TGFβ is decreased in cells that have compromised TGFβ signaling through RNA interference of Smad4 and is decreased in NER-deficient cells and cells with compromised NER through RNA interference of excision repair cross-complementing group 1 (ERCC1). Increased interaction and nuclear localization of ERCC1/xeroderma pigmentosum (XP) F and ERCC1/XPA proteins is observed after TGFβ treatment. Our study represents the first experimental evidence of a role for TGFβ in the repair of bulky DNA damage resulting from promotion of the interaction and localization of repair protein complexes involved in the incision step of NER.
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Affiliation(s)
- Huiyuan Zheng
- Unit of Biochemical Toxicology, Karolinska Institutet, Stockholm, Sweden
| | - Ian W H Jarvis
- Unit of Biochemical Toxicology, Karolinska Institutet, Stockholm, Sweden
| | - Matteo Bottai
- Unit of Biostatistics, Institute of Environmental Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Kristian Dreij
- Unit of Biochemical Toxicology, Karolinska Institutet, Stockholm, Sweden
| | - Ulla Stenius
- Unit of Biochemical Toxicology, Karolinska Institutet, Stockholm, Sweden
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8
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Gentile F, Elmenoufy AH, Ciniero G, Jay D, Karimi-Busheri F, Barakat KH, Weinfeld M, West FG, Tuszynski JA. Computer-aided drug design of small molecule inhibitors of the ERCC1-XPF protein-protein interaction. Chem Biol Drug Des 2020; 95:460-471. [PMID: 31891209 DOI: 10.1111/cbdd.13660] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 11/15/2019] [Accepted: 12/17/2019] [Indexed: 01/09/2023]
Abstract
The heterodimer of DNA excision repair protein ERCC-1 and DNA repair endonuclease XPF (ERCC1-XPF) is a 5'-3' structure-specific endonuclease essential for the nucleotide excision repair (NER) pathway, and it is also involved in other DNA repair pathways. In cancer cells, ERCC1-XPF plays a central role in repairing DNA damage induced by chemotherapeutics including platinum-based and cross-linking agents; thus, its inhibition is a promising strategy to enhance the effect of these therapies. In this study, we rationally modified the structure of F06, a small molecule inhibitor of the ERCC1-XPF interaction (Molecular Pharmacology, 84, 2013 and 12), to improve its binding to the target. We followed a multi-step computational approach to investigate potential modification sites of F06, rationally design and rank a library of analogues, and identify candidates for chemical synthesis and in vitro testing. Our top compound, B5, showed an improved half-maximum inhibitory concentration (IC50 ) value of 0.49 µM for the inhibition of ERCC1-XPF endonuclease activit, and lays the foundation for further testing and optimization. Also, the computational approach reported here can be used to develop DNA repair inhibitors targeting the ERCC1-XPF complex.
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Affiliation(s)
| | - Ahmed H Elmenoufy
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada.,Department of Pharmaceutical Chemistry, College of Pharmacy, Misr University for Science and Technology, 6th of October City, Egypt
| | - Gloria Ciniero
- Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy.,Università di Torino, Torino, Italy
| | - David Jay
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
| | | | - Khaled H Barakat
- Faculty of Pharmacy and Pharmaceutical Sciences, University of Alberta, Edmonton, AB, Canada
| | - Michael Weinfeld
- Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada.,Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Frederick G West
- Department of Chemistry, University of Alberta, Edmonton, AB, Canada.,Cancer Research Institute of Northern Alberta, University of Alberta, Edmonton, AB, Canada
| | - Jack A Tuszynski
- Department of Physics, University of Alberta, Edmonton, AB, Canada.,Department of Mechanical and Aerospace Engineering, Politecnico di Torino, Torino, Italy.,Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, AB, Canada
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9
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Jager M, Blokzijl F, Kuijk E, Bertl J, Vougioukalaki M, Janssen R, Besselink N, Boymans S, de Ligt J, Pedersen JS, Hoeijmakers J, Pothof J, van Boxtel R, Cuppen E. Deficiency of nucleotide excision repair is associated with mutational signature observed in cancer. Genome Res 2019; 29:1067-1077. [PMID: 31221724 PMCID: PMC6633256 DOI: 10.1101/gr.246223.118] [Citation(s) in RCA: 55] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2018] [Accepted: 06/07/2019] [Indexed: 12/24/2022]
Abstract
Nucleotide excision repair (NER) is one of the main DNA repair pathways that protect cells against genomic damage. Disruption of this pathway can contribute to the development of cancer and accelerate aging. Mutational characteristics of NER-deficiency may reveal important diagnostic opportunities, as tumors deficient in NER are more sensitive to certain treatments. Here, we analyzed the genome-wide somatic mutational profiles of adult stem cells (ASCs) from NER-deficient Ercc1 -/Δ mice. Our results indicate that NER-deficiency increases the base substitution load twofold in liver but not in small intestinal ASCs, which coincides with the tissue-specific aging pathology observed in these mice. Moreover, NER-deficient ASCs of both tissues show an increased contribution of Signature 8 mutations, which is a mutational pattern with unknown etiology that is recurrently observed in various cancer types. The scattered genomic distribution of the base substitutions indicates that deficiency of global-genome NER (GG-NER) underlies the observed mutational consequences. In line with this, we observe increased Signature 8 mutations in a GG-NER-deficient human organoid culture, in which XPC was deleted using CRISPR-Cas9 gene-editing. Furthermore, genomes of NER-deficient breast tumors show an increased contribution of Signature 8 mutations compared with NER-proficient tumors. Elevated levels of Signature 8 mutations could therefore contribute to a predictor of NER-deficiency based on a patient's mutational profile.
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Affiliation(s)
- Myrthe Jager
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Francis Blokzijl
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Ewart Kuijk
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Johanna Bertl
- Department of Molecular Medicine, Aarhus University, 8200 Aarhus N, Denmark
| | | | - Roel Janssen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Nicolle Besselink
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Sander Boymans
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Joep de Ligt
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | | | | | - Joris Pothof
- Erasmus Medical Center, 3015 CN Rotterdam, The Netherlands
| | - Ruben van Boxtel
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
| | - Edwin Cuppen
- Center for Molecular Medicine and Oncode Institute, University Medical Center Utrecht, Utrecht University, 3584 CG Utrecht, The Netherlands
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10
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Yang L, Wei W, Zhou L, Wang J, Hu G. High/positive expression of ERCC1 predicts poor treatment response and survival prognosis in nasopharyngeal carcinoma: A systematic meta-analysis from 21 studies. Medicine (Baltimore) 2019; 98:e15641. [PMID: 31124943 PMCID: PMC6571253 DOI: 10.1097/md.0000000000015641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Excision repair cross-complementation group 1 (ERCC1) protein is a member of the nucleotide excision repair (NER) system, which plays an important role in DNA damage repair. Recently, its predictive and prognostic value in nasopharyngeal carcinoma (NPC) has been investigated by several studies. However, their results remain controversial. OBJECTIVES In an attempt to address this issue, we conducted the present comprehensive meta-analysis. DATA SOURCES Studies published until November 2017 were searched. Finally, total 21 literatures involving 22 cohorts and 2921 NPC patients fulfilled the inclusion criteria. RESULTS The pooled results showed that high/positive expression of ERCC1 predicted poor objective response rate (ORR) [odds ratio (OR) = 2.83; 95% confidence interval (CI) = 2.11-3.80; P <.001], overall survival (OS) [hazard ratio (HR) = 1.77; 95% CI = 1.48-2.12; P <.001], and disease-free survival (DFS) (HR = 1.60; 95% CI = 1.43-1.79; P <.001) in NPC. Low heterogeneity was detected among these studies (ORR: I = 0.0%, P = .776; DFS: I = 38.7%, P = .148; OS: I = 0.0%; P = .530). The results of sensitivity analyses and publication bias verified the reliability of our findings. CONCLUSIONS This study suggested ERCC1 as a potential predictive and prognostic biomarker for the treatment response and survival prognosis of NPC patients.
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Affiliation(s)
- Lin Yang
- Department of Oncology, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, Hubei, P.R. China
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11
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Servant G, Streva VA, Deininger PL. Transcription coupled repair and biased insertion of human retrotransposon L1 in transcribed genes. Mob DNA 2017; 8:18. [PMID: 29225704 PMCID: PMC5717806 DOI: 10.1186/s13100-017-0100-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2017] [Accepted: 11/06/2017] [Indexed: 11/26/2022] Open
Abstract
Background L1 retrotransposons inserted within genes in the human genome show a strong bias against sense orientation with respect to the gene. One suggested explanation for this observation was the possibility that L1 inserted randomly, but that there was negative selection against sense-oriented insertions. However, multiple studies have now found that de novo and polymorphic L1 insertions, which have little opportunity for selection to act, also show the same bias. Results Here we show that the transcription-coupled sub-pathway of nucleotide excision repair does not affect the overall rate of insertion of L1 elements, which is in contrast with the regulation by the global sub-pathway of nucleotide excision repair. The transcription-coupled subpathway does cause a strong bias against insertion in the sense orientation relative to genes. Conclusions This suggests that a major portion of the L1 orientation bias might be generated during the process of insertion through the action of transcription-coupled nucleotide excision repair. Electronic supplementary material The online version of this article (10.1186/s13100-017-0100-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Geraldine Servant
- Tulane University, Tulane Cancer Center and the Department of Epidemiology, 1430 Tulane Ave, New Orleans, LA 70112 USA
| | - Vincent A Streva
- Tulane University, Tulane Cancer Center and the Department of Epidemiology, 1430 Tulane Ave, New Orleans, LA 70112 USA.,Present Address: Division of Infectious Diseases, Boston Children's Hospital and Harvard Medical School, 300 Longwood Ave, Boston, MA 02115 USA
| | - Prescott L Deininger
- Tulane University, Tulane Cancer Center and the Department of Epidemiology, 1430 Tulane Ave, New Orleans, LA 70112 USA.,Tulane Cancer Center, SL66, Tulane University Health Sciences Center, 1430 Tulane Ave., New Orleans, LA 70112 USA
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12
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Jacobsen F, Taskin B, Melling N, Sauer C, Wittmer C, Hube-Magg C, Kluth M, Simon R, Pehrke D, Beyer B, Steuber T, Thederan I, Sauter G, Schlomm T, Wilczak W, Möller K, Weidemann SA, Burdak-Rothkamm S. Increased ERCC1 expression is linked to chromosomal aberrations and adverse tumor biology in prostate cancer. BMC Cancer 2017; 17:504. [PMID: 28747165 PMCID: PMC5530529 DOI: 10.1186/s12885-017-3489-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 07/17/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Animal model experiments have suggested a role of the DNA repair protein ERCC1 (Excision Repair Cross-Complementation Group 1) in prostate cancer progression. METHODS To better understand the impact of ERCC1 protein expression in human prostate cancer, a preexisting tissue microarray (TMA) containing more than 12,000 prostate cancer specimens was analyzed by immunohistochemistry and data were compared with tumor phenotype, PSA recurrence and several of the most common genomic alterations (TMPRSS2:ERG fusions: deletions of PTEN, 6q, 5q, 3p). RESULTS ERCC1 staining was seen in 64.7% of 10,436 interpretable tissues and was considered weak in 37.1%, moderate in 22.6% and strong in 5% of tumors. High-level ERCC1 staining was linked to advanced pT stage, high Gleason grade, positive lymph nodes, high pre-operative serum PSA, and positive surgical margin status (p < 0.0001 each). High ERCC1 expression was strongly associated with an elevated risk of PSA recurrence (p < 0.0001). This was independent of established prognostic features. A subgroup analysis of cancers defined by comparable quantitative Gleason grades revealed that the prognostic impact was mostly driven by low-grade tumors with a Gleason 3 + 3 or 3 + 4 (Gleason 4: ≤5%). High ERCC1 expression was strongly associated with the presence of genomic alterations and expression levels increased with the number of deletions present in the tumor. These latter data suggest a functional relationship of ERCC1 expression with genomic instability. CONCLUSION The results of our study demonstrate that expression of ERCC1 - a potential surrogate for genomic instability - is an independent prognostic marker in prostate cancer with particular importance in low-grade tumors.
