1
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Lv Z, Wu X, Lu P, Xu X, Wang J, Zhang C, Liu W, Gao Y, Lu C, Zhang Y, Kou H. POLE2 knockdown suppresses lymphoma progression via downregulating Wnt/β-catenin signaling pathway. Mol Cell Biochem 2024; 479:487-497. [PMID: 37097331 DOI: 10.1007/s11010-023-04738-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2023] [Accepted: 04/09/2023] [Indexed: 04/26/2023]
Abstract
Lymphoma is the most common malignant tumor arising from immune system. Recently, DNA polymerase epsilon subunit 2 (POLE2) was identified to be a tumor promotor in a variety of malignant tumors. However, the biological role of POLE2 in lymphoma is still largely unclear. In our present study, the expression patterns of POLE2 in lymphoma tissues were identified by immunohistochemistry (IHC) staining of human tissue microarray. Cell viability was determined by CCK-8 assay. Cell apoptosis and cycle distribution were evaluated by Annexin V and PI staining, respectively. Cell migration was analyzed by transwell assay. Tumor growth in vivo was observed by a xenograft model of mice. The potential signaling was explored by human phospho-kinase array and immunoblotting. POLE2 was significantly upregulated in human lymphoma tissues and cells. POLE2 knockdown attenuated the proliferation, migration capabilities of lymphoma cells, as well as induced cell apoptosis and cycle arrest. Moreover, POLE2 depletion impaired the tumor growth in mice. Furthermore, POLE2 knockdown apparently inhibited the activation of β-Catenin and downregulated the expression of Wnt/β-Catenin signaling-related proteins. POLE2 knockdown suppressed the proliferation and migration of lymphoma cells by inhibiting Wnt/β-Catenin signaling pathway. POLE2 may serve as a novel therapeutic target for lymphoma.
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Affiliation(s)
- Zhenhui Lv
- Department of Hematology, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Xueqiong Wu
- Department of Hematology, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Ping Lu
- Department of Hematology, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Xinxin Xu
- Department of Hematology, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Jiaju Wang
- Department of Hematology, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Cui Zhang
- Department of Hematology, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Wenting Liu
- Department of Hematology, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Yan Gao
- Department of Hematology, Zibo Central Hospital, Zibo, 255000, Shandong, China
| | - Cong Lu
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Yinqiang Zhang
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China
| | - Haiming Kou
- Department of Hematology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Wuhan, 430030, China.
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2
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Day M, Tetik B, Parlak M, Almeida-Hernández Y, Räschle M, Kaschani F, Siegert H, Marko A, Sanchez-Garcia E, Kaiser M, Barker IA, Pearl LH, Oliver AW, Boos D. TopBP1 utilises a bipartite GINS binding mode to support genome replication. Nat Commun 2024; 15:1797. [PMID: 38413589 PMCID: PMC10899662 DOI: 10.1038/s41467-024-45946-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2023] [Accepted: 02/07/2024] [Indexed: 02/29/2024] Open
Abstract
Activation of the replicative Mcm2-7 helicase by loading GINS and Cdc45 is crucial for replication origin firing, and as such for faithful genetic inheritance. Our biochemical and structural studies demonstrate that the helicase activator GINS interacts with TopBP1 through two separate binding surfaces, the first involving a stretch of highly conserved amino acids in the TopBP1-GINI region, the second a surface on TopBP1-BRCT4. The two surfaces bind to opposite ends of the A domain of the GINS subunit Psf1. Mutation analysis reveals that either surface is individually able to support TopBP1-GINS interaction, albeit with reduced affinity. Consistently, either surface is sufficient for replication origin firing in Xenopus egg extracts and becomes essential in the absence of the other. The TopBP1-GINS interaction appears sterically incompatible with simultaneous binding of DNA polymerase epsilon (Polε) to GINS when bound to Mcm2-7-Cdc45, although TopBP1-BRCT4 and the Polε subunit PolE2 show only partial competitivity in binding to Psf1. Our TopBP1-GINS model improves the understanding of the recently characterised metazoan pre-loading complex. It further predicts the coordination of three molecular origin firing processes, DNA polymerase epsilon arrival, TopBP1 ejection and GINS integration into Mcm2-7-Cdc45.
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Affiliation(s)
- Matthew Day
- School of Biological and Behavioural Sciences, Blizard Institute, Queen Mary University of London, London, E1 2AT, UK.
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Bilal Tetik
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Milena Parlak
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Yasser Almeida-Hernández
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Räschle
- Molecular Genetics, Technical University Kaiserslautern, Paul-Ehrlich Straße 24, 67663, Kaiserslautern, Germany
| | - Farnusch Kaschani
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Heike Siegert
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Anika Marko
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Elsa Sanchez-Garcia
- Computational Bioengineering, Fakultät Bio- und Chemieingenieurwesen, Technical University Dortmund, Emil-Figge Str. 66, 44227, Dortmund, Germany
- Computational Biochemistry, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
| | - Markus Kaiser
- Analytics Core Facility Essen, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany
- Chemical Biology, Center of Medical Biotechnology, University Duisburg-Essen, Fakultät Biologie, Essen, Germany
| | - Isabel A Barker
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK
| | - Laurence H Pearl
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
- Division of Structural Biology, Institute of Cancer Research, Chester Beatty Laboratories, 237 Fulham Road, London, SW1E 6BT, UK.
| | - Antony W Oliver
- Cancer Research UK DNA Repair Enzymes Group, Genome Damage and Stability Centre, School of Life Sciences, University of Sussex, Falmer, Brighton, BN1 9RQ, UK.
| | - Dominik Boos
- Molecular Genetics II, Center of Medical Biotechnology, University of Duisburg-Essen, Universitätsstraße 2-5, 45141, Essen, Germany.
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3
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Takeuchi I, Tanase-Nakao K, Ogawa A, Sugawara T, Migita O, Kashima M, Yamazaki T, Iguchi A, Naiki Y, Uchiyama T, Tamaoki J, Maeda H, Shimizu H, Kawai T, Taniguchi K, Hirata H, Kobayashi M, Matsumoto K, Naruse K, Hata K, Akutsu H, Kato T, Narumi S, Arai K, Ishiguro A. Congenital anaemia associated with loss-of-function variants in DNA polymerase epsilon 1. J Med Genet 2024; 61:239-243. [PMID: 37833059 DOI: 10.1136/jmg-2023-109444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2023] [Accepted: 09/25/2023] [Indexed: 10/15/2023]
Abstract
DNA polymerase epsilon (Pol ε), a component of the core replisome, is involved in DNA replication. Although genetic defects of Pol ε have been reported to cause immunodeficiency syndromes, its role in haematopoiesis remains unknown. Here, we identified compound heterozygous variants (p.[Asp1131fs];[Thr1891del]) in POLE, encoding Pol ε catalytic subunit A (POLE1), in siblings with a syndromic form of severe congenital transfusion-dependent anaemia. In contrast to Diamond-Blackfan anaemia, marked reticulocytopenia or marked erythroid hypoplasia was not found. Their bone marrow aspirates during infancy revealed erythroid dysplasia with strongly positive TP53 in immunostaining. Repetitive examinations demonstrated trilineage myelodysplasia within 2 years from birth. They had short stature and facial dysmorphism. HEK293 cell-based expression experiments and analyses of patient-derived induced pluripotent stem cells (iPSCs) disclosed a reduced mRNA level of Asp1131fs-POLE1 and defective nuclear translocation of Thr1891del-POLE1. Analysis of iPSCs showed compensatory mRNA upregulation of the other replisome components and increase of the TP53 protein, both suggesting dysfunction of the replisome. We created Pole-knockout medaka fish and found that heterozygous fishes were viable, but with decreased RBCs. Our observations expand the phenotypic spectrum of the Pol ε defect in humans, additionally providing unique evidence linking Pol ε to haematopoiesis.
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Affiliation(s)
- Ichiro Takeuchi
- Center for Pediatric Inflammatory Bowel Disease, Division of Gastroenterology, National Center for Child Health and Development, Tokyo, Japan
| | - Kanako Tanase-Nakao
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Ayame Ogawa
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
- Integrative Bioscience and Biomedical Engineering, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Tohru Sugawara
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Osuke Migita
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
- Department of Laboratory Medicine, St. Marianna University School of Medicine, Kawasaki, Kanagawa, Japan
| | - Makoto Kashima
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Sagamihara, Kanagawa, Japan
| | - Touko Yamazaki
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Akihiro Iguchi
- Children Cancer's Center, Division of Hematology, National Center for Child Health and Development, Tokyo, Japan
| | - Yasuhiro Naiki
- Division of Endocrinology and Metabolism, National Center for Child Health and Development, Tokyo, Japan
| | - Toru Uchiyama
- Department of Genome Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Junya Tamaoki
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hiroki Maeda
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Hirotaka Shimizu
- Center for Pediatric Inflammatory Bowel Disease, Division of Gastroenterology, National Center for Child Health and Development, Tokyo, Japan
| | - Toshinao Kawai
- Division of Immunology, National Center for Child Health and Development, Tokyo, Japan
| | - Kosuke Taniguchi
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hiromi Hirata
- Department of Chemistry and Biological Science, Aoyama Gakuin University, Sagamihara, Kanagawa, Japan
| | - Makoto Kobayashi
- Department of Molecular and Developmental Biology, Institute of Medicine, University of Tsukuba, Tsukuba, Ibaraki, Japan
| | - Kimikazu Matsumoto
- Children Cancer's Center, Division of Hematology, National Center for Child Health and Development, Tokyo, Japan
| | - Kiyoshi Naruse
- Laboratory of Bioresources, National Institute for Basic Biology, Okazaki, Aichi, Japan
| | - Kenichiro Hata
- Department of Maternal-Fetal Biology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Hidenori Akutsu
- Center for Regenerative Medicine, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Takashi Kato
- Department of Biology, Faculty of Education and Integrated Arts and Sciences, Waseda University, Tokyo, Japan
- Integrative Bioscience and Biomedical Engineering, Graduate School of Advanced Science and Engineering, Waseda University, Tokyo, Japan
| | - Satoshi Narumi
- Department of Molecular Endocrinology, National Research Institute for Child Health and Development, Tokyo, Japan
| | - Katsuhiro Arai
- Center for Pediatric Inflammatory Bowel Disease, Division of Gastroenterology, National Center for Child Health and Development, Tokyo, Japan
| | - Akira Ishiguro
- Children Cancer's Center, Division of Hematology, National Center for Child Health and Development, Tokyo, Japan
- Center for Postgraduate Education and Training, National Center for Child Health and Development, Tokyo, Japan
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4
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Ostroverkhova D, Tyryshkin K, Beach AK, Moore EA, Masoudi-Sobhanzadeh Y, Barbari SR, Rogozin IB, Shaitan KV, Panchenko AR, Shcherbakova PV. DNA polymerase ε and δ variants drive mutagenesis in polypurine tracts in human tumors. Cell Rep 2024; 43:113655. [PMID: 38219146 PMCID: PMC10830898 DOI: 10.1016/j.celrep.2023.113655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/07/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024] Open
Abstract
Alterations in the exonuclease domain of DNA polymerase ε cause ultramutated cancers. These cancers accumulate AGA>ATA transversions; however, their genomic features beyond the trinucleotide motifs are obscure. We analyze the extended DNA context of ultramutation using whole-exome sequencing data from 524 endometrial and 395 colorectal tumors. We find that G>T transversions in POLE-mutant tumors predominantly affect sequences containing at least six consecutive purines, with a striking preference for certain positions within polypurine tracts. Using this signature, we develop a machine-learning classifier to identify tumors with hitherto unknown POLE drivers and validate two drivers, POLE-E978G and POLE-S461L, by functional assays in yeast. Unlike other pathogenic variants, the E978G substitution affects the polymerase domain of Pol ε. We further show that tumors with POLD1 drivers share the extended signature of POLE ultramutation. These findings expand the understanding of ultramutation mechanisms and highlight peculiar mutagenic properties of polypurine tracts in the human genome.
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Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Kathrin Tyryshkin
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Annette K Beach
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Elizabeth A Moore
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yosef Masoudi-Sobhanzadeh
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada.
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
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5
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Tang M, Yin S, Zeng H, Huang A, Huang Y, Hu Z, Shah AR, Zhang S, Li H, Chen G. The P286R mutation of DNA polymerase ε activates cancer-cell-intrinsic immunity and suppresses endometrial tumorigenesis via the cGAS-STING pathway. Cell Death Dis 2024; 15:69. [PMID: 38238314 PMCID: PMC10796917 DOI: 10.1038/s41419-023-06418-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Revised: 12/15/2023] [Accepted: 12/22/2023] [Indexed: 01/22/2024]
Abstract
Endometrial carcinoma (EC) is a prevalent gynecological tumor in women, and its treatment and prevention are significant global health concerns. The mutations in DNA polymerase ε (POLE) are recognized as key features of EC and may confer survival benefits in endometrial cancer patients undergoing anti-PD-1/PD-L1 therapy. However, the anti-tumor mechanism of POLE mutations remains largely elusive. This study demonstrates that the hot POLE P286R mutation impedes endometrial tumorigenesis by inducing DNA breakage and activating the cGAS-STING signaling pathway. The POLE mutations were found to inhibit the proliferation and stemness of primary human EC cells. Mechanistically, the POLE mutants enhance DNA damage and suppress its repair through the interaction with DNA repair proteins, leading to genomic instability and the upregulation of cytoplasmic DNA. Additionally, the POLE P286R mutant also increases cGAS level, promotes TBK1 phosphorylation, and stimulates inflammatory gene expression and anti-tumor immune response. Furthermore, the POLE P286R mutation inhibits tumor growth and facilitates the infiltration of cytotoxic T cells in human endometrial cancers. These findings uncover a novel mechanism of POLE mutations in antagonizing tumorigenesis and provide a promising direction for effective cancer therapy.
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Affiliation(s)
- Ming Tang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Shasha Yin
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
- Department of Biochemistry and Molecular Biology, Hollings Cancer Center, Medical University of South Carolina, Charleston, SC, USA
| | - Hongliang Zeng
- Center of Medical Laboratory Animal, Hunan Academy of Chinese Medicine, Changsha, 410013, China
| | - Ao Huang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
- Center of Medical Laboratory Animal, Hunan Academy of Chinese Medicine, Changsha, 410013, China
| | - Yujia Huang
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Zhiyi Hu
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China
| | - Ab Rauf Shah
- Department of Pathology and Microbiology, UNMC, Omaha, USA
| | - Shuyong Zhang
- Key Laboratory of Prevention and Treatment of Cardiovascular and Cerebrovascular Diseases, Gannan Medical University, Ministry of Education, Ganzhou, 341000, China.
- School of Basic Medicine, Gannan Medical University, Ganzhou, 341000, China.
| | - Haisen Li
- School of Life Sciences, Fudan University, Shanghai, 200438, China.
- AoBio Medical Co., Shanghai, 200438, China.
| | - Guofang Chen
- Shanghai Key Laboratory of Maternal Fetal Medicine, Shanghai Institute of Maternal-Fetal Medicine and Gynecologic Oncology, Clinical and Translational Research Center, Shanghai First Maternity and Infant Hospital, School of Medicine, Tongji University, Shanghai, 200092, China.
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6
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Selves J, de Castro E Gloria H, Brunac AC, Saffi J, Guimbaud R, Brousset P, Hoffmann JS. Exploring the basis of heterogeneity of cancer aggressiveness among the mutated POLE variants. Life Sci Alliance 2024; 7:e202302290. [PMID: 37891003 PMCID: PMC10610022 DOI: 10.26508/lsa.202302290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/04/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Germline pathogenic variants in the exonuclease domain of the replicative DNA polymerase Pol ε encoded by the POLE gene, predispose essentially to colorectal and endometrial tumors by inducing an ultramutator phenotype. It is still unclear whether all the POLE alterations influence similar strength tumorigenesis, immune microenvironment, and treatment response. In this review, we summarize the current understanding of the mechanisms and consequences of POLE mutations in human malignancies; we highlight the heterogeneity of mutation rate and cancer aggressiveness among POLE variants, propose some mechanistic basis underlining such heterogeneity, and discuss novel considerations for the choice and efficacy of therapies of POLE tumors.
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Affiliation(s)
- Janick Selves
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
| | - Helena de Castro E Gloria
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Anne-Cécile Brunac
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Jenifer Saffi
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Rosine Guimbaud
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
- Department of Digestive Oncology, Centre Hospitalier Universitaire (CHU), Toulouse, France
- Department of Digestive Surgery, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Pierre Brousset
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Toulouse, France
| | - Jean-Sébastien Hoffmann
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Toulouse, France
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7
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Ahmad T, Kawasumi R, Taniguchi T, Abe T, Terada K, Tsuda M, Shimizu N, Tsurimoto T, Takeda S, Hirota K. The proofreading exonuclease of leading-strand DNA polymerase epsilon prevents replication fork collapse at broken template strands. Nucleic Acids Res 2023; 51:12288-12302. [PMID: 37944988 PMCID: PMC10711444 DOI: 10.1093/nar/gkad999] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2023] [Revised: 10/03/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023] Open
Abstract
Leading-strand DNA replication by polymerase epsilon (Polϵ) across single-strand breaks (SSBs) causes single-ended double-strand breaks (seDSBs), which are repaired via homology-directed repair (HDR) and suppressed by fork reversal (FR). Although previous studies identified many molecules required for hydroxyurea-induced FR, FR at seDSBs is poorly understood. Here, we identified molecules that specifically mediate FR at seDSBs. Because FR at seDSBs requires poly(ADP ribose)polymerase 1 (PARP1), we hypothesized that seDSB/FR-associated molecules would increase tolerance to camptothecin (CPT) but not the PARP inhibitor olaparib, even though both anti-cancer agents generate seDSBs. Indeed, we uncovered that Polϵ exonuclease and CTF18, a Polϵ cofactor, increased tolerance to CPT but not olaparib. To explore potential functional interactions between Polϵ exonuclease, CTF18, and PARP1, we created exonuclease-deficient POLE1exo-/-, CTF18-/-, PARP1-/-, CTF18-/-/POLE1exo-/-, PARP1-/-/POLE1exo-/-, and CTF18-/-/PARP1-/- cells. Epistasis analysis indicated that Polϵ exonuclease and CTF18 were interdependent and required PARP1 for CPT tolerance. Remarkably, POLE1exo-/- and HDR-deficient BRCA1-/- cells exhibited similar CPT sensitivity. Moreover, combining POLE1exo-/- with BRCA1-/- mutations synergistically increased CPT sensitivity. In conclusion, the newly identified PARP1-CTF18-Polϵ exonuclease axis and HDR act independently to prevent fork collapse at seDSBs. Olaparib inhibits this axis, explaining the pronounced cytotoxic effects of olaparib on HDR-deficient cells.