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Affiliation(s)
- Frank Jacobsen
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Billurvan Taskin
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Nathaniel Melling
- General, Visceral and Thoracic Surgery Department and Clinic, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Charlotte Sauer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Corinna Wittmer
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Claudia Hube-Magg
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Martina Kluth
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Ronald Simon
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany.
| | - Dirk Pehrke
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Burkhard Beyer
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Thomas Steuber
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Imke Thederan
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Thorsten Schlomm
- Martini-Clinic, Prostate Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.,Department of Urology, Section for translational Prostate Cancer Research, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Waldemar Wilczak
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Katharina Möller
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Sören A Weidemann
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
| | - Susanne Burdak-Rothkamm
- Institute of Pathology, University Medical Center Hamburg-Eppendorf, Martinistr. 52, 20246, Hamburg, Germany
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13
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Disruption of DNA repair in cancer cells by ubiquitination of a destabilising dimerization domain of nucleotide excision repair protein ERCC1. Oncotarget 2017; 8:55246-55264. [PMID: 28903417 PMCID: PMC5589656 DOI: 10.18632/oncotarget.19422] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2017] [Accepted: 07/11/2017] [Indexed: 11/25/2022] Open
Abstract
DNA repair pathways present in all cells serve to preserve genome stability, but in cancer cells they also act reduce the efficacy of chemotherapy. The endonuclease ERCC1-XPF has an important role in the repair of DNA damage caused by a variety of chemotherapeutic agents and there has been intense interest in the use of ERCC1 as a predictive marker of therapeutic response in non-small cell lung carcinoma, squamous cell carcinoma and ovarian cancer. We have previously validated ERCC1 as a therapeutic target in melanoma, but all small molecule ERCC1-XPF inhibitors reported to date have lacked sufficient potency and specificity for clinical use. In an alternative approach to prevent the repair activity of ERCC1-XPF, we investigated the mechanism of ERCC1 ubiquitination and found that the key region was the C-terminal (HhH)2 domain which heterodimerizes with XPF. This ERCC1 region was modified by non-conventional lysine-independent, but proteasome-dependent polyubiquitination, involving Lys33 of ubiquitin and a linear ubiquitin chain. XPF was not polyubiquitinated and its expression was dependent on presence of ERCC1, but not vice versa. To our surprise we found that ERCC1 can also homodimerize through its C-terminal (HhH)2 domain. We exploited the ability of a peptide containing this C-terminal domain to destabilise both endogenous ERCC1 and XPF in human melanoma cells and fibroblasts, resulting in reductions of up to 85% in nucleotide excision repair and near two-fold increased sensitivity to DNA damaging agents. We suggest that the ERCC1 (HhH)2 domain could be used in an alternative strategy to treat cancer.
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14
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Lehmann J, Seebode C, Smolorz S, Schubert S, Emmert S. XPF knockout via CRISPR/Cas9 reveals that ERCC1 is retained in the cytoplasm without its heterodimer partner XPF. Cell Mol Life Sci 2017; 74:2081-2094. [PMID: 28130555 PMCID: PMC11107539 DOI: 10.1007/s00018-017-2455-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/01/2016] [Accepted: 01/03/2017] [Indexed: 01/05/2023]
Abstract
The XPF/ERCC1 heterodimeric complex is essentially involved in nucleotide excision repair (NER), interstrand crosslink (ICL), and double-strand break repair. Defects in XPF lead to severe diseases like xeroderma pigmentosum (XP). Up until now, XP-F patient cells have been utilized for functional analyses. Due to the multiple roles of the XPF/ERCC1 complex, these patient cells retain at least one full-length allele and residual repair capabilities. Despite the essential function of the XPF/ERCC1 complex for the human organism, we successfully generated a viable immortalised human XPF knockout cell line with complete loss of XPF using the CRISPR/Cas9 technique in fetal lung fibroblasts (MRC5Vi cells). These cells showed a markedly increased sensitivity to UVC, cisplatin, and psoralen activated by UVA as well as reduced repair capabilities for NER and ICL repair as assessed by reporter gene assays. Using the newly generated knockout cells, we could show that human XPF is markedly involved in homologous recombination repair (HRR) but dispensable for non-homologous end-joining (NHEJ). Notably, ERCC1 was not detectable in the nucleus of the XPF knockout cells indicating the necessity of a functional XPF/ERCC1 heterodimer to allow ERCC1 to enter the nucleus. Overexpression of wild-type XPF could reverse this effect as well as the repair deficiencies.
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Affiliation(s)
- Janin Lehmann
- Clinic and Policlinic for Dermatology and Venereology, University Medical Centre Rostock, Strempelstrasse 13, 18057, Rostock, Germany
- Department of Dermatology, Venereology and Allergology, University Medical Centre Goettingen, Robert-Koch-Strasse 40, 37075, Goettingen, Germany
| | - Christina Seebode
- Clinic and Policlinic for Dermatology and Venereology, University Medical Centre Rostock, Strempelstrasse 13, 18057, Rostock, Germany
| | - Sabine Smolorz
- Department of Dermatology, Venereology and Allergology, University Medical Centre Goettingen, Robert-Koch-Strasse 40, 37075, Goettingen, Germany
| | - Steffen Schubert
- Department of Dermatology, Venereology and Allergology, University Medical Centre Goettingen, Robert-Koch-Strasse 40, 37075, Goettingen, Germany
| | - Steffen Emmert
- Clinic and Policlinic for Dermatology and Venereology, University Medical Centre Rostock, Strempelstrasse 13, 18057, Rostock, Germany.
- Department of Dermatology, Venereology and Allergology, University Medical Centre Goettingen, Robert-Koch-Strasse 40, 37075, Goettingen, Germany.
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15
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Das D, Faridounnia M, Kovacic L, Kaptein R, Boelens R, Folkers GE. Single-stranded DNA Binding by the Helix-Hairpin-Helix Domain of XPF Protein Contributes to the Substrate Specificity of the ERCC1-XPF Protein Complex. J Biol Chem 2016; 292:2842-2853. [PMID: 28028171 DOI: 10.1074/jbc.m116.747857] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2016] [Revised: 12/24/2016] [Indexed: 11/06/2022] Open
Abstract
The nucleotide excision repair protein complex ERCC1-XPF is required for incision of DNA upstream of DNA damage. Functional studies have provided insights into the binding of ERCC1-XPF to various DNA substrates. However, because no structure for the ERCC1-XPF-DNA complex has been determined, the mechanism of substrate recognition remains elusive. Here we biochemically characterize the substrate preferences of the helix-hairpin-helix (HhH) domains of XPF and ERCC-XPF and show that the binding to single-stranded DNA (ssDNA)/dsDNA junctions is dependent on joint binding to the DNA binding domain of ERCC1 and XPF. We reveal that the homodimeric XPF is able to bind various ssDNA sequences but with a clear preference for guanine-containing substrates. NMR titration experiments and in vitro DNA binding assays also show that, within the heterodimeric ERCC1-XPF complex, XPF specifically recognizes ssDNA. On the other hand, the HhH domain of ERCC1 preferentially binds dsDNA through the hairpin region. The two separate non-overlapping DNA binding domains in the ERCC1-XPF heterodimer jointly bind to an ssDNA/dsDNA substrate and, thereby, at least partially dictate the incision position during damage removal. Based on structural models, NMR titrations, DNA-binding studies, site-directed mutagenesis, charge distribution, and sequence conservation, we propose that the HhH domain of ERCC1 binds to dsDNA upstream of the damage, and XPF binds to the non-damaged strand within a repair bubble.
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Affiliation(s)
- Devashish Das
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Maryam Faridounnia
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Lidija Kovacic
- the Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, 1000 Ljubljana, Slovenia
| | - Robert Kaptein
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Rolf Boelens
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
| | - Gert E Folkers
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands and
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16
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The Nucleotide Excision Repair Pathway Limits L1 Retrotransposition. Genetics 2016; 205:139-153. [PMID: 28049704 PMCID: PMC5223499 DOI: 10.1534/genetics.116.188680] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Accepted: 10/30/2016] [Indexed: 12/25/2022] Open
Abstract
Long interspersed elements 1 (L1) are active mobile elements that constitute almost 17% of the human genome. They amplify through a “copy-and-paste” mechanism termed retrotransposition, and de novo insertions related to these elements have been reported to cause 0.2% of genetic diseases. Our previous data demonstrated that the endonuclease complex ERCC1-XPF, which cleaves a 3′ DNA flap structure, limits L1 retrotransposition. Although the ERCC1-XPF endonuclease participates in several different DNA repair pathways, such as single-strand annealing, or in telomere maintenance, its recruitment to DNA lesions is best characterized in the nucleotide excision repair (NER) pathway. To determine if the NER pathway prevents the insertion of retroelements in the genome, we monitored the retrotransposition efficiencies of engineered L1 elements in NER-deficient cells and in their complemented versions. Core proteins of the NER pathway, XPD and XPA, and the lesion binding protein, XPC, are involved in limiting L1 retrotransposition. In addition, sequence analysis of recovered de novo L1 inserts and their genomic locations in NER-deficient cells demonstrated the presence of abnormally large duplications at the site of insertion, suggesting that NER proteins may also play a role in the normal L1 insertion process. Here, we propose new functions for the NER pathway in the maintenance of genome integrity: limitation of insertional mutations caused by retrotransposons and the prevention of potentially mutagenic large genomic duplications at the site of retrotransposon insertion events.
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17
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Heo SJ, Jung I, Lee CK, Kim JH, Lim SM, Moon YW, Shim HS, Jeong J, Kim JH, Kim HR, Cho BC. A randomized phase II trial of ERCC1 and RRM1 mRNA expression-based chemotherapy versus docetaxel/carboplatin in advanced non-small cell lung cancer. Cancer Chemother Pharmacol 2016; 77:539-48. [PMID: 26811178 DOI: 10.1007/s00280-016-2968-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2015] [Accepted: 11/05/2015] [Indexed: 11/29/2022]
Abstract
OBJECTIVES To evaluate whether the selection of first-line chemotherapy based on ERCC1 and RRM1 mRNA expression levels would improve clinical outcomes in advanced non-small cell lung cancer (NSCLC) patients. MATERIALS AND METHODS Eligible patients were randomly assigned 1:1 to the experimental and control arms; the experimental arm received gemcitabine/carboplatin (GC) if ERCC1 and RRM1 expression was low, gemcitabine/vinorelbine (GV) if ERCC1 was high and RRM1 was low, docetaxel/carboplatin (DC) if ERCC1 was low and RRM1 was high, and docetaxel/vinorelbine (DV) if both were high. In the control arm, patients received DC. RESULTS This study was prematurely terminated after the futility analysis of 43 progression-free survival (PFS) events. A total of 55 patients (n = 26 in the experimental arm, n = 29 in the control arm) were evaluable for efficacy and toxicity. Nineteen (73.1%) patients were assigned to receive GC, 0 (0.0%) to GV, 4 (15.4%) to DC, and 3 (11.5%) to DV in the experimental arm. The overall response rates were 42.3 and 48.3% in the experimental and control arms, respectively, which were not statistically different (P = 0.657). The median PFS was 5.2 months in the experimental arm and 5.4 months in the control arm (P = 0.286). The median overall survival was 17.4 months in the experimental arm and 12.6 months in the control arm (P = 0.638). The occurrence of grade 3 or higher neutropenia (69.2 vs. 93.1%, P = 0.035) and febrile neutropenia (3.8 vs. 24.1%, P = 0.054) was more common in the control arm. CONCLUSION ERCC1 and RRM1 mRNA expression-based chemotherapy did not improve clinical outcomes in advanced NSCLC (NCT01648517).
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Affiliation(s)
- Su Jin Heo
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-Gu, Seoul, 120-752, Korea
| | - Inkyung Jung
- Department of Biostatistics and Medical Informatics, Yonsei University College of Medicine, Seoul, Korea
| | - Choong-Kun Lee
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-Gu, Seoul, 120-752, Korea
| | - Jee Hung Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-Gu, Seoul, 120-752, Korea
| | - Sun Min Lim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-Gu, Seoul, 120-752, Korea
| | - Yong Wha Moon
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-Gu, Seoul, 120-752, Korea
| | - Hyo Sup Shim
- Department of Pathology, Yonsei University College of Medicine, Seoul, Korea
| | - Jaeheon Jeong
- Division of Medical Oncology and Hematology, Department of Internal Medicine, School of Medicine, Kyunghee University, Seoul, Korea
| | - Joo-Hang Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-Gu, Seoul, 120-752, Korea
| | - Hye Ryun Kim
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-Gu, Seoul, 120-752, Korea.
| | - Byoung Chul Cho
- Division of Medical Oncology, Department of Internal Medicine, Yonsei Cancer Center, Yonsei University College of Medicine, 50 Yonsei-ro, Seodaemun-Gu, Seoul, 120-752, Korea.
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Muggia FM, Bonetti A, Hoeschele JD, Rozencweig M, Howell SB. Platinum Antitumor Complexes: 50 Years Since Barnett Rosenberg's Discovery. J Clin Oncol 2015; 33:4219-26. [PMID: 26503202 DOI: 10.1200/jco.2015.60.7481] [Citation(s) in RCA: 119] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Franco M Muggia
- Franco M. Muggia, New York University School of Medicine, New York, NY; Andrea Bonetti, Mater Salutis Hospitaļ Legnago, Italy; James D. Hoeschele, Eastern Michigan University, Ypsilanti, MI; Marcel Rozencweig, Innate Pharma, Marseille, France; and Stephen B. Howell, University of California San Diego (UCSD) and Moores UCSD Cancer Center, La Jolla, CA.
| | - Andrea Bonetti
- Franco M. Muggia, New York University School of Medicine, New York, NY; Andrea Bonetti, Mater Salutis Hospitaļ Legnago, Italy; James D. Hoeschele, Eastern Michigan University, Ypsilanti, MI; Marcel Rozencweig, Innate Pharma, Marseille, France; and Stephen B. Howell, University of California San Diego (UCSD) and Moores UCSD Cancer Center, La Jolla, CA
| | - James D Hoeschele
- Franco M. Muggia, New York University School of Medicine, New York, NY; Andrea Bonetti, Mater Salutis Hospitaļ Legnago, Italy; James D. Hoeschele, Eastern Michigan University, Ypsilanti, MI; Marcel Rozencweig, Innate Pharma, Marseille, France; and Stephen B. Howell, University of California San Diego (UCSD) and Moores UCSD Cancer Center, La Jolla, CA
| | - Marcel Rozencweig
- Franco M. Muggia, New York University School of Medicine, New York, NY; Andrea Bonetti, Mater Salutis Hospitaļ Legnago, Italy; James D. Hoeschele, Eastern Michigan University, Ypsilanti, MI; Marcel Rozencweig, Innate Pharma, Marseille, France; and Stephen B. Howell, University of California San Diego (UCSD) and Moores UCSD Cancer Center, La Jolla, CA
| | - Stephen B Howell
- Franco M. Muggia, New York University School of Medicine, New York, NY; Andrea Bonetti, Mater Salutis Hospitaļ Legnago, Italy; James D. Hoeschele, Eastern Michigan University, Ypsilanti, MI; Marcel Rozencweig, Innate Pharma, Marseille, France; and Stephen B. Howell, University of California San Diego (UCSD) and Moores UCSD Cancer Center, La Jolla, CA
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19
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Faridounnia M, Wienk H, Kovačič L, Folkers GE, Jaspers NGJ, Kaptein R, Hoeijmakers JHJ, Boelens R. The Cerebro-oculo-facio-skeletal Syndrome Point Mutation F231L in the ERCC1 DNA Repair Protein Causes Dissociation of the ERCC1-XPF Complex. J Biol Chem 2015; 290:20541-55. [PMID: 26085086 DOI: 10.1074/jbc.m114.635169] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2015] [Indexed: 12/15/2022] Open
Abstract
The ERCC1-XPF heterodimer, a structure-specific DNA endonuclease, is best known for its function in the nucleotide excision repair (NER) pathway. The ERCC1 point mutation F231L, located at the hydrophobic interaction interface of ERCC1 (excision repair cross-complementation group 1) and XPF (xeroderma pigmentosum complementation group F), leads to severe NER pathway deficiencies. Here, we analyze biophysical properties and report the NMR structure of the complex of the C-terminal tandem helix-hairpin-helix domains of ERCC1-XPF that contains this mutation. The structures of wild type and the F231L mutant are very similar. The F231L mutation results in only a small disturbance of the ERCC1-XPF interface, where, in contrast to Phe(231), Leu(231) lacks interactions stabilizing the ERCC1-XPF complex. One of the two anchor points is severely distorted, and this results in a more dynamic complex, causing reduced stability and an increased dissociation rate of the mutant complex as compared with wild type. These data provide a biophysical explanation for the severe NER deficiencies caused by this mutation.
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Affiliation(s)
- Maryam Faridounnia
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Hans Wienk
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Lidija Kovačič
- the Department of Molecular and Biomedical Sciences, Jožef Stefan Institute, Jamova cesta 39, SI-1000 Ljubljana, Slovenia, and
| | - Gert E Folkers
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Nicolaas G J Jaspers
- the Department of Genetics, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Robert Kaptein
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
| | - Jan H J Hoeijmakers
- the Department of Genetics, Erasmus Medical Center, PO Box 2040, 3000 CA Rotterdam, The Netherlands
| | - Rolf Boelens
- From the Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands,
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Manandhar M, Boulware KS, Wood RD. The ERCC1 and ERCC4 (XPF) genes and gene products. Gene 2015; 569:153-61. [PMID: 26074087 DOI: 10.1016/j.gene.2015.06.026] [Citation(s) in RCA: 93] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2015] [Revised: 05/01/2015] [Accepted: 06/09/2015] [Indexed: 12/22/2022]
Abstract
The ERCC1 and ERCC4 genes encode the two subunits of the ERCC1-XPF nuclease. This enzyme plays an important role in repair of DNA damage and in maintaining genomic stability. ERCC1-XPF nuclease nicks DNA specifically at junctions between double-stranded and single-stranded DNA, when the single-strand is oriented 5' to 3' away from a junction. ERCC1-XPF is a core component of nucleotide excision repair and also plays a role in interstrand crosslink repair, some pathways of double-strand break repair by homologous recombination and end-joining, as a backup enzyme in base excision repair, and in telomere length regulation. In many of these activities, ERCC1-XPF complex cleaves the 3' tails of DNA intermediates in preparation for further processing. ERCC1-XPF interacts with other proteins including XPA, RPA, SLX4 and TRF2 to perform its functions. Disruption of these interactions or direct targeting of ERCC1-XPF to decrease its DNA repair function might be a useful strategy to increase the sensitivity of cancer cells to some DNA damaging agents. Complete deletion of either ERCC1 or ERCC4 is not compatible with viability in mice or humans. However, mutations in the ERCC1 or ERCC4 genes cause a remarkable array of rare inherited human disorders. These include specific forms of xeroderma pigmentosum, Cockayne syndrome, Fanconi anemia, XFE progeria and cerebro-oculo-facio-skeletal syndrome.
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Affiliation(s)
- Mandira Manandhar
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Karen S Boulware
- The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA
| | - Richard D Wood
- Department of Epigenetics & Molecular Carcinogenesis, The University of Texas MD Anderson Cancer Center, Smithville, TX 78957, USA; The University of Texas Graduate School of Biomedical Sciences at Houston, Houston, TX 77030, USA.
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21
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McNeil EM, Astell KR, Ritchie AM, Shave S, Houston DR, Bakrania P, Jones HM, Khurana P, Wallace C, Chapman T, Wear MA, Walkinshaw MD, Saxty B, Melton DW. Inhibition of the ERCC1-XPF structure-specific endonuclease to overcome cancer chemoresistance. DNA Repair (Amst) 2015; 31:19-28. [PMID: 25956741 DOI: 10.1016/j.dnarep.2015.04.002] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Revised: 04/07/2015] [Accepted: 04/10/2015] [Indexed: 01/23/2023]
Abstract
ERCC1-XPF is a structure-specific endonuclease that is required for the repair of DNA lesions, generated by the widely used platinum-containing cancer chemotherapeutics such as cisplatin, through the Nucleotide Excision Repair and Interstrand Crosslink Repair pathways. Based on mouse xenograft experiments, where ERCC1-deficient melanomas were cured by cisplatin therapy, we proposed that inhibition of ERCC1-XPF could enhance the effectiveness of platinum-based chemotherapy. Here we report the identification and properties of inhibitors against two key targets on ERCC1-XPF. By targeting the ERCC1-XPF interaction domain we proposed that inhibition would disrupt the ERCC1-XPF heterodimer resulting in destabilisation of both proteins. Using in silico screening, we identified an inhibitor that bound to ERCC1-XPF in a biophysical assay, reduced the level of ERCC1-XPF complexes in ovarian cancer cells, inhibited Nucleotide Excision Repair and sensitised melanoma cells to cisplatin. We also utilised high throughput and in silico screening to identify the first reported inhibitors of the other key target, the XPF endonuclease domain. We demonstrate that two of these compounds display specificity in vitro for ERCC1-XPF over two other endonucleases, bind to ERCC1-XPF, inhibit Nucleotide Excision Repair in two independent assays and specifically sensitise Nucleotide Excision Repair-proficient, but not Nucleotide Excision Repair-deficient human and mouse cells to cisplatin.