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Affiliation(s)
- Tasnim Ahmad
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Ryotaro Kawasumi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Tomoya Taniguchi
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Takuya Abe
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
| | - Kazuhiro Terada
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
| | - Masataka Tsuda
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
- Division of Genetics and Mutagenesis, National Institute of Health Sciences, 3-25-26 Tonomachi, Kawasaki-ku, Kawasaki 210-9501, Japan
| | - Naoto Shimizu
- Department of Radiation Genetics, Graduate School of Medicine, Kyoto University, Yoshidakonoe, Sakyo-ku, Kyoto 606-8501, Japan
- Program of Mathematical and Life Sciences, Graduate School of Integrated Sciences for Life, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8526, Japan
| | - Toshiki Tsurimoto
- Department of Biology, Faculty of Science, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Shunichi Takeda
- Shenzhen University, School of Medicine, Shenzhen, Guangdong 518060, China
| | - Kouji Hirota
- Department of Chemistry, Graduate School of Science, Tokyo Metropolitan University, Minamiosawa 1-1, Hachioji-shi, Tokyo 192-0397, Japan
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8
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Crevel G, Kearsey S, Cotterill S. A simple bypass assay for DNA polymerases shows that cancer-associated hypermutating variants exhibit differences in vitro. FEBS J 2023; 290:5744-5758. [PMID: 37592814 PMCID: PMC10953417 DOI: 10.1111/febs.16936] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2023] [Revised: 07/13/2023] [Accepted: 08/16/2023] [Indexed: 08/19/2023]
Abstract
Errors made by DNA polymerases contribute to both natural variation and, in extreme cases, genome instability and its associated diseases. Recently, the importance of polymerase misincorporation in disease has been highlighted by the identification of cancer-associated polymerase variants with mutations in the exonuclease domain. A subgroup of these variants have a hypermutation phenotype in tumours, and when modelled in yeast, they show mutation rates in excess of that seen with polymerase with simple loss of proofreading activity. We have developed a bypass assay to rapidly determine the tendency of a polymerase to misincorporate in vitro. We have used the assay to compare misincorporation by wild-type, exonuclease-defective and two hypermutating human DNA polymerase ε variants, P286R and V411L. The assay clearly distinguished between the misincorporation rates of wild-type, exonuclease dead and P286R polymerases. However, the V411L polymerase showed misincorporation rate comparable to the exonuclease dead enzyme rather than P286R, suggesting that there may be some differences in the way that these variants cause hypermutation. Using this assay, misincorporation opposite a templated C nucleotide was consistently higher than for other nucleotides, and this caused predominantly C-to-T transitions. This is consistent with the observation that C-to-T transitions are commonly seen in DNA polymerase ε mutant tumours.
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9
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Dmowski M, Makiela-Dzbenska K, Sharma S, Chabes A, Fijalkowska IJ. Impairment of the non-catalytic subunit Dpb2 of DNA Pol ɛ results in increased involvement of Pol δ on the leading strand. DNA Repair (Amst) 2023; 129:103541. [PMID: 37481989 DOI: 10.1016/j.dnarep.2023.103541] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 05/29/2023] [Accepted: 07/05/2023] [Indexed: 07/25/2023]
Abstract
The generally accepted model assumes that leading strand synthesis is performed by Pol ε, while lagging-strand synthesis is catalyzed by Pol δ. Pol ε has been shown to target the leading strand by interacting with the CMG helicase [Cdc45 Mcm2-7 GINS(Psf1-3, Sld5)]. Proper functioning of the CMG-Pol ɛ, the helicase-polymerase complex is essential for its progression and the fidelity of DNA replication. Dpb2p, the essential non-catalytic subunit of Pol ε plays a key role in maintaining the correct architecture of the replisome by acting as a link between Pol ε and the CMG complex. Using a temperature-sensitive dpb2-100 mutant previously isolated in our laboratory, and a genetic system which takes advantage of a distinct mutational signature of the Pol δ-L612M variant which allows detection of the involvement of Pol δ in the replication of particular DNA strands we show that in yeast cells with an impaired Dpb2 subunit, the contribution of Pol δ to the replication of the leading strand is significantly increased.
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Affiliation(s)
- Michal Dmowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland.
| | - Karolina Makiela-Dzbenska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-901 87 Umeå, Sweden
| | - Iwona J Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5A, 02-106 Warsaw, Poland.
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10
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Fenstermaker TK, Petruk S, Kovermann SK, Brock HW, Mazo A. RNA polymerase II associates with active genes during DNA replication. Nature 2023; 620:426-433. [PMID: 37468626 DOI: 10.1038/s41586-023-06341-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 06/19/2023] [Indexed: 07/21/2023]
Abstract
The transcriptional machinery is thought to dissociate from DNA during replication. Certain proteins, termed epigenetic marks, must be transferred from parent to daughter DNA strands in order to maintain the memory of transcriptional states1,2. These proteins are believed to re-initiate rebuilding of chromatin structure, which ultimately recruits RNA polymerase II (Pol II) to the newly replicated daughter strands. It is believed that Pol II is recruited back to active genes only after chromatin is rebuilt3,4. However, there is little experimental evidence addressing the central questions of when and how Pol II is recruited back to the daughter strands and resumes transcription. Here we show that immediately after passage of the replication fork, Pol II in complex with other general transcription proteins and immature RNA re-associates with active genes on both leading and lagging strands of nascent DNA, and rapidly resumes transcription. This suggests that the transcriptionally active Pol II complex is retained in close proximity to DNA, with a Pol II-PCNA interaction potentially underlying this retention. These findings indicate that the Pol II machinery may not require epigenetic marks to be recruited to the newly synthesized DNA during the transition from DNA replication to resumption of transcription.
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Affiliation(s)
- Tyler K Fenstermaker
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Svetlana Petruk
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA
| | - Sina K Kovermann
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Hugh W Brock
- Department of Zoology, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alexander Mazo
- Department of Biochemistry and Molecular Biology, Sidney Kimmel Medical College, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, USA.
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11
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Johnson RE, Prakash L, Prakash S. DNA polymerase ε leading strand signature mutations result from defects in its proofreading activity. J Biol Chem 2023; 299:104913. [PMID: 37307920 PMCID: PMC10371845 DOI: 10.1016/j.jbc.2023.104913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 06/05/2023] [Accepted: 06/07/2023] [Indexed: 06/14/2023] Open
Abstract
The evidence that purified pol2-M644G DNA polymerase (Pol)ε exhibits a highly elevated bias for forming T:dTTP mispairs over A:dATP mispairs and that yeast cells harboring this Polε mutation accumulate A > T signature mutations in the leading strand have been used to assign a role for Polε in replicating the leading strand. Here, we determine whether A > T signature mutations result from defects in Polε proofreading activity by analyzing their rate in Polε proofreading defective pol2-4 and pol2-M644G cells. Since purified pol2-4 Polε exhibits no bias for T:dTTP mispair formation, A > T mutations are expected to occur at a much lower rate in pol2-4 than in pol2-M644G cells if Polε replicated the leading strand. Instead, we find that the rate of A > T signature mutations are as highly elevated in pol2-4 cells as in pol2-M644G cells; furthermore, the highly elevated rate of A > T signature mutations is severely curtailed in the absence of PCNA ubiquitination or Polζ in both the pol2-M644G and pol2-4 strains. Altogether, our evidence supports the conclusion that the leading strand A > T signature mutations derive from defects in Polε proofreading activity and not from the role of Polε as a leading strand replicase, and it conforms with the genetic evidence for a major role of Polδ in replication of both the DNA strands.
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Affiliation(s)
- Robert E Johnson
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch at Galveston, Galveston, Texas, USA.