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Affiliation(s)
- Ewan M McNeil
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Katy R Astell
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Ann-Marie Ritchie
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
| | - Steven Shave
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Douglas R Houston
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Preeti Bakrania
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Hayley M Jones
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Puneet Khurana
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Claire Wallace
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Tim Chapman
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - Martin A Wear
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Malcolm D Walkinshaw
- Centre for Translational and Chemical Biology, School of Biological Sciences, University of Edinburgh, Michael Swann Building, The King's Buildings, Mayfield Road, Edinburgh EH9 3JR, UK
| | - Barbara Saxty
- Centre for Therapeutics Discovery, MRC Technology, 1-3 Burtonhole Lane, Mill Hill, London NW7 1AD, UK
| | - David W Melton
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK.
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22
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Zhao J, Li X, McGowan S, Niedernhofer LJ, Robbins PD. NF-κB activation with aging: characterization and therapeutic inhibition. Methods Mol Biol 2015; 1280:543-557. [PMID: 25736771 DOI: 10.1007/978-1-4939-2422-6_32] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Aging is a condition characterized by progressive decline in tissue homeostasis due, at least in part, to the accumulation of replicative, oxidative, and genotoxic stress over time. The activity of the transcription factor NF-κB is upregulated in both naturally aged mice and multiple progeroid mouse models of accelerated aging. Suppressing NF-κB activity genetically or pharmacologically has been shown to delay the onset and progression of aging pathology and therefore prolong the healthspan in progeroid mouse models. Here, we describe the methods for measuring aging endpoints along with NF-κΒ activation in mice, as well as after pharmacologic intervention to prevent NF-κB activation using a NEMO-binding domain (NBD)-protein transduction domain (PTD) fusion peptide.
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Affiliation(s)
- Jing Zhao
- Department of Metabolism and Aging, The Scripps Research Institute, 130 Scripps Way, #3B3, Jupiter, FL, 33458, USA
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23
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Smith DH, Fiehn AMK, Fogh L, Christensen IJ, Hansen TP, Stenvang J, Nielsen HJ, Nielsen KV, Hasselby JP, Brünner N, Jensen SS. Measuring ERCC1 protein expression in cancer specimens: validation of a novel antibody. Sci Rep 2014; 4:4313. [PMID: 24603753 PMCID: PMC3945488 DOI: 10.1038/srep04313] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2014] [Accepted: 02/20/2014] [Indexed: 12/17/2022] Open
Abstract
Platinum chemotherapy remains part of standard therapies in the management of a variety of cancers. Severe side effects and a high degree of resistance to platinum drugs have led numerous researchers to search for predictive biomarkers, which could aid in identifying patients that are the most likely to respond to therapy. The ERCC1-ERCC4 endonuclease plays a critical role in the repair of platinum-DNA damage and has widely been studied in relation to sensitivity to platinum chemotherapy. The standard method to evaluate ERCC1 protein expression is through the use of immunohistochemistry with monoclonal antibody 8F1, an antibody that was recently found to bind an unrelated protein. The present study determines the specificity of a novel antibody, monoclonal antibody 4F9, and presents a method to evaluate ERCC1 expression in colorectal tumor specimens. Using relevant cell lines as controls, the specificity of antibody 4F9 was tested by immunoblotting, immunohistochemistry and immunofluorescence. Scoring guidelines to aid in the evaluation of ERCC1 tumor expression were developed and evaluated in archival formalin-fixed paraffin embedded colorectal cancer specimens. Antibody 4F9 was found to be specific by all methods applied and it was possible to evaluate the ERCC1 expression in the majority (85%) of colorectal cancer tumor specimens.
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Affiliation(s)
- David Hersi Smith
- 1] R&D, Dako A/S, Produktionsvej 42, DK-2600 Glostrup, Denmark [2] Section for Molecular Disease Biology, Institute of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Strandboulevarden 49, DK-2100 Copenhagen Ø, Denmark
| | - Anne-Marie Kanstrup Fiehn
- Department of Pathology, Copenhagen University Hospital, Blegdamsvej 9, DK-2100 Copenhagen Ø, Denmark
| | - Louise Fogh
- Section for Molecular Disease Biology, Institute of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Strandboulevarden 49, DK-2100 Copenhagen Ø, Denmark
| | - Ib Jarle Christensen
- Finsen Laboratory, Rigshospitalet and Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen Biocenter, Ole Maaloevs Vej 5, building 3, 3rd floor, DK-2200 Copenhagen N, Denmark
| | - Tine Plato Hansen
- Department of Pathology, Odense University Hospital, Winslowparken 15, DK-5000 Odense C, Denmark
| | - Jan Stenvang
- Section for Molecular Disease Biology, Institute of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Strandboulevarden 49, DK-2100 Copenhagen Ø, Denmark
| | - Hans Jørgen Nielsen
- 1] Department of Surgical Gastroenterology 360, Hvidovre Hospital, Kettegård Allé 30, DK-2650 Hvidovre, Denmark [2] Institute of Clinical Medicine, Faculty of Health and Medical Sciences, University of Copenhagen, Blegdamsvej 3B, DK-2200 Copenhagen N, Denmark
| | | | - Jane Preuss Hasselby
- Department of Pathology, Copenhagen University Hospital, Blegdamsvej 9, DK-2100 Copenhagen Ø, Denmark
| | - Nils Brünner
- Section for Molecular Disease Biology, Institute of Veterinary Disease Biology, Faculty of Health and Medical Sciences, Strandboulevarden 49, DK-2100 Copenhagen Ø, Denmark
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24
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Postel-Vinay S, Bajrami I, Friboulet L, Elliott R, Fontebasso Y, Dorvault N, Olaussen KA, André F, Soria JC, Lord CJ, Ashworth A. A high-throughput screen identifies PARP1/2 inhibitors as a potential therapy for ERCC1-deficient non-small cell lung cancer. Oncogene 2013; 32:5377-87. [PMID: 23934192 DOI: 10.1038/onc.2013.311] [Citation(s) in RCA: 71] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2013] [Revised: 06/08/2013] [Accepted: 06/10/2013] [Indexed: 12/29/2022]
Abstract
Excision repair cross-complementation group 1 (ERCC1) is a DNA repair enzyme that is frequently defective in non-small cell lung cancer (NSCLC). Although low ERCC1 expression correlates with platinum sensitivity, the clinical effectiveness of platinum therapy is limited, highlighting the need for alternative treatment strategies. To discover new mechanism-based therapeutic strategies for ERCC1-defective tumours, we performed high-throughput drug screens in an isogenic NSCLC model of ERCC1 deficiency and dissected the mechanism underlying ERCC1-selective effects by studying molecular biomarkers of tumour cell response. The high-throughput screens identified multiple clinical poly (ADP-ribose) polymerase 1 and 2 (PARP1/2) inhibitors, such as olaparib (AZD-2281), niraparib (MK-4827) and BMN 673, as being selective for ERCC1 deficiency. We observed that ERCC1-deficient cells displayed a significant delay in double-strand break repair associated with a profound and prolonged G₂/M arrest following PARP1/2 inhibitor treatment. Importantly, we found that ERCC1 isoform 202, which has recently been shown to mediate platinum sensitivity, also modulated PARP1/2 sensitivity. A PARP1/2 inhibitor-synthetic lethal siRNA screen revealed that ERCC1 deficiency was epistatic with homologous recombination deficiency. However, ERCC1-deficient cells did not display a defect in RAD51 foci formation, suggesting that ERCC1 might be required to process PARP1/2 inhibitor-induced DNA lesions before DNA strand invasion. PARP1 silencing restored PARP1/2 inhibitor resistance in ERCC1-deficient cells but had no effect in ERCC1-proficient cells, supporting the hypothesis that PARP1 might be required for the ERCC1 selectivity of PARP1/2 inhibitors. This study suggests that PARP1/2 inhibitors as a monotherapy could represent a novel therapeutic strategy for NSCLC patients with ERCC1-deficient tumours.
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Affiliation(s)
- S Postel-Vinay
- 1] The Breakthrough Breast Cancer Research Centre and CRUK Gene Function Laboratory, Institute of Cancer Research, London, UK [2] Département de médecine-Unité INSERM 981, Institut Gustave Roussy, Villejuif, France
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25
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Friboulet L, Postel-Vinay S, Sourisseau T, Adam J, Stoclin A, Ponsonnailles F, Dorvault N, Commo F, Saulnier P, Salome-Desmoulez S, Pottier G, André F, Kroemer G, Soria JC, Olaussen KA. ERCC1 function in nuclear excision and interstrand crosslink repair pathways is mediated exclusively by the ERCC1-202 isoform. Cell Cycle 2013; 12:3298-306. [PMID: 24036546 DOI: 10.4161/cc.26309] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
ERCC1 (excision repair cross-complementation group 1) plays essential roles in the removal of DNA intrastrand crosslinks by nucleotide excision repair, and that of DNA interstrand crosslinks by the Fanconi anemia (FA) pathway and homology-directed repair processes (HDR). The function of ERCC1 thus impacts on the DNA damage response (DDR), particularly in anticancer therapy when DNA damaging agents are employed. ERCC1 expression has been proposed as a predictive biomarker of the response to platinum-based therapy. However, the assessment of ERCC1 expression in clinical samples is complicated by the existence of 4 functionally distinct protein isoforms, which differently impact on DDR. Here, we explored the functional competence of each ERCC1 protein isoform and obtained evidence that the 202 isoform is the sole one endowed with ERCC1 activity in DNA repair pathways. The ERCC1 isoform 202 interacts with RPA, XPA, and XPF, and XPF stability requires expression of the ERCC1 202 isoform (but none of the 3 others). ERCC1-deficient non-small cell lung cancer cells show abnormal mitosis, a phenotype reminiscent of the FA phenotype that can be rescued by isoform 202 only. Finally, we could not observe any dominant-negative interaction between ERCC1 isoforms. These data suggest that the selective assessment of the ERCC1 isoform 202 in clinical samples should accurately reflect the DDR-related activity of the gene and hence constitute a useful biomarker for customizing anticancer therapies.