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12
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Klassen R, Gangavarapu V, Johnson RE, Prakash L, Prakash S. Mismatch repair operates at the replication fork in direct competition with mismatch extension by DNA polymerase δ. J Biol Chem 2023; 299:104598. [PMID: 36898578 PMCID: PMC10124943 DOI: 10.1016/j.jbc.2023.104598] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2023] [Revised: 03/05/2023] [Accepted: 03/06/2023] [Indexed: 03/12/2023] Open
Abstract
DNA mismatch repair (MMR) in eukaryotes is believed to occur post-replicatively, wherein nicks or gaps in the nascent DNA strand are suggested to serve as strand discrimination signals. However, how such signals are generated in the nascent leading strand has remained unclear. Here we examine the alternative possibility that MMR occurs in conjunction with the replication fork. To this end, we utilize mutations in the PCNA interacting peptide (PIP) domain of the Pol3 or Pol32 subunit of DNA polymerase δ (Polδ) and show that these pip mutations suppress the greatly elevated mutagenesis in yeast strains harboring the pol3-01 mutation defective in Polδ proofreading activity. And strikingly, they suppress the synthetic lethality of pol3-01 pol2-4 double mutant strains, which arises from the vastly enhanced mutability due to defects in the proofreading functions of both Polδ and Polε. Our finding that suppression of elevated mutagenesis in pol3-01 by the Polδ pip mutations requires intact MMR supports the conclusion that MMR operates at the replication fork in direct competition with other mismatch removal processes and with extension of synthesis from the mispair by Polδ. Furthermore, the evidence that Polδ pip mutations eliminate almost all the mutability of pol2-4 msh2Δ or pol3-01 pol2-4 adds strong support for a major role of Polδ in replication of both the leading and lagging DNA strands.
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Affiliation(s)
- Roland Klassen
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Venkat Gangavarapu
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Robert E Johnson
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.
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13
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Rocque MJ, Leipart V, Kumar Singh A, Mur P, Olsen MF, Engebretsen LF, Martin-Ramos E, Aligué R, Sætrom P, Valle L, Drabløs F, Otterlei M, Sjursen W. Characterization of POLE c.1373A > T p.(Tyr458Phe), causing high cancer risk. Mol Genet Genomics 2023; 298:555-566. [PMID: 36856825 PMCID: PMC10133059 DOI: 10.1007/s00438-023-02000-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023]
Abstract
The cancer syndrome polymerase proofreading-associated polyposis results from germline mutations in the POLE and POLD1 genes. Mutations in the exonuclease domain of these genes are associated with hyper- and ultra-mutated tumors with a predominance of base substitutions resulting from faulty proofreading during DNA replication. When a new variant is identified by gene testing of POLE and POLD1, it is important to verify whether the variant is associated with PPAP or not, to guide genetic counseling of mutation carriers. In 2015, we reported the likely pathogenic (class 4) germline POLE c.1373A > T p.(Tyr458Phe) variant and we have now characterized this variant to verify that it is a class 5 pathogenic variant. For this purpose, we investigated (1) mutator phenotype in tumors from two carriers, (2) mutation frequency in cell-based mutagenesis assays, and (3) structural consequences based on protein modeling. Whole-exome sequencing of two tumors identified an ultra-mutator phenotype with a predominance of base substitutions, the majority of which are C > T. A SupF mutagenesis assay revealed increased mutation frequency in cells overexpressing the variant of interest as well as in isogenic cells encoding the variant. Moreover, exonuclease repair yeast-based assay supported defect in proofreading activity. Lastly, we present a homology model of human POLE to demonstrate structural consequences leading to pathogenic impact of the p.(Tyr458Phe) mutation. The three lines of evidence, taken together with updated co-segregation and previously published data, allow the germline variant POLE c.1373A > T p.(Tyr458Phe) to be reclassified as a class 5 variant. That means the variant is associated with PPAP.
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Affiliation(s)
- Mariève J Rocque
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Vilde Leipart
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
| | - Ashish Kumar Singh
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maren F Olsen
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Lars F Engebretsen
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Edgar Martin-Ramos
- Department of Biomedical Sciences, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Rosa Aligué
- Department of Biomedical Sciences, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Department of Computer and Information Science, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Bioinformatics Core Facility-BioCore, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Finn Drabløs
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
| | - Wenche Sjursen
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway.
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway.
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14
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Abstract
DNA replication is complex and highly regulated, and DNA replication errors can lead to human diseases such as cancer. DNA polymerase ε (polε) is a key player in DNA replication and contains a large subunit called POLE, which possesses both a DNA polymerase domain and a 3'-5' exonuclease domain (EXO). Mutations at the EXO domain and other missense mutations on POLE with unknown significance have been detected in a variety of human cancers. Based on cancer genome databases, Meng and colleagues (pp. 74-79) previously identified several missense mutations in POPS (pol2 family-specific catalytic core peripheral subdomain), and mutations at the conserved residues of yeast Pol2 (pol2-REL) showed reduced DNA synthesis and growth. In this issue of Genes & Development, Meng and colleagues (pp. 74-79) found unexpectedly that mutations at the EXO domain rescue the growth defects of pol2-REL. They further discovered that EXO-mediated polymerase backtracking impedes forward movement of the enzyme when POPS is defective, revealing a novel interplay between the EXO domain and POPS of Pol2 for efficient DNA synthesis. Additional molecular insight into this interplay will likely inform the impact of cancer-associated mutations found in both the EXO domain and POPS on tumorigenesis and uncover future novel therapeutic strategies.
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Affiliation(s)
- Matthew Gallitto
- Institute for Cancer Genetics, Department of Pediatrics, Department of Genetics and Development, Irving Cancer Research Center, Columbia University, New York, New York 10032, USA
| | - Zhiguo Zhang
- Institute for Cancer Genetics, Department of Pediatrics, Department of Genetics and Development, Irving Cancer Research Center, Columbia University, New York, New York 10032, USA
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15
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Meng X, Claussin C, Regan-Mochrie G, Whitehouse I, Zhao X. Balancing act of a leading strand DNA polymerase-specific domain and its exonuclease domain promotes genome-wide sister replication fork symmetry. Genes Dev 2023; 37:74-79. [PMID: 36702483 PMCID: PMC10069448 DOI: 10.1101/gad.350054.122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Accepted: 12/19/2022] [Indexed: 01/28/2023]
Abstract
Pol2 is the leading-strand DNA polymerase in budding yeast. Here we describe an antagonism between its conserved POPS (Pol2 family-specific catalytic core peripheral subdomain) and exonuclease domain and the importance of this antagonism in genome replication. We show that multiple defects caused by POPS mutations, including impaired growth and DNA synthesis, genome instability, and reliance on other genome maintenance factors, were rescued by exonuclease inactivation. Single-molecule data revealed that the rescue stemmed from allowing sister replication forks to progress at equal rates. Our data suggest that balanced activity of Pol2's POPS and exonuclease domains is vital for genome replication and stability.
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Affiliation(s)
- Xiangzhou Meng
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Clémence Claussin
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Gemma Regan-Mochrie
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
- Gerstner Sloan Kettering Graduate School of Biomedical Sciences, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Iestyn Whitehouse
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA;
| | - Xiaolan Zhao
- Molecular Biology Program, Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA;
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16
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Acharya N, Prakash L, Prakash S. Yeast 9-1-1 complex acts as a sliding clamp for DNA synthesis by DNA polymerase ε. J Biol Chem 2023; 299:102727. [PMID: 36410434 PMCID: PMC9791402 DOI: 10.1016/j.jbc.2022.102727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 11/10/2022] [Accepted: 11/13/2022] [Indexed: 11/21/2022] Open
Abstract
Eukaryotic cells harbor two DNA-binding clamps, proliferating cell nuclear antigen (PCNA), and another clamp commonly referred to as 9-1-1 clamp. In contrast to the essential role of PCNA in DNA replication as a sliding clamp for DNA polymerase (Pol) δ, no such role in DNA synthesis has been identified for the human 9-1-1 clamp or the orthologous yeast 17-3-1 clamp. The only role identified for either the 9-1-1 or 17-3-1 clamp is in the recruitment of signal transduction kinases, which affect the activation of cell cycle checkpoints in response to DNA damage. However, unlike the loading of PCNA by the replication factor C (RFC) clamp loader onto 3'-recessed DNA junctions for processive DNA synthesis by Polδ, the 17-3-1 clamp or the 9-1-1 clamp is loaded by their respective clamp loader Rad24-RFC or RAD17-RFC onto the 5'-recessed DNA junction of replication protein A-coated DNA for the recruitment of signal transduction kinases. Here, we identify a novel role of 17-3-1 clamp as a sliding clamp for DNA synthesis by Polε. We provide evidence that similar to the loading of PCNA by RFC, the 17-3-1 clamp is loaded by the Rad24-RFC clamp loader at the 3'-recessed DNA junction in an ATP-dependent manner. However, unlike PCNA, the 17-3-1 clamp does not enhance the processivity of DNA synthesis by Polε; instead, it greatly increases the catalytic efficiency of Polε for correct nucleotide incorporation. Furthermore, we show that the same PCNA-interacting peptide domain in the polymerase 2 catalytic subunit mediates Polε interaction with the 17-3-1 clamp and with PCNA.
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Affiliation(s)
- Narottam Acharya
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Louise Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA
| | - Satya Prakash
- Department of Biochemistry and Molecular Biology, University of Texas Medical Branch, Galveston, Texas, USA.
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17
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Vipat S, Gupta D, Jonchhe S, Anderspuk H, Rothenberg E, Moiseeva TN. The non-catalytic role of DNA polymerase epsilon in replication initiation in human cells. Nat Commun 2022; 13:7099. [PMID: 36402816 PMCID: PMC9675812 DOI: 10.1038/s41467-022-34911-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 11/10/2022] [Indexed: 11/21/2022] Open
Abstract
DNA polymerase epsilon (PolE) in an enzyme essential for DNA replication. Deficiencies and mutations in PolE cause severe developmental abnormalities and cancers. Paradoxically, the catalytic domain of yeast PolE catalytic subunit is dispensable for survival, and its non-catalytic essential function is linked with replicative helicase (CMG) assembly. Less is known about the PolE role in replication initiation in human cells. Here we use an auxin-inducible degron system to study the effect of POLE1 depletion on replication initiation in U2OS cells. POLE1-depleted cells were able to assemble CMG helicase and initiate DNA synthesis that failed shortly after. Expression of POLE1 non-catalytic domain rescued this defect resulting in slow, but continuous DNA synthesis. We propose a model where in human U2OS cells POLE1/POLE2 are dispensable for CMG assembly, but essential during later steps of replication initiation. Our study provides some insights into the role of PolE in replication initiation in human cells.
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Affiliation(s)
- Sameera Vipat
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Dipika Gupta
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Sagun Jonchhe
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Hele Anderspuk
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia
| | - Eli Rothenberg
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY, 10016, USA
| | - Tatiana N Moiseeva
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, 12618, Estonia.
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18
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Loganathan L, Al-Haidose A, Ganesh Kumar A, Sujatha LB, Carlus FH, Alharbi A, Alhyassat S, Muthusamy K, Carlus SJ, Abdallah AM. An in silico analysis of the impact of POLE mutations on cladribine docking. Eur Rev Med Pharmacol Sci 2022; 26:7580-7593. [PMID: 36314330 DOI: 10.26355/eurrev_202210_30033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/16/2023]
Abstract
OBJECTIVE Polymerase ε exonuclease (POLE) is an enzyme involved in DNA replication and may be an attractive therapeutic target in various cancers. Here we sought to model the impact of specific POLE mutations on protein function. Due to the lack of a crystal structure, the tertiary structures of the wild type and four common mutants were modeled using I-Tasser server. MATERIALS AND METHODS Molecular docking and dynamic simulation studies were performed, and the structure and function of the mutants analyzed through residue conservation analysis and protein folding energy changes. RESULTS All mutants of POLE gene had favorable binding affinities compared with their wild type of counterpart. The P286R variant, but not the other variants, disrupted cladribine binding to the protein. Similarly, dynamics studies revealed instability of the P286R mutant, while V411L, L424V, and L424F appeared to favor cladribine binding. CONCLUSIONS Since P286R is a hotspot mutation in endometrioid carcinomas, patients with this variant may not respond to cladribine. Population-based pharmacogenomics studies will be required to validate our results.
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Affiliation(s)
- L Loganathan
- Department of Bioinformatics, Alagappa University, Karaikudi, Tamil Nadu, India.
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19
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Gong Z, Liu ZG, Du KY, Wu JH, Yang N, Malhotra A, Shu JK. RETRACTED: Potential of β-elemene induced ferroptosis through Pole2-mediated p53 and PI3K/AKT signaling in lung cancer cells. Chem Biol Interact 2022; 365:110088. [PMID: 35940278 DOI: 10.1016/j.cbi.2022.110088] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 07/29/2022] [Accepted: 07/30/2022] [Indexed: 12/24/2022]
Abstract
This article has been retracted: please see Elsevier Policy on Article Withdrawal (http://www.elsevier.com/locate/withdrawalpolicy). This article has been retracted at the request of the Editor-in-Chief. After a thorough investigation, the Editor has concluded that the acceptance of this article was partly based upon the positive advice of one illegitimate reviewer report. The report was submitted from an email account which was provided to the journal as a suggested reviewer during the submission of the article. Although purportedly a real reviewer account, the Editor has concluded that this was not of an appropriate, independent reviewer. Further inquiry revealed that the name of the author Anshoo Malhotra was added after the acceptance of the article without notifying the author and the handling Editor, which is contrary to the journal policy on changes to authorship. This manipulation of the peer-review process represents a clear violation of the fundamentals of peer review, our publishing policies, and publishing ethics standards. Apologies are offered to the reviewer whose identity was assumed and to the readers of the journal that this deception was not detected during the submission process.
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Affiliation(s)
- Zheng Gong
- Department of Thoracic Surgery, Affiliated Hospital of Yunnan University, Kunming, 650000, China
| | - Ze-Gang Liu
- Department of General Surgery, The 920 Hospital of PLA Joint Service Support Force, Kunming, 650000, China
| | - Kun-Yu Du
- Department of Respiratory and Critical Care MedicineⅡ, The First Affiliated Hospital of Kunming Medical University, Kunming, 650000, China
| | - Jiang-Hai Wu
- Department of Respiratory and Critical Care MedicineⅡ, The First Affiliated Hospital of Kunming Medical University, Kunming, 650000, China
| | - Na Yang
- Department of Respiratory, Affiliated Hospital of Yunnan University, Kunming, 650000, China
| | | | - Jing-Kui Shu
- Department of Respiratory and Critical Care MedicineⅡ, The First Affiliated Hospital of Kunming Medical University, Kunming, 650000, China.
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Zhou ZX, Kunkel TA. Extrinsic proofreading. DNA Repair (Amst) 2022; 117:103369. [PMID: 35850061 PMCID: PMC9561950 DOI: 10.1016/j.dnarep.2022.103369] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2022] [Revised: 07/01/2022] [Accepted: 07/02/2022] [Indexed: 11/24/2022]
Abstract
The high fidelity of replication of the nuclear DNA genome in eukaryotes involves three processes. Correct rather than incorrect dNTPs are almost always incorporated by the three major replicases, DNA polymerases α, δ and ε. When an incorrect base is occasionally inserted, the latter Pols δ and ε also have a 3 ´ to 5 ´ exonuclease activity that can remove the mismatch to allow correct DNA synthesis to proceed. Lastly, rare mismatches that escape proofreading activity and are present in newly replicated DNA can be removed by DNA mismatch repair. In this review, we consider evidence supporting the hypothesis that the second mechanism, proofreading, can operate in two different ways. Primer terminal mismatches made by either Pol δ or Pol ε can be 'intrinsically' proofread. This mechanism occurs by direct transfer of a misinserted base made at the polymerase active site to the exonuclease active site that is located a short distance away. Intrinsic proofreading allows mismatch excision without intervening enzyme dissociation. Alternatively, considerable evidence suggests that mismatches made by any of the three replicases can also be proofread by 'extrinsic' proofreading by Pol δ. Extrinsic proofreading occurs when a mismatch made by any of the three replicases is initially abandoned, thereby allowing the exonuclease active site of Pol δ to bind directly to and remove the mismatch before replication continues. Here we review the evidence that extrinsic proofreading significantly enhances the fidelity of nuclear DNA replication, and we then briefly consider the implications of this process for evolution and disease.
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Affiliation(s)
- Zhi-Xiong Zhou
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA
| | - Thomas A Kunkel
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, NIH, DHHS, Research Triangle Park, NC 27709, USA.
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21
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Wen L, Chen Z, Ji X, Fong WP, Shao Q, Ren C, Cai Y, Li B, Yuan Y, Wang D, Li Y. Pathological complete response to immune checkpoint inhibitor in patients with colorectal cancer liver metastases harboring POLE exonuclease domain mutation. J Immunother Cancer 2022; 10:e004487. [PMID: 35793867 PMCID: PMC9260839 DOI: 10.1136/jitc-2022-004487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/15/2022] [Indexed: 11/03/2022] Open
Abstract
Patients with polymerase epsilon (POLE) exonuclease domain mutation (EDM) exhibits distinct clinical characteristics and extremely high tumor mutation burden (TMB). There is a paucity of data on the therapeutic efficacy of immune checkpoint inhibitors (ICIs) for the treatment of colorectal cancer liver metastases (CRLM) patients with POLE EDM. Clinical characteristics, radiological and pathological response, as well as oncological outcomes of four CRLM patients harboring POLE EDM and treated by ICI plus chemotherapy were retrospectively collected and analyzed. TMB and genomic mutation profiling were also assessed in resected CRLM patients harboring different molecular characteristics. The four CRLM patients received toripalimab or sintilimab plus chemotherapy (FOLFOX or FOLFIRI or XELOX) with or without bevacizumab after POLE EDM were detected. All four patients achieved a radiological partial response. Staged or simultaneous complete surgical resection of the primary tumor and liver metastases was conducted. Pathological complete response was achieved in all four patients. After a median follow-up of 14 (range 9-20) months, all four patients maintained non-evidence of disease status until the last follow-up. POLE EDM patients showed a larger set of mutational genes compared with non-POLE EDM patients. TMB of patients harboring POLE EDM was significantly higher than those with microsatellite instability-high (median, 313.92 vs 42.24 mutations/Mb, p<0.05), POLE non-EDM (313.92 vs 4.80, p<0.001), and MSS subtypes (313.92 vs 4.80, p<0.001). Despite being a rare phenotype, CRLM patients with POLE EDM exhibit ultra-high TMB and, more importantly, significant clinical response to ICI-based combination therapy. Therefore, the complete sequencing of POLE exonuclease domains is recommended in CRLM patients clinically.