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Affiliation(s)
- Luc Friboulet
- Gustave Roussy; Villejuif, France; INSERM, U981; IRCIV; Villejuif, France; Département Hospitalo-Universitaire Thorax Innovation (DHU TORINO); Villejuif, France; Université Paris Sud; Kremlin-Bicêtre, France
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26
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Williamson EA, Hromas R. Repressing DNA repair to enhance chemotherapy: targeting MyD88 in colon cancer. J Natl Cancer Inst 2013; 105:926-7. [PMID: 23766531 DOI: 10.1093/jnci/djt148] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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27
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Sepe S, Payan-Gomez C, Milanese C, Hoeijmakers JH, Mastroberardino PG. Nucleotide excision repair in chronic neurodegenerative diseases. DNA Repair (Amst) 2013; 12:568-77. [PMID: 23726220 DOI: 10.1016/j.dnarep.2013.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
Impaired DNA repair involving the nucleotide excision repair (NER)/transcription-coupled repair (TCR) pathway cause human pathologies associated with severe neurological symptoms. These clinical observations suggest that defective NER/TCR might also play a critical role in chronic neurodegenerative disorders (ND), such as Alzheimer's and Parkinson's disease. Involvement of NER/TCR in these disorders is also substantiated by the evidence that aging constitutes the principal risk factor for chronic ND and that this DNA repair mechanism is very relevant for the aging process itself. Our understanding of the exact role of NER/TCR in chronic ND, however, is extremely rudimentary; while there is no doubt that defective NER/TCR can lead to neuronal death, evidence for its participation in the etiopathogenesis of ND is inconclusive thus far. Here we summarize the experimental observations supporting a role for NER/TCR in chronic ND and suggest questions and lines of investigation that might help in addressing this important issue. We also present a preliminary yet unprecedented meta-analysis on human brain microarray data to understand the expression levels of the various NER factors in the anatomical areas relevant for chronic ND pathogenesis. In summary, this review intends to highlight elements supporting a role of NER/TCR in these devastating disorders and to propose potential strategies of investigation.
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Affiliation(s)
- Sara Sepe
- Department of Genetics, Erasmus Medical Center, Rotterdam, The Netherlands
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28
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Chen Q, Liu K, Robinson AR, Clauson CL, Blair HC, Robbins PD, Niedernhofer LJ, Ouyang H. DNA damage drives accelerated bone aging via an NF-κB-dependent mechanism. J Bone Miner Res 2013; 28:1214-28. [PMID: 23281008 PMCID: PMC3662975 DOI: 10.1002/jbmr.1851] [Citation(s) in RCA: 89] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2012] [Revised: 11/15/2012] [Accepted: 11/26/2012] [Indexed: 12/21/2022]
Abstract
Advanced age is one of the most important risk factors for osteoporosis. Accumulation of oxidative DNA damage has been proposed to contribute to age-related deregulation of osteoblastic and osteoclastic cells. Excision repair cross complementary group 1-xeroderma pigmentosum group F (ERCC1-XPF) is an evolutionarily conserved structure-specific endonuclease that is required for multiple DNA repair pathways. Inherited mutations affecting expression of ERCC1-XPF cause a severe progeroid syndrome in humans, including early onset of osteopenia and osteoporosis, or anomalies in skeletal development. Herein, we used progeroid ERCC1-XPF-deficient mice, including Ercc1-null (Ercc1(-/-)) and hypomorphic (Ercc1(-/Δ)) mice, to investigate the mechanism by which DNA damage leads to accelerated bone aging. Compared to their wild-type littermates, both Ercc1(-/-) and Ercc1(-/Δ) mice display severe, progressive osteoporosis caused by reduced bone formation and enhanced osteoclastogenesis. ERCC1 deficiency leads to atrophy of osteoblastic progenitors in the bone marrow stromal cell (BMSC) population. There is increased cellular senescence of BMSCs and osteoblastic cells, as characterized by reduced proliferation, accumulation of DNA damage, and a senescence-associated secretory phenotype (SASP). This leads to enhanced secretion of inflammatory cytokines known to drive osteoclastogenesis, such as interleukin-6 (IL-6), tumor necrosis factor α (TNFα), and receptor activator of NF-κB ligand (RANKL), and thereby induces an inflammatory bone microenvironment favoring osteoclastogenesis. Furthermore, we found that the transcription factor NF-κB is activated in osteoblastic and osteoclastic cells of the Ercc1 mutant mice. Importantly, we demonstrated that haploinsufficiency of the p65 NF-κB subunit partially rescued the osteoporosis phenotype of Ercc1(-/Δ) mice. Finally, pharmacological inhibition of the NF-κB signaling via an I-κB kinase (IKK) inhibitor reversed cellular senescence and SASP in Ercc1(-/Δ) BMSCs. These results demonstrate that DNA damage drives osteoporosis through an NF-κB-dependent mechanism. Therefore, the NF-κB pathway represents a novel therapeutic target to treat aging-related bone disease.
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Affiliation(s)
- Qian Chen
- Department of Medicine, University of Pittsburgh School of Medicine, 1218 Scaife Hall 3550 Terrace Street, Pittsburgh, PA 15261
| | - Kai Liu
- Department of Restorative Dentistry and Comprehensive Care, University of Pittsburgh School of Dental Medicine, 3023 Salk Annex, 3501 Terrace Street, Pittsburgh, PA 15261 USA
| | - Andria R. Robinson
- Department of Human Genetics, University of Pittsburgh School of Public Health, 130 DeSoto Street, Pittsburgh, PA 15261 USA
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Hillman Cancer Center, 2.6, Pittsburgh, PA 15213 USA
| | - Cheryl L. Clauson
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Hillman Cancer Center, 2.6, Pittsburgh, PA 15213 USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 427 Bridgeside Point II, 450 Technology Drive, Pittsburgh, PA 15219 USA
| | - Harry C. Blair
- Pittsburgh Veteran’s Affairs Medical Center, Laboratory Service-646, 7180 Highland Drive, Pittsburgh, PA 15206 USA
- Department of Pathology, University of Pittsburgh School of Medicine, Scaife Hall S705, 3501 Terrace Street, Pittsburgh, PA 15261 USA
| | - Paul D. Robbins
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Hillman Cancer Center, 2.6, Pittsburgh, PA 15213 USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 427 Bridgeside Point II, 450 Technology Drive, Pittsburgh, PA 15219 USA
| | - Laura J. Niedernhofer
- University of Pittsburgh Cancer Institute, 5117 Centre Ave, Hillman Cancer Center, 2.6, Pittsburgh, PA 15213 USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 427 Bridgeside Point II, 450 Technology Drive, Pittsburgh, PA 15219 USA
| | - Hongjiao Ouyang
- Department of Restorative Dentistry and Comprehensive Care, University of Pittsburgh School of Dental Medicine, 3023 Salk Annex, 3501 Terrace Street, Pittsburgh, PA 15261 USA
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, 427 Bridgeside Point II, 450 Technology Drive, Pittsburgh, PA 15219 USA
- McGowan Institute for Regenerative Medicine, 450 Technology Drive Suite 300 Pittsburgh, PA 15219 USA
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29
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Friboulet L, Olaussen KA, Pignon JP, Shepherd FA, Tsao MS, Graziano S, Kratzke R, Douillard JY, Seymour L, Pirker R, Filipits M, André F, Solary E, Ponsonnailles F, Robin A, Stoclin A, Dorvault N, Commo F, Adam J, Vanhecke E, Saulnier P, Thomale J, Le Chevalier T, Dunant A, Rousseau V, Le Teuff G, Brambilla E, Soria JC. ERCC1 isoform expression and DNA repair in non-small-cell lung cancer. N Engl J Med 2013; 368:1101-10. [PMID: 23514287 PMCID: PMC4054818 DOI: 10.1056/nejmoa1214271] [Citation(s) in RCA: 297] [Impact Index Per Article: 27.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
BACKGROUND The excision repair cross-complementation group 1 (ERCC1) protein is a potential prognostic biomarker of the efficacy of cisplatin-based chemotherapy in non-small-cell lung cancer (NSCLC). Although several ongoing trials are evaluating the level of expression of ERCC1, no consensus has been reached regarding a method for evaluation. METHODS We used the 8F1 antibody to measure the level of expression of ERCC1 protein by means of immunohistochemical analysis in a validation set of samples obtained from 494 patients in two independent phase 3 trials (the National Cancer Institute of Canada Clinical Trials Group JBR.10 and the Cancer and Leukemia Group B 9633 trial from the Lung Adjuvant Cisplatin Evaluation Biology project). We compared the results of repeated staining of the entire original set of samples obtained from 589 patients in the International Adjuvant Lung Cancer Trial Biology study, which had led to the initial correlation between the absence of ERCC1 expression and platinum response, with our previous results in the same tumors. We mapped the epitope recognized by 16 commercially available ERCC1 antibodies and investigated the capacity of the different ERCC1 isoforms to repair platinum-induced DNA damage. RESULTS We were unable to validate the predictive effect of immunostaining for ERCC1 protein. The discordance in the results of staining for ERCC1 suggested a change in the performance of the 8F1 antibody since 2006. We found that none of the 16 antibodies could distinguish among the four ERCC1 protein isoforms, whereas only one isoform produced a protein that had full capacities for nucleotide excision repair and cisplatin resistance. CONCLUSIONS Immunohistochemical analysis with the use of currently available ERCC1 antibodies did not specifically detect the unique functional ERCC1 isoform. As a result, its usefulness in guiding therapeutic decision making is limited. (Funded by Eli Lilly and others.).
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Affiliation(s)
- Luc Friboulet
- INSERM Unité 981, and Département Hospitalo-Universitaire Thorax Innovation, Institut Gustave-Roussy, Villejuif, France
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Abstract
The quest for markers of sensitivity to cytotoxic agents has been ongoing for decades. In non-small-cell lung cancer, platinum compounds represent the cornerstone of systemic therapy. They target DNA and induce damage that cancer cells struggle to overcome. Somatic excision repair cross-complementing rodent repair deficiency, complementation group 1 (ERCC1), and ribonucleotide reductase M1 (RRM1) expression levels have been extensively explored as markers of DNA repair capacity in tumor cells. Although low ERCC1 and/or RRM1 expression is generally associated with sensitivity to platinum, the results published in retrospective and prospective studies are not always consistent. Against this background, we will examine in this review the function of these two biomarkers as well as the tools available for their assessment and the associated technical issues. Their prognostic and predictive values will be summarized and considered in terms of customizing systemic therapy according to biomarker (ERCC1 and RRM1) expression levels. We will also discuss why the use of both markers should at this point be restricted to clinical research and underline that functional readouts of DNA repair will help boost future strategies for biomarker discovery in the field.
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31
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McNeil EM, Melton DW. DNA repair endonuclease ERCC1-XPF as a novel therapeutic target to overcome chemoresistance in cancer therapy. Nucleic Acids Res 2012; 40:9990-10004. [PMID: 22941649 PMCID: PMC3488251 DOI: 10.1093/nar/gks818] [Citation(s) in RCA: 139] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The ERCC1–XPF complex is a structure-specific endonuclease essential for the repair of DNA damage by the nucleotide excision repair pathway. It is also involved in other key cellular processes, including DNA interstrand crosslink (ICL) repair and DNA double-strand break (DSB) repair. New evidence has recently emerged, increasing our understanding of its requirement in these additional roles. In this review, we focus on the protein–protein and protein–DNA interactions made by the ERCC1 and XPF proteins and discuss how these coordinate ERCC1–XPF in its various roles. In a number of different cancers, high expression of ERCC1 has been linked to a poor response to platinum-based chemotherapy. We discuss prospects for the development of DNA repair inhibitors that target the activity, stability or protein interactions of the ERCC1–XPF complex as a novel therapeutic strategy to overcome chemoresistance.