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Affiliation(s)
- Lei Wen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Medical Oncology, Sun Yat‑sen University Cancer Center, Guangzhou, China
| | - Zhigang Chen
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Medical Oncology, Sun Yat‑sen University Cancer Center, Guangzhou, China
| | - Xiaomeng Ji
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Medical Oncology, Sun Yat‑sen University Cancer Center, Guangzhou, China
| | - William Pat Fong
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Medical Oncology, Sun Yat‑sen University Cancer Center, Guangzhou, China
| | - Qiong Shao
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Molecular Diagnostics, Sun Yat‑sen University Cancer Center, Guangzhou, China
| | - Chao Ren
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Medical Oncology, Sun Yat‑sen University Cancer Center, Guangzhou, China
| | - Yanyu Cai
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Medical Oncology, Sun Yat‑sen University Cancer Center, Guangzhou, China
| | - Binkui Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Hepatobiliary Surgery, Sun Yat‑sen University Cancer Center, Guangzhou, China
| | - Yunfei Yuan
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Hepatobiliary Surgery, Sun Yat‑sen University Cancer Center, Guangzhou, China
| | - Deshen Wang
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Medical Oncology, Sun Yat‑sen University Cancer Center, Guangzhou, China
| | - Yuhong Li
- State Key Laboratory of Oncology in South China, Collaborative Innovation Center for Cancer Medicine, Sun Yat‑sen University Cancer Center, Guangzhou, Guangdong, China
- Department of Medical Oncology, Sun Yat‑sen University Cancer Center, Guangzhou, China
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22
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Jumaah AS, Al-Haddad HS, McAllister KA, Yasseen AA. The clinicopathology and survival characteristics of patients with POLE proofreading mutations in endometrial carcinoma: A systematic review and meta-analysis. PLoS One 2022; 17:e0263585. [PMID: 35139130 PMCID: PMC8827442 DOI: 10.1371/journal.pone.0263585] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Accepted: 01/21/2022] [Indexed: 12/17/2022] Open
Abstract
Background Endometrial carcinoma (EC) is classified into four distinct molecular subgroups. Patients with polymerase epsilon exonuclease domain mutated (POLE-EDM) tumors have the best prognosis of all. This meta-analysis consolidated the clinicopathology variations reported in the POLE-mutant subtype and survival parameters in patients with EC. Methods The following internet data bases were searched: PubMed, Web of science, Embase and Scimage directory. Data was extracted from eligible studies including sample size, number of positive POLE-mutant cases, EDM sequencing information, clinicopathologic, and survival data. Meta-analysis and a random-effects model produced pooled estimates of POLE prognostic parameters using 95% confidence intervals (CI), hazard ratios (HR), and odds ratios (OR). Results The meta-analysis included 11 cohort studies comprising 5508 EC patients (442 POLE EDM tumors). Patients with POLE mutant EC were associated with improved disease specific survival (HR = 0.408, 95% CI: 0.306 to 0.543) and progression-free survival (HR = 0.231, 95% CI: 0.117 to 0.456). POLE-mutated tumors were mostly endometrioid histology (84.480%; 95% CI: 77.237 to 90.548), although not significantly more than wild type tumors (OR = 1.386; p = 0.073). The POLE mutant tumors significantly present (p<0.001) at Federation of International of Gynecologists and Obstetricians (FIGO) lower stages I-II (OR = 2.955, p<0.001) and highest grade III (OR = 1.717, P = 0.003). The tumors are significantly associated with invasion less than half (<50%) of the myometrium (OR = 1.765, p = 0.001), but not deeply invasive EC (MI>50%, OR = 0.83, p = 0.34). POLE mutations significantly protected against lymph node metastases (OR = 0.202, p = 0.001), and have no clear association with lymph-vascular space invasion (OR = 0.967, 95% 0.713–1.310, p = 0.826). The tumors are predominantly of low ESMO risk stratification distribution (40.356%; 95% CI: 27.577 to 53.838). Conclusions POLE mutations serve as an important biomarker of favorable prognosis in EC. The tumors are characteristically high grade, early stage, and remain localized in the endometrium with reduced likelihood of lymph node metastasis for improved survival prospects and the lowest risk classification. These findings have implications for medical management of EC.
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Affiliation(s)
- Alaa Salah Jumaah
- Department of Pathology and Forensic Medicine, Faculty of Medicine, University of Kufa, Kufa, Iraq
| | | | - Katherine Ann McAllister
- School of Biomedical Sciences, Ulster University, Coleraine, Northern Ireland, United Kingdom
- * E-mail:
| | - Akeel Abed Yasseen
- Department of Pathology and Forensic Medicine, Faculty of Medicine, University of Kufa, Kufa, Iraq
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Zhang P, Chen X, Zhang L, Cao D, Chen Y, Guo Z, Chen J. POLE2 facilitates the malignant phenotypes of glioblastoma through promoting AURKA-mediated stabilization of FOXM1. Cell Death Dis 2022; 13:61. [PMID: 35039475 PMCID: PMC8763902 DOI: 10.1038/s41419-021-04498-7] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 12/06/2021] [Accepted: 12/20/2021] [Indexed: 02/08/2023]
Abstract
Glioblastoma (GBM) is a type of brain cancer with high morbidity and mortality worldwide. The clinical significance, biological roles, and underlying molecular mechanisms of DNA poly ε-B subunit (POLE2) in GBM were investigated in the study. Firstly, the Cancer Genome Atlas (TCGA) database found that POLE2 was highly expressed in GBM. Immunohistochemistry (IHC) results further confirmed that POLE2 was abnormally elevated in GBM. In addition, loss-of-function assays revealed that POLE2 knockdown could inhibit the malignant behaviors of GBM, especially reduce cell viability, weaken cell clone formation, enhance the sensitivity of apoptosis, restrain migration and inhibit epithelial-mesenchymal transition (EMT) in vitro. In vivo experiments further clarified the suppressive effects of reduced POLE2 expression on tumors. Mechanically, POLE2 knockdown promoted the ubiquitination as well as reduced the stability of Forkhead transcription factor (FOXM1), which is a known tumor promotor in GBM, through Aurora kinase A (AURKA). Moreover, the knockdown of FOXM1 could weaken the promoting effects of POLE2 on malignant behaviors of GBM. In conclusion, our study revealed crucial roles and a novel mechanism of POLE2 involved in GBM through AURKA-mediated stability of FOXM1 and may provide the theoretical basis of molecular therapy for GBM.
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Affiliation(s)
- Peng Zhang
- Department of Neurosurgery of the First Affiliated Hospital of Zhengzhou University, Zhengzhou, No.1 Jianshe East Road, Zhengzhou City, Henan Province, China
| | - Xu Chen
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Ave, Wuhan City, Hubei Province, China.
| | - LingYun Zhang
- Department of Thyroid and Parathyroid Surgery, West China Hospital, Sichuan University, No. 37 Guoxue Alley, Chengdu City, Sichuan Province, China
| | - Dan Cao
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Ave, Wuhan City, Hubei Province, China
| | - Yong Chen
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Ave, Wuhan City, Hubei Province, China
| | - ZhengQian Guo
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Ave, Wuhan City, Hubei Province, China
| | - Jian Chen
- Department of Neurosurgery, Tongji Hospital, Tongji Medical College, Huazhong University of Science and Technology, No. 1095 Jiefang Ave, Wuhan City, Hubei Province, China
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Jones ML, Baris Y, Taylor MRG, Yeeles JTP. Structure of a human replisome shows the organisation and interactions of a DNA replication machine. EMBO J 2021; 40:e108819. [PMID: 34694004 PMCID: PMC8634136 DOI: 10.15252/embj.2021108819] [Citation(s) in RCA: 50] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2021] [Revised: 09/28/2021] [Accepted: 09/30/2021] [Indexed: 02/01/2023] Open
Abstract
The human replisome is an elaborate arrangement of molecular machines responsible for accurate chromosome replication. At its heart is the CDC45-MCM-GINS (CMG) helicase, which, in addition to unwinding the parental DNA duplex, arranges many proteins including the leading-strand polymerase Pol ε, together with TIMELESS-TIPIN, CLASPIN and AND-1 that have key and varied roles in maintaining smooth replisome progression. How these proteins are coordinated in the human replisome is poorly understood. We have determined a 3.2 Å cryo-EM structure of a human replisome comprising CMG, Pol ε, TIMELESS-TIPIN, CLASPIN and AND-1 bound to replication fork DNA. The structure permits a detailed understanding of how AND-1, TIMELESS-TIPIN and Pol ε engage CMG, reveals how CLASPIN binds to multiple replisome components and identifies the position of the Pol ε catalytic domain. Furthermore, the intricate network of contacts contributed by MCM subunits and TIMELESS-TIPIN with replication fork DNA suggests a mechanism for strand separation.