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Affiliation(s)
- Ewan M McNeil
- MRC Institute of Genetics and Molecular Medicine, University of Edinburgh, MRC Human Genetics Unit, Western General Hospital, Crewe Road, Edinburgh EH4 2XU, UK
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32
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Borst P. Cancer drug pan-resistance: pumps, cancer stem cells, quiescence, epithelial to mesenchymal transition, blocked cell death pathways, persisters or what? Open Biol 2012; 2:120066. [PMID: 22724067 PMCID: PMC3376736 DOI: 10.1098/rsob.120066] [Citation(s) in RCA: 137] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2012] [Accepted: 04/27/2012] [Indexed: 12/11/2022] Open
Abstract
Although chemotherapy of tumours has scored successes, drug resistance remains the major cause of death of cancer patients. Initial treatment often leaves residual disease, from which the tumour regrows. Eventually, most tumours become resistant to all available chemotherapy. I call this pan-resistance to distinguish it from multi-drug resistance, usually describing resistance caused by upregulation of drug transporters, such as P-glycoprotein. In this review, I discuss mechanisms proposed to explain both residual disease and pan-resistance. Although plausible explanations are at hand for residual disease, pan-resistance is still a mystery. My conclusion is that it is time for a major effort to solve this mystery using the new genetically modified mouse tumour models that produce real tumours resembling cancer in human patients.
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MESH Headings
- ATP Binding Cassette Transporter, Subfamily B, Member 1/antagonists & inhibitors
- ATP Binding Cassette Transporter, Subfamily B, Member 1/physiology
- ATP-Binding Cassette Transporters/physiology
- Animals
- Antineoplastic Agents/chemistry
- Antineoplastic Agents/pharmacokinetics
- Antineoplastic Agents/pharmacology
- Antineoplastic Agents/therapeutic use
- Biological Availability
- Blood-Brain Barrier
- Cell Cycle
- Cell Death/drug effects
- Chromatin Assembly and Disassembly
- Clonal Evolution
- DNA Repair
- DNA, Neoplasm/drug effects
- Drug Resistance, Neoplasm/genetics
- Drug Resistance, Neoplasm/physiology
- Epigenesis, Genetic
- Epithelial-Mesenchymal Transition
- Humans
- Mice
- Models, Biological
- Neoplasm Proteins/antagonists & inhibitors
- Neoplasm Proteins/physiology
- Neoplasm, Residual
- Neoplasms, Experimental/drug therapy
- Neoplastic Stem Cells/cytology
- Neoplastic Stem Cells/drug effects
- Neoplastic Stem Cells/metabolism
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Affiliation(s)
- Piet Borst
- Molecular Oncology , NKI-AVL , Plesmanlaan 121, Amsterdam, The Netherlands.
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33
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Accelerated age-related cognitive decline and neurodegeneration, caused by deficient DNA repair. J Neurosci 2011; 31:12543-53. [PMID: 21880916 DOI: 10.1523/jneurosci.1589-11.2011] [Citation(s) in RCA: 92] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Age-related cognitive decline and neurodegenerative diseases are a growing challenge for our societies with their aging populations. Accumulation of DNA damage has been proposed to contribute to these impairments, but direct proof that DNA damage results in impaired neuronal plasticity and memory is lacking. Here we take advantage of Ercc1(Δ/-) mutant mice, which are impaired in DNA nucleotide excision repair, interstrand crosslink repair, and double-strand break repair. We show that these mice exhibit an age-dependent decrease in neuronal plasticity and progressive neuronal pathology, suggestive of neurodegenerative processes. A similar phenotype is observed in mice where the mutation is restricted to excitatory forebrain neurons. Moreover, these neuron-specific mutants develop a learning impairment. Together, these results suggest a causal relationship between unrepaired, accumulating DNA damage, and age-dependent cognitive decline and neurodegeneration. Hence, accumulated DNA damage could therefore be an important factor in the onset and progression of age-related cognitive decline and neurodegenerative diseases.
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Karpac J, Younger A, Jasper H. Dynamic coordination of innate immune signaling and insulin signaling regulates systemic responses to localized DNA damage. Dev Cell 2011; 20:841-54. [PMID: 21664581 DOI: 10.1016/j.devcel.2011.05.011] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2010] [Revised: 03/02/2011] [Accepted: 05/14/2011] [Indexed: 12/19/2022]
Abstract
Metazoans adapt to changing environmental conditions and to harmful challenges by attenuating growth and metabolic activities systemically. Recent studies in mice and flies indicate that endocrine signaling interactions between insulin/IGF signaling (IIS) and innate immune signaling pathways are critical for this adaptation, yet the temporal and spatial hierarchy of these signaling events remains elusive. Here, we identify and characterize a program of signaling interactions that regulates the systemic response of the Drosophila larva to localized DNA damage. We provide evidence that epidermal DNA damage induces an innate immune response that is kept in check by systemic repression of IIS activity. IIS repression induces NFκB/Relish signaling in the fat body, which is required for recovery of IIS activity in a second phase of the systemic response to DNA damage. This systemic response to localized DNA damage thus coordinates growth and metabolic activities across tissues, ensuring growth homeostasis and survival of the animal.
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Affiliation(s)
- Jason Karpac
- Department of Biology, University of Rochester, NY 14627, USA
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35
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Gregg SQ, Robinson AR, Niedernhofer LJ. Physiological consequences of defects in ERCC1-XPF DNA repair endonuclease. DNA Repair (Amst) 2011; 10:781-91. [PMID: 21612988 DOI: 10.1016/j.dnarep.2011.04.026] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
ERCC1-XPF is a structure-specific endonuclease required for nucleotide excision repair, interstrand crosslink repair, and the repair of some double-strand breaks. Mutations in ERCC1 or XPF cause xeroderma pigmentosum, XFE progeroid syndrome or cerebro-oculo-facio-skeletal syndrome, characterized by increased risk of cancer, accelerated aging and severe developmental abnormalities, respectively. This review provides a comprehensive overview of the health impact of ERCC1-XPF deficiency, based on these rare diseases and mouse models of them. This offers an understanding of the tremendous health impact of DNA damage derived from environmental and endogenous sources.
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Affiliation(s)
- Siobhán Q Gregg
- Department of Microbiology and Molecular Genetics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15219, USA
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36
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Wang C, Lambert MW. The Fanconi anemia protein, FANCG, binds to the ERCC1-XPF endonuclease via its tetratricopeptide repeats and the central domain of ERCC1. Biochemistry 2010; 49:5560-9. [PMID: 20518486 DOI: 10.1021/bi100584c] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
There is evidence that Fanconi anemia (FA) proteins play an important role in the repair of DNA interstrand cross-links (ICLs), but the precise mechanism by which this occurs is not clear. One of the critical steps in the ICL repair process involves unhooking of the cross-link from DNA by incisions on one strand on either side of the ICL and its subsequent removal. The ERCC1-XPF endonuclease is involved in this unhooking step and in the removal of the cross-link. We have previously shown that several of the FA proteins are needed to produce incisions created by ERCC1-XPF at sites of ICLs. To more clearly establish a link between FA proteins and the incision step(s) mediated by ERCC1-XPF, we undertook yeast two-hybrid analysis to determine whether FANCA, FANCC, FANCF, and FANCG directly interact with ERCC1 and XPF and, if so, to determine the sites of interaction. One of these FA proteins, FANCG, was found to have a strong affinity for ERCC1 and a moderate affinity for XPF. FANCG has been shown to contain seven tetratricopeptide repeat (TPR) motifs, which are motifs that mediate protein-protein interactions. Mapping the sites of interaction of FANCG with ERCC1, using site-directed mutagenesis, demonstrated that TPRs 1, 3, 5, and 6 are needed for binding of FANCG to ERCC1. ERCC1, in turn, was shown to interact with FANCG via its central domain, which is different from the region of ERCC1 that binds to XPF. This binding between FANCG and the ERCC1-XPF endonuclease, combined with our previous studies which show that FANCG is involved in the incision step mediated by ERCC1-XPF, establishes a link between an FA protein and the critical unhooking step of the ICL repair process.
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Affiliation(s)
- Chuan Wang
- Department of Pathology and Laboratory Medicine, New Jersey Medical School and Graduate School of Biomedical Sciences, University of Medicine and Dentistry of New Jersey, Newark, New Jersey 07103, USA
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Orelli B, McClendon TB, Tsodikov OV, Ellenberger T, Niedernhofer LJ, Schärer OD. The XPA-binding domain of ERCC1 is required for nucleotide excision repair but not other DNA repair pathways. J Biol Chem 2009; 285:3705-3712. [PMID: 19940136 DOI: 10.1074/jbc.m109.067538] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
The endonuclease ERCC1-XPF incises the damaged strand of DNA 5' to a lesion during nucleotide excision repair (NER) and has additional, poorly characterized functions in interstrand cross-link repair, double-strand break repair, and homologous recombination. XPA, another key factor in NER, interacts with ERCC1 and recruits it to sites of damage. We identified ERCC1 residues that are critical for the interaction with XPA and assessed their importance for NER in vitro and in vivo. Mutation of two conserved residues (Asn-110 and Tyr-145) located in the XPA-binding site of ERCC1 dramatically affected NER but not nuclease activity on model DNA substrates. In ERCC1-deficient cells expressing ERCC1(N110A/Y145A), the nuclease was not recruited to sites of UV damage. The repair of UV-induced (6-4)photoproducts was severely impaired in these cells, and they were hypersensitive to UV irradiation. Remarkably, the ERCC1(N110A/Y145A) protein rescues the sensitivity of ERCC1-deficient cells to cross-linking agents. Our studies suggest that ERCC1-XPF engages in different repair pathways through specific protein-protein interactions and that these functions can be separated through the selective disruption of these interactions. We discuss the impact of these findings for understanding how ERCC1 contributes to resistance of tumor cells to therapeutic agents such as cisplatin.
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Affiliation(s)
- Barbara Orelli
- From the Department of Pharmacological Sciences and Chemistry, Stony Brook University, Stony Brook, New York 11794-3400
| | - T Brooke McClendon
- the Department of Microbiology and Molecular Genetics and Cancer Institute, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15213-1863
| | - Oleg V Tsodikov
- the Department of Medicinal Chemistry, College of Pharmacy, University of Michigan, Ann Arbor, Michigan 48109-2676, and
| | - Tom Ellenberger
- the Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110
| | - Laura J Niedernhofer
- the Department of Microbiology and Molecular Genetics and Cancer Institute, Hillman Cancer Center, University of Pittsburgh, Pittsburgh, Pennsylvania 15213-1863
| | - Orlando D Schärer
- From the Department of Pharmacological Sciences and Chemistry, Stony Brook University, Stony Brook, New York 11794-3400.