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25
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Soriano I, Vazquez E, De Leon N, Bertrand S, Heitzer E, Toumazou S, Bo Z, Palles C, Pai CC, Humphrey TC, Tomlinson I, Cotterill S, Kearsey SE. Expression of the cancer-associated DNA polymerase ε P286R in fission yeast leads to translesion synthesis polymerase dependent hypermutation and defective DNA replication. PLoS Genet 2021; 17:e1009526. [PMID: 34228709 PMCID: PMC8284607 DOI: 10.1371/journal.pgen.1009526] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2021] [Revised: 07/16/2021] [Accepted: 06/11/2021] [Indexed: 12/15/2022] Open
Abstract
Somatic and germline mutations in the proofreading domain of the replicative DNA polymerase ε (POLE-exonuclease domain mutations, POLE-EDMs) are frequently found in colorectal and endometrial cancers and, occasionally, in other tumours. POLE-associated cancers typically display hypermutation, and a unique mutational signature, with a predominance of C > A transversions in the context TCT and C > T transitions in the context TCG. To understand better the contribution of hypermutagenesis to tumour development, we have modelled the most recurrent POLE-EDM (POLE-P286R) in Schizosaccharomyces pombe. Whole-genome sequencing analysis revealed that the corresponding pol2-P287R allele also has a strong mutator effect in vivo, with a high frequency of base substitutions and relatively few indel mutations. The mutations are equally distributed across different genomic regions, but in the immediate vicinity there is an asymmetry in AT frequency. The most abundant base-pair changes are TCT > TAT transversions and, in contrast to human mutations, TCG > TTG transitions are not elevated, likely due to the absence of cytosine methylation in fission yeast. The pol2-P287R variant has an increased sensitivity to elevated dNTP levels and DNA damaging agents, and shows reduced viability on depletion of the Pfh1 helicase. In addition, S phase is aberrant and RPA foci are elevated, suggestive of ssDNA or DNA damage, and the pol2-P287R mutation is synthetically lethal with rad3 inactivation, indicative of checkpoint activation. Significantly, deletion of genes encoding some translesion synthesis polymerases, most notably Pol κ, partially suppresses pol2-P287R hypermutation, indicating that polymerase switching contributes to this phenotype.
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Affiliation(s)
- Ignacio Soriano
- ZRAB, University of Oxford, Oxford, United Kingdom
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Enrique Vazquez
- Genomics Unit, Centro Nacional de Investigaciones Cardiovasculares (CNIC), Madrid, Spain
| | - Nagore De Leon
- ZRAB, University of Oxford, Oxford, United Kingdom
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | | | - Ellen Heitzer
- Institute of Human Genetics, Diagnostic & Research Center for Molecular BioMedicine, Medical University of Graz, Graz, Austria
| | - Sophia Toumazou
- ZRAB, University of Oxford, Oxford, United Kingdom
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Zhihan Bo
- ZRAB, University of Oxford, Oxford, United Kingdom
| | - Claire Palles
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, United Kingdom
| | - Chen-Chun Pai
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Timothy C. Humphrey
- MRC Oxford Institute for Radiation Oncology, Department of Oncology, University of Oxford, Oxford, United Kingdom
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Western General Hospital, Edinburgh, United Kingdom
| | - Sue Cotterill
- St. George’s, University of London, Cranmer Terrace, Tooting, London, United Kingdom
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Nisa M, Bergis C, Pedroza-Garcia JA, Drouin-Wahbi J, Mazubert C, Bergounioux C, Benhamed M, Raynaud C. The plant DNA polymerase theta is essential for the repair of replication-associated DNA damage. Plant J 2021; 106:1197-1207. [PMID: 33989439 DOI: 10.1111/tpj.15295] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 04/15/2021] [Accepted: 04/21/2021] [Indexed: 06/12/2023]
Abstract
Safeguarding of genome integrity is a key process in all living organisms. Due to their sessile lifestyle, plants are particularly exposed to all kinds of stress conditions that could induce DNA damage. However, very few genes involved in the maintenance of genome integrity are indispensable to plants' viability. One remarkable exception is the POLQ gene, which encodes DNA polymerase theta (Pol θ), a non-replicative polymerase involved in trans-lesion synthesis during DNA replication and double-strand break (DSB) repair. The Arabidopsis tebichi (teb) mutants, deficient in Pol θ, have been reported to display severe developmental defects, leading to the conclusion that Pol θ is required for normal plant development. However, this essential role of Pol θ in plants is challenged by contradictory reports regarding the phenotypic defects of teb mutants and the recent finding that rice (Oryza sativa) null mutants develop normally. Here we show that the phenotype of teb mutants is highly variable. Taking advantage of hypomorphic mutants for the replicative DNA polymerase epsilon, which display constitutive replicative stress, we show that Pol θ allows maintenance of meristem activity when DNA replication is partially compromised. Furthermore, we found that the phenotype of Pol θ mutants can be aggravated by modifying their growth conditions, suggesting that environmental conditions impact the basal level of replicative stress and providing evidence for a link between plants' responses to adverse conditions and mechanisms involved in the maintenance of genome integrity.
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Affiliation(s)
- Maherun Nisa
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Clara Bergis
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Jose-Antonio Pedroza-Garcia
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Jeannine Drouin-Wahbi
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Christelle Mazubert
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Catherine Bergounioux
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
- Institut Universitaire de France (IUF), France
| | - Cécile Raynaud
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, Univ Evry, Orsay, 91405, France
- Institute of Plant Sciences Paris Saclay, Université de Paris, CNRS, INRAE, Orsay, (IPS2) 91405, France
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Raffone A, Travaglino A, Gabrielli O, Micheli M, Zuccalà V, Bitonti G, Camastra C, Gargiulo V, Insabato L, Zullo F. Clinical features of ProMisE groups identify different phenotypes of patients with endometrial cancer. Arch Gynecol Obstet 2021; 303:1393-1400. [PMID: 33754186 PMCID: PMC8087601 DOI: 10.1007/s00404-021-06028-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2020] [Accepted: 03/12/2021] [Indexed: 12/19/2022]
Abstract
BACKGROUND The Proactive Molecular Risk Classifier for Endometrial Cancer (ProMisE) groups has identified four molecular prognostic groups of endometrial cancer (EC): POLE-mutated (POLE-mt), mismatch repair-deficient (MMR-d), p53-abnormal (p53-abn), p53-wild-type (p53-wt). These groups might have different pathogenesis and risk factors, and might occur in different phenotypes of patients. However, these data are still lacking. OBJECTIVE To provide a clinical characterization of the ProMisE groups of EC. METHODS A systematic review and meta-analysis was performed by searching seven electronic databases from their inception to December 2020, for all studies reporting clinical characteristics of EC patients in each ProMisE group. Pooled means of age and BMI and pooled prevalence of FIGO stage I and adjuvant treatment in each ProMisE group were calculated. RESULTS Six studies with 1, 879 women were included in the systematic review. Pooled means (with standard error) and prevalence values were: in the MMR-d group, age = 66.5 ± 0.6; BMI = 30.6 ± 1.2; stage I = 72.6%; adjuvant treatment = 47.3%; in the POLE-mt group, age = 58.6 ± 2.7; BMI = 27.2 ± 0.9; stage I = 93.7%; adjuvant treatment = 53.6%; in the p53-wt group, age = 64.2 ± 1.9; BMI = 32.3 ± 1.4; stage I = 80.5%; adjuvant treatment = 45.3%; in the p53-abn group, age = 71.1 ± 0.5; BMI = 29.1 ± 0.5; stage I = 50.8%; adjuvant treatment = 64.4%. CONCLUSION The ProMisE groups identify different phenotypes of patients. The POLE-mt group included the youngest women, with the lower BMI and the highest prevalence of stage I. The p53-wt group included patients with the highest BMI. The p53-abn group included the oldest women, with the highest prevalence of adjuvant treatment and the lowest prevalence of stage I. The MMR-d group showed intermediate values among the ProMisE groups for all clinical features.
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Affiliation(s)
- Antonio Raffone
- Gynecology and Obstetrics Unit, Department of Neuroscience, Reproductive Sciences and Dentistry, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Antonio Travaglino
- Anatomic Pathology Unit, Department of Advanced Biomedical Sciences, School of Medicine, University of Naples Federico II, Via Sergio Pansini, 5, 80131, Naples, Italy.