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Giglia-Mari G, Theil AF, Mari PO, Mourgues S, Nonnekens J, Andrieux LO, de Wit J, Miquel C, Wijgers N, Maas A, Fousteri M, Hoeijmakers JHJ, Vermeulen W. Differentiation driven changes in the dynamic organization of Basal transcription initiation. PLoS Biol 2009; 7:e1000220. [PMID: 19841728 PMCID: PMC2754661 DOI: 10.1371/journal.pbio.1000220] [Citation(s) in RCA: 46] [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: 12/15/2008] [Accepted: 09/07/2009] [Indexed: 01/01/2023] Open
Abstract
A novel mouse model reveals that the dynamic behavior of transcription factors can vary considerably between different cells of an organism. Studies based on cell-free systems and on in vitro–cultured living cells support the concept that many cellular processes, such as transcription initiation, are highly dynamic: individual proteins stochastically bind to their substrates and disassemble after reaction completion. This dynamic nature allows quick adaptation of transcription to changing conditions. However, it is unknown to what extent this dynamic transcription organization holds for postmitotic cells embedded in mammalian tissue. To allow analysis of transcription initiation dynamics directly into living mammalian tissues, we created a knock-in mouse model expressing fluorescently tagged TFIIH. Surprisingly and in contrast to what has been observed in cultured and proliferating cells, postmitotic murine cells embedded in their tissue exhibit a strong and long-lasting transcription-dependent immobilization of TFIIH. This immobilization is both differentiation driven and development dependent. Furthermore, although very statically bound, TFIIH can be remobilized to respond to new transcriptional needs. This divergent spatiotemporal transcriptional organization in different cells of the soma revisits the generally accepted highly dynamic concept of the kinetic framework of transcription and shows how basic processes, such as transcription, can be organized in a fundamentally different fashion in intact organisms as previously deduced from in vitro studies. The accepted model of eukaryotic mRNA production is that transcription factors spend most of their time diffusing throughout the cell nucleus, encountering gene promoters (their substrate) in a random fashion and binding to them for a very short time. A similar modus operandi has been accepted as a paradigm for interactions within most of the chromatin-associated enzymatic processes (transcription, replication, DNA damage response). However, it is not known whether such behavior is indeed a common characteristic for all cells in the organism. To answer this question, we generated a knock-in mouse that expresses in all cells a fluorescently tagged transcription factor (TFIIH) that functions in both transcription initiation and DNA repair. This new tool, when combined with quantitative imaging techniques, allowed us to monitor the mobility of this transcription factor in virtually all living tissues. In this study, we show that, in contrast to the aforementioned paradigm, in highly differentiated postmitotic cells such as neurons, hepatocytes, and cardiac myocytes, TFIIH is effectively immobilized on the chromatin during transcription, whereas in proliferative cells, TFIIH has the same dynamic behavior as in cultured cells. Our study also points out that results obtained from in vitro or cultured cell systems cannot always be directly extrapolated to the whole organism. More importantly, this raises a question for researchers in the transcription field: why do some cells opt for a dynamic framework for transcription, whereas others exhibit a static one?
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Affiliation(s)
- Giuseppina Giglia-Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
- * E-mail: (GG-M); (WV)
| | - Arjan F. Theil
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Pierre-Olivier Mari
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Sophie Mourgues
- CNRS, IPBS (Institut de Pharmacologie et de Biologie Structurale), Toulouse, France
- Université de Toulouse, UPS, IPBS, Toulouse, France
| | - Julie Nonnekens
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Jan de Wit
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | | | - Nils Wijgers
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Alex Maas
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
| | - Maria Fousteri
- Department of Toxicogenetics, LUMC, Leiden, The Netherlands
| | | | - Wim Vermeulen
- Department of Genetics, Erasmus MC, Rotterdam, The Netherlands
- * E-mail: (GG-M); (WV)
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The nucleotide excision repair of DNA in human cells and its association with xeroderma pigmentosum. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2009; 637:113-9. [PMID: 19181116 DOI: 10.1007/978-0-387-09599-8_12] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/19/2023]
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40
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Das D, Tripsianes K, Jaspers NGJ, Hoeijmakers JHJ, Kaptein R, Boelens R, Folkers GE. The HhH domain of the human DNA repair protein XPF forms stable homodimers. Proteins 2008; 70:1551-63. [PMID: 17912758 DOI: 10.1002/prot.21635] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The human XPF-ERCC1 protein complex plays an essential role in nucleotide excision repair by catalysing positioned nicking of a DNA strand at the 5' side of the damage. We have recently solved the structure of the heterodimeric complex of the C-terminal domains of XPF and ERCC1 (Tripsianes et al., Structure 2005;13:1849-1858). We found that this complex comprises a pseudo twofold symmetry axis and that the helix-hairpin-helix motif of ERCC1 is required for DNA binding, whereas the corresponding domain of XPF is functioning as a scaffold for complex formation with ERCC1. Despite the functional importance of heterodimerization, the C-terminal domain of XPF can also form homodimers in vitro. We here compare the stabilities of homodimeric and heterodimeric complexes of the C-terminal domains of XPF and ERCC1. The higher stability of the XPF HhH complexes under various experimental conditions, determined using CD and NMR spectroscopy and mass spectrometry, is well explained by the structural differences that exist between the HhH domains of the two complexes. The XPF HhH homodimer has a larger interaction interface, aromatic stacking interactions, and additional hydrogen bond contacts as compared to the XPF/ERCC1 HhH complex, which accounts for its higher stability.
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Affiliation(s)
- Devashish Das
- Bijvoet Center for Biomolecular Research, Utrecht University, 3584 CH Utrecht, The Netherlands
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Kulkarni A, Wilson DM. The involvement of DNA-damage and -repair defects in neurological dysfunction. Am J Hum Genet 2008; 82:539-66. [PMID: 18319069 PMCID: PMC2427185 DOI: 10.1016/j.ajhg.2008.01.009] [Citation(s) in RCA: 50] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 12/17/2007] [Accepted: 01/03/2008] [Indexed: 10/22/2022] Open
Abstract
A genetic link between defects in DNA repair and neurological abnormalities has been well established through studies of inherited disorders such as ataxia telangiectasia and xeroderma pigmentosum. In this review, we present a comprehensive summary of the major types of DNA damage, the molecular pathways that function in their repair, and the connection between defective DNA-repair responses and specific neurological disease. Particular attention is given to describing the nature of the repair defect and its relationship to the manifestation of the associated neurological dysfunction. Finally, the review touches upon the role of oxidative stress, a leading precursor to DNA damage, in the development of certain neurodegenerative pathologies, such as Alzheimer's and Parkinson's.
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Affiliation(s)
- Avanti Kulkarni
- Laboratory of Molecular Gerontology, National Institute of Aging, National Institutes of Health, Baltimore, MD 21224, USA
| | - David M. Wilson
- Laboratory of Molecular Gerontology, National Institute of Aging, National Institutes of Health, Baltimore, MD 21224, USA
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Structural basis for the recruitment of ERCC1-XPF to nucleotide excision repair complexes by XPA. EMBO J 2007; 26:4768-76. [PMID: 17948053 DOI: 10.1038/sj.emboj.7601894] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2007] [Accepted: 09/25/2007] [Indexed: 12/16/2022] Open
Abstract
The nucleotide excision repair (NER) pathway corrects DNA damage caused by sunlight, environmental mutagens and certain antitumor agents. This multistep DNA repair reaction operates by the sequential assembly of protein factors at sites of DNA damage. The efficient recognition of DNA damage and its repair are orchestrated by specific protein-protein and protein-DNA interactions within NER complexes. We have investigated an essential protein-protein interaction of the NER pathway, the binding of the XPA protein to the ERCC1 subunit of the repair endonuclease ERCC1-XPF. The structure of ERCC1 in complex with an XPA peptide shows that only a small region of XPA interacts with ERCC1 to form a stable complex exhibiting submicromolar binding affinity. However, this XPA peptide is a potent inhibitor of NER activity in a cell-free assay, blocking the excision of a cisplatin adduct from DNA. The structure of the peptide inhibitor bound to its target site reveals a binding interface that is amenable to the development of small molecule peptidomimetics that could be used to modulate NER repair activities in vivo.
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Zhang N, Liu X, Li L, Legerski R. Double-strand breaks induce homologous recombinational repair of interstrand cross-links via cooperation of MSH2, ERCC1-XPF, REV3, and the Fanconi anemia pathway. DNA Repair (Amst) 2007; 6:1670-8. [PMID: 17669695 PMCID: PMC2586762 DOI: 10.1016/j.dnarep.2007.06.002] [Citation(s) in RCA: 69] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2007] [Revised: 06/12/2007] [Accepted: 06/12/2007] [Indexed: 11/16/2022]
Abstract
DNA interstrand cross-linking agents have been widely used in chemotherapeutic treatment of cancer. The majority of interstrand cross-links (ICLs) in mammalian cells are removed via a complex process that involves the formation of double-strand breaks at replication forks, incision of the ICL, and subsequent error-free repair by homologous recombination. How double-strand breaks effect the removal of ICLs and the downstream homologous recombination process is not clear. Here, we describe a plasmid-based recombination assay in which one copy of the CFP gene is inactivated by a site-specific psoralen ICL and can be repaired by gene conversion with a mutated homologous donor sequence. We found that the homology-dependent recombination (HDR) is inhibited by the ICL. However, when we introduced a double-strand break adjacent to the site of the ICL, the removal of the ICL was enhanced and the substrate was funneled into a HDR repair pathway. This process was not dependent on the nucleotide excision repair pathway, but did require the ERCC1-XPF endonuclease and REV3. In addition, both the Fanconi anemia pathway and the mismatch repair protein MSH2 were required for the recombinational repair processing of the ICL. These results suggest that the juxtaposition of an ICL and a DSB stimulates repair of ICLs through a process requiring components of mismatch repair, ERCC1-XPF, REV3, Fanconi anemia proteins, and homologous recombination repair factors.
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Affiliation(s)
- Nianxiang Zhang
- Department of Cancer Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Xiuping Liu
- Department of Cancer Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Lei Li
- Department of Experimental Radiation Oncology, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
| | - Randy Legerski
- Department of Cancer Genetics, The University of Texas M.D. Anderson Cancer Center, Houston, Texas 77030
- *Corresponding author. Fax. 713-792-1474; E-Mail:
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Francis MA, Bagga P, Athwal R, Rainbow AJ. Partial Complementation of the DNA Repair Defects in Cells from Xeroderma Pigmentosum Groups A, C, D and F but not G by the denV Gene from Bacteriophage T4 ¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0720365pcotdr2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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45
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Jaspers NGJ, Raams A, Silengo MC, Wijgers N, Niedernhofer LJ, Robinson AR, Giglia-Mari G, Hoogstraten D, Kleijer WJ, Hoeijmakers JHJ, Vermeulen W. First reported patient with human ERCC1 deficiency has cerebro-oculo-facio-skeletal syndrome with a mild defect in nucleotide excision repair and severe developmental failure. Am J Hum Genet 2007; 80:457-66. [PMID: 17273966 PMCID: PMC1821117 DOI: 10.1086/512486] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2006] [Accepted: 01/05/2007] [Indexed: 01/21/2023] Open
Abstract
Nucleotide excision repair (NER) is a genome caretaker mechanism responsible for removing helix-distorting DNA lesions, most notably ultraviolet photodimers. Inherited defects in NER result in profound photosensitivity and the cancer-prone syndrome xeroderma pigmentosum (XP) or two progeroid syndromes: Cockayne and trichothiodystrophy syndromes. The heterodimer ERCC1-XPF is one of two endonucleases required for NER. Mutations in XPF are associated with mild XP and rarely with progeria. Mutations in ERCC1 have not been reported. Here, we describe the first case of human inherited ERCC1 deficiency. Patient cells showed moderate hypersensitivity to ultraviolet rays and mitomycin C, yet the clinical features were very severe and, unexpectedly, were compatible with a diagnosis of cerebro-oculo-facio-skeletal syndrome. This discovery represents a novel complementation group of patients with defective NER. Further, the clinical severity, coupled with a relatively mild repair defect, suggests novel functions for ERCC1.
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Giglia-Mari G, Miquel C, Theil AF, Mari PO, Hoogstraten D, Ng JMY, Dinant C, Hoeijmakers JHJ, Vermeulen W. Dynamic interaction of TTDA with TFIIH is stabilized by nucleotide excision repair in living cells. PLoS Biol 2006; 4:e156. [PMID: 16669699 PMCID: PMC1457016 DOI: 10.1371/journal.pbio.0040156] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2005] [Accepted: 03/15/2006] [Indexed: 01/11/2023] Open
Abstract
Transcription/repair factor IIH (TFIIH) is essential for RNA polymerase II transcription and nucleotide excision repair (NER). This multi-subunit complex consists of ten polypeptides, including the recently identified small 8-kDa trichothiodystrophy group A (TTDA)/ hTFB5 protein. Patients belonging to the rare neurodevelopmental repair syndrome TTD-A carry inactivating mutations in the
TTDA/hTFB5 gene. One of these mutations completely inactivates the protein, whereas other TFIIH genes only tolerate point mutations that do not compromise the essential role in transcription. Nevertheless, the severe NER-deficiency in TTD-A suggests that the TTDA protein is critical for repair. Using a fluorescently tagged and biologically active version of TTDA, we have investigated the involvement of TTDA in repair and transcription in living cells. Under non-challenging conditions, TTDA is present in two distinct kinetic pools: one bound to TFIIH, and a free fraction that shuttles between the cytoplasm and nucleus. After induction of NER-specific DNA lesions, the equilibrium between these two pools dramatically shifts towards a more stable association of TTDA to TFIIH. Modulating transcriptional activity in cells did not induce a similar shift in this equilibrium. Surprisingly, DNA conformations that only provoke an abortive-type of NER reaction do not result into a more stable incorporation of TTDA into TFIIH. These findings identify TTDA as the first TFIIH subunit with a primarily NER-dedicated role in vivo and indicate that its interaction with TFIIH reflects productive NER.
Transcription/repair factor IIH (TFIIH) is a multi-subunit protein complex essential for RNA polymerase II transcription and nucleotide excision repair (NER). The authors show that the TTDA subunit is associated with TFIIH specifically during NER.
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Affiliation(s)
- Giuseppina Giglia-Mari
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Catherine Miquel
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Arjan F Theil
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Pierre-Olivier Mari
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Deborah Hoogstraten
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Jessica M. Y Ng
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Christoffel Dinant
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Jan H. J Hoeijmakers
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
| | - Wim Vermeulen
- 1Department of Cell Biology and Genetics, Medical Genetics Center, Erasmus Medical Center, Rotterdam, Netherlands
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Tripsianes K, Folkers G, Ab E, Das D, Odijk H, Jaspers NGJ, Hoeijmakers JHJ, Kaptein R, Boelens R. The structure of the human ERCC1/XPF interaction domains reveals a complementary role for the two proteins in nucleotide excision repair. Structure 2006; 13:1849-58. [PMID: 16338413 DOI: 10.1016/j.str.2005.08.014] [Citation(s) in RCA: 92] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 08/26/2005] [Accepted: 08/28/2005] [Indexed: 11/21/2022]
Abstract
The human ERCC1/XPF complex is a structure-specific endonuclease with defined polarity that participates in multiple DNA repair pathways. We report the heterodimeric structure of the C-terminal domains of both proteins responsible for ERCC1/XPF complex formation. Both domains exhibit the double helix-hairpin-helix motif (HhH)2, and they are related by a pseudo-2-fold symmetry axis. In the XPF domain, the hairpin of the second motif is replaced by a short turn. The ERCC1 domain folds properly only in the presence of the XPF domain, which implies a role for XPF as a scaffold for the folding of ERCC1. The intersubunit interactions are largely hydrophobic in nature. NMR titration data show that only the ERCC1 domain of the ERCC1/XPF complex is involved in DNA binding. On the basis of these findings, we propose a model for the targeting of XPF nuclease via ERCC1-mediated interactions in the context of nucleotide excision repair.
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Affiliation(s)
- Konstantinos Tripsianes
- Department of NMR Spectroscopy, Bijvoet Center for Biomolecular Research, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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Tsodikov OV, Enzlin JH, Schärer OD, Ellenberger T. Crystal structure and DNA binding functions of ERCC1, a subunit of the DNA structure-specific endonuclease XPF-ERCC1. Proc Natl Acad Sci U S A 2005; 102:11236-41. [PMID: 16076955 PMCID: PMC1183572 DOI: 10.1073/pnas.0504341102] [Citation(s) in RCA: 128] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2005] [Indexed: 11/18/2022] Open
Abstract
Human XPF-ERCC1 is a DNA endonuclease that incises a damaged DNA strand on the 5' side of a lesion during nucleotide excision repair and has additional role(s) in homologous recombination and DNA interstrand crosslink repair. We show that a truncated form of XPF lacking the N-terminal helicase-like domain in complex with ERCC1 exhibits a structure-specific endonuclease activity with similar specificity to that of full-length XPF-ERCC1. Two domains of ERCC1, a central domain and a C-terminal tandem helix-hairpin-helix (HhH2) dimerization domain, bind to ssDNA. The central domain of ERCC1 binds ssDNA/dsDNA junctions with a defined polarity, preferring a 5' single-stranded overhang. The XPF-ERCC1 HhH2 domain heterodimer contains two independent ssDNA-binding surfaces, which are revealed by a crystal structure of the protein complex. A crystal structure of the central domain of ERCC1 shows its fold is strikingly similar to that of the nuclease domains of the archaeal Mus81/XPF homologs, despite very low sequence homology. A groove lined with basic and aromatic residues on the surface of ERCC1 has apparently been adapted to interact with ssDNA. On the basis of these crystallographic and biochemical studies, we propose a model in which XPF-ERCC1 recognizes a branched DNA substrate by binding the two ssDNA arms with the two HhH2 domains of XPF and ERCC1 and by binding the 5'-ssDNA arm with the central domain of ERCC1.
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Affiliation(s)
- Oleg V Tsodikov
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, 240 Longwood Avenue, Boston, MA 02115, USA
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Choi YJ, Ryu KS, Ko YM, Chae YK, Pelton JG, Wemmer DE, Choi BS. Biophysical Characterization of the Interaction Domains and Mapping of the Contact Residues in the XPF-ERCC1 Complex. J Biol Chem 2005; 280:28644-52. [PMID: 15932882 DOI: 10.1074/jbc.m501083200] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
XPF and ERCC1 exist as a heterodimer to be stable and active in cells and catalyze DNA cleavage on the 5'-side of a lesion during nucleotide excision repair. To characterize the specific interaction between XPF and ERCC1, we expressed the human ERCC1 binding domain of XPF (XPF-EB) and the XPF binding domain of ERCC1 (ERCC1-FB) in Escherichia coli. Milligram quantities of a heterodimer were characterized with gel filtration chromatography, an Ni(2+)-NTA binding assay, and analytical ultracentrifugation. Cross-linking experiments at high salt concentrations revealed that XPF interacts with ERCC1 mainly through hydrophobic interactions. XPF-EB was also shown to homodimerize in the absence of ERCC1. NMR cross-saturation methods were applied to map the residues involved in formation of the XPF-EB.XPF-EB homodimer and the XPF-EB.ERCC1-FB heterodimer. Helix H3 and the C-terminal region of XPF-EB were either within or in close proximity to the homodimer interface, whereas the ERCC1-FB binding site of XPF-EB was distributed across helix H1, a small part of H2, H3, and the C-terminal region, most of which exhibited large changes in chemical shift upon ERCC1 binding. The XPF-EB heterodimeric interface is larger than the XPF-EB homodimeric one, which could explain why XPF has a stronger affinity for ERCC1 than for a second molecule of XPF. The XPF binding sites of ERCC1 were located in helices H1 and H3 and in the C-terminal region, similar to the involved surface of XPF. We used cross-saturation data and the crystal structure of related proteins to model the two complexes.
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Affiliation(s)
- Yun-Jeong Choi
- Department of Chemistry and National Creative Research Initiative Center, Korea Advanced Institute of Science and Technology, 373-1 Guseong-dong, Yuseong-gu, Daejon 305-701, Korea
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Zhou W, Liu G, Park S, Wang Z, Wain JC, Lynch TJ, Su L, Christiani DC. Gene-smoking interaction associations for the ERCC1 polymorphisms in the risk of lung cancer. Cancer Epidemiol Biomarkers Prev 2005; 14:491-6. [PMID: 15734977 DOI: 10.1158/1055-9965.epi-04-0612] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Cigarette smoking may induce DNA damage. Lower DNA repair capacities have been associated with higher risk of lung cancer. Excision repair cross-complementing group 1 (ERCC1) is the lead enzyme in the nucleotide excision repair process, and low expression of ERCC1 mRNA levels has been associated with higher risk of cancers. We examined the association between two polymorphisms of ERCC1, 8092C > A (rs3212986) and 19007T > C (codon 118, rs11615), which are associated with altered ERCC1 mRNA stability and mRNA levels, in 1,752 Caucasian lung cancer patients and 1,358 controls. The results were analyzed using logistic regression models, adjusting for relevant covariates. The two polymorphisms were in Hardy-Weinberg disequilibrium and in linkage disequilibrium. There was no overall association between ERCC1 polymorphisms and lung cancer risk, with the adjusted odds ratios (AOR) of 1.26 [95% confidence interval (95% CI), 0.81-1.96] for the 8092C > A polymorphism (A/A versus C/C) and 0.93 (95% CI, 0.67-1.30) for the 19007T > C polymorphism (C/C versus T/T). Stratified analyses revealed that the AORs for the 8092C > A polymorphism (A/A versus C/C) decreased significantly as pack-years increased, with the AOR of 2.11 (95% CI, 1.03-4.31) in never smokers and 0.50 (95% CI, 0.25-1.01) in heavy smokers (>/=56 pack-years), respectively. Consistent results were found when gene-smoking interaction was incorporated by joint effects and interactions models that considered both discrete and continuous variables for cumulative smoking exposure. The same direction for the gene-smoking interaction was found for the 19007T > C polymorphism, although the interaction was not statistically significant. In conclusion, ERCC1 8092C > A polymorphism may modify the associations between cumulative cigarette smoking and lung cancer risk.
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Affiliation(s)
- Wei Zhou
- Occupational Health Program, Department of Environmental Health, Harvard School of Public Health, 665 Huntington Avenue, Boston, MA 02115, USA
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