| | - Olimpia Gabrielli
- Gynecology and Obstetrics Unit, Department of Neuroscience, Reproductive Sciences and Dentistry, School of Medicine, University of Naples Federico II, Naples, Italy
| | | | | | - Giovanna Bitonti
- Department of Obstetrics and Gynecology, Magna Grecia University, Catanzaro, Italy
| | - Caterina Camastra
- Department of Health Sciences, University of Catanzaro Magna Græcia, Catanzaro, Italy
| | - Valentina Gargiulo
- Gynecology and Obstetrics Unit, Department of Neuroscience, Reproductive Sciences and Dentistry, School of Medicine, University of Naples Federico II, Naples, Italy
| | - Luigi Insabato
- Anatomic Pathology Unit, Department of Advanced Biomedical Sciences, School of Medicine, University of Naples Federico II, Via Sergio Pansini, 5, 80131, Naples, Italy
| | - Fulvio Zullo
- Gynecology and Obstetrics Unit, Department of Neuroscience, Reproductive Sciences and Dentistry, School of Medicine, University of Naples Federico II, Naples, Italy
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Herzog M, Alonso-Perez E, Salguero I, Warringer J, Adams D, Jackson SP, Puddu F. Mutagenic mechanisms of cancer-associated DNA polymerase ϵ alleles. Nucleic Acids Res 2021; 49:3919-3931. [PMID: 33764464 PMCID: PMC8053093 DOI: 10.1093/nar/gkab160] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2021] [Accepted: 03/03/2021] [Indexed: 01/08/2023] Open
Abstract
A single amino acid residue change in the exonuclease domain of human DNA polymerase ϵ, P286R, is associated with the development of colorectal cancers, and has been shown to impart a mutator phenotype. The corresponding Pol ϵ allele in the yeast Saccharomyces cerevisiae (pol2-P301R), was found to drive greater mutagenesis than an entirely exonuclease-deficient Pol ϵ (pol2-4), an unexpected phenotype of ultra-mutagenesis. By studying the impact on mutation frequency, type, replication-strand bias, and sequence context, we show that ultra-mutagenesis is commonly observed in yeast cells carrying a range of cancer-associated Pol ϵ exonuclease domain alleles. Similarities between mutations generated by these alleles and those generated in pol2-4 cells indicate a shared mechanism of mutagenesis that yields a mutation pattern similar to cancer Signature 14. Comparison of POL2 ultra-mutator with pol2-M644G, a mutant in the polymerase domain decreasing Pol ϵ fidelity, revealed unexpected analogies in the sequence context and strand bias of mutations. Analysis of mutational patterns unique to exonuclease domain mutant cells suggests that backtracking of the polymerase, when the mismatched primer end cannot be accommodated in the proofreading domain, results in the observed insertions and T>A mutations in specific sequence contexts.
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Affiliation(s)
- Mareike Herzog
- The Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
- The Wellcome Sanger Institute, Hinxton CB10 1HH, UK
| | - Elisa Alonso-Perez
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9 C, 413 90, Göteborg, Sweden
| | - Israel Salguero
- The Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Jonas Warringer
- Department of Chemistry and Molecular Biology, University of Gothenburg, Medicinaregatan 9 C, 413 90, Göteborg, Sweden
| | | | - Stephen P Jackson
- The Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
| | - Fabio Puddu
- The Wellcome/Cancer Research UK Gurdon Institute and Department of Biochemistry, University of Cambridge, Tennis Court Road, Cambridge CB2 1QN, UK
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Denkiewicz-Kruk M, Jedrychowska M, Endo S, Araki H, Jonczyk P, Dmowski M, Fijalkowska IJ. Recombination and Pol ζ Rescue Defective DNA Replication upon Impaired CMG Helicase-Pol ε Interaction. Int J Mol Sci 2020; 21:ijms21249484. [PMID: 33322195 PMCID: PMC7762974 DOI: 10.3390/ijms21249484] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2020] [Revised: 12/06/2020] [Accepted: 12/09/2020] [Indexed: 11/22/2022] Open
Abstract
The CMG complex (Cdc45, Mcm2–7, GINS (Psf1, 2, 3, and Sld5)) is crucial for both DNA replication initiation and fork progression. The CMG helicase interaction with the leading strand DNA polymerase epsilon (Pol ε) is essential for the preferential loading of Pol ε onto the leading strand, the stimulation of the polymerase, and the modulation of helicase activity. Here, we analyze the consequences of impaired interaction between Pol ε and GINS in Saccharomyces cerevisiae cells with the psf1-100 mutation. This significantly affects DNA replication activity measured in vitro, while in vivo, the psf1-100 mutation reduces replication fidelity by increasing slippage of Pol ε, which manifests as an elevated number of frameshifts. It also increases the occurrence of single-stranded DNA (ssDNA) gaps and the demand for homologous recombination. The psf1-100 mutant shows elevated recombination rates and synthetic lethality with rad52Δ. Additionally, we observe increased participation of DNA polymerase zeta (Pol ζ) in DNA synthesis. We conclude that the impaired interaction between GINS and Pol ε requires enhanced involvement of error-prone Pol ζ, and increased participation of recombination as a rescue mechanism for recovery of impaired replication forks.
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Affiliation(s)
- Milena Denkiewicz-Kruk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Malgorzata Jedrychowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Shizuko Endo
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; (S.E.); (H.A.)
| | - Hiroyuki Araki
- National Institute of Genetics, 1111 Yata, Mishima, Shizuoka 411-8540, Japan; (S.E.); (H.A.)
| | - Piotr Jonczyk
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
| | - Michal Dmowski
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
- Correspondence: (M.D.); (I.J.F.); Tel.: +48-22-5921128 (M.D.); +48-22-5921113 (I.J.F.)
| | - Iwona J. Fijalkowska
- Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, 02-106 Warsaw, Poland; (M.D.-K.); (M.J.); (P.J.)
- Correspondence: (M.D.); (I.J.F.); Tel.: +48-22-5921128 (M.D.); +48-22-5921113 (I.J.F.)
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30
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Zahurancik WJ, Suo Z. Kinetic investigation of the polymerase and exonuclease activities of human DNA polymerase ε holoenzyme. J Biol Chem 2020; 295:17251-17264. [PMID: 33051204 PMCID: PMC7863874 DOI: 10.1074/jbc.ra120.013903] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2020] [Revised: 10/09/2020] [Indexed: 12/31/2022] Open
Abstract
In eukaryotic DNA replication, DNA polymerase ε (Polε) is responsible for leading strand synthesis, whereas DNA polymerases α and δ synthesize the lagging strand. The human Polε (hPolε) holoenzyme is comprised of the catalytic p261 subunit and the noncatalytic p59, p17, and p12 small subunits. So far, the contribution of the noncatalytic subunits to hPolε function is not well understood. Using pre-steady-state kinetic methods, we established a minimal kinetic mechanism for DNA polymerization and editing catalyzed by the hPolε holoenzyme. Compared with the 140-kDa N-terminal catalytic fragment of p261 (p261N), which we kinetically characterized in our earlier studies, the presence of the p261 C-terminal domain (p261C) and the three small subunits increased the DNA binding affinity and the base substitution fidelity. Although the small subunits enhanced correct nucleotide incorporation efficiency, there was a wide range of rate constants when incorporating a correct nucleotide over a single-base mismatch. Surprisingly, the 3'→5' exonuclease activity of the hPolε holoenzyme was significantly slower than that of p261N when editing both matched and mismatched DNA substrates. This suggests that the presence of p261C and the three small subunits regulates the 3'→5' exonuclease activity of the hPolε holoenzyme. Together, the 3'→5' exonuclease activity and the variable mismatch extension activity modulate the overall fidelity of the hPolε holoenzyme by up to 3 orders of magnitude. Thus, the presence of p261C and the three noncatalytic subunits optimizes the dual enzymatic activities of the catalytic p261 subunit and makes the hPolε holoenzyme an efficient and faithful replicative DNA polymerase.
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Affiliation(s)
- Walter J Zahurancik
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA
| | - Zucai Suo
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio, USA; Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida, USA.
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Bourguet P, López-González L, Gómez-Zambrano Á, Pélissier T, Hesketh A, Potok ME, Pouch-Pélissier MN, Perez M, Da Ines O, Latrasse D, White CI, Jacobsen SE, Benhamed M, Mathieu O. DNA polymerase epsilon is required for heterochromatin maintenance in Arabidopsis. Genome Biol 2020; 21:283. [PMID: 33234150 PMCID: PMC7687843 DOI: 10.1186/s13059-020-02190-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 10/27/2020] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Chromatin organizes DNA and regulates its transcriptional activity through epigenetic modifications. Heterochromatic regions of the genome are generally transcriptionally silent, while euchromatin is more prone to transcription. During DNA replication, both genetic information and chromatin modifications must be faithfully passed on to daughter strands. There is evidence that DNA polymerases play a role in transcriptional silencing, but the extent of their contribution and how it relates to heterochromatin maintenance is unclear. RESULTS We isolate a strong hypomorphic Arabidopsis thaliana mutant of the POL2A catalytic subunit of DNA polymerase epsilon and show that POL2A is required to stabilize heterochromatin silencing genome-wide, likely by preventing replicative stress. We reveal that POL2A inhibits DNA methylation and histone H3 lysine 9 methylation. Hence, the release of heterochromatin silencing in POL2A-deficient mutants paradoxically occurs in a chromatin context of increased levels of these two repressive epigenetic marks. At the nuclear level, the POL2A defect is associated with fragmentation of heterochromatin. CONCLUSION These results indicate that POL2A is critical to heterochromatin structure and function, and that unhindered replisome progression is required for the faithful propagation of DNA methylation throughout the cell cycle.
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Affiliation(s)
- Pierre Bourguet
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Leticia López-González
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Ángeles Gómez-Zambrano
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
- Present Address: Instituto de Bioquímica Vegetal y Fotosíntesis, CSIC-Cartuja, Avda, Américo Vespucio, 49., 41092, Sevilla, Spain
| | - Thierry Pélissier
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Amy Hesketh
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Magdalena E Potok
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Marie-Noëlle Pouch-Pélissier
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Magali Perez
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Olivier Da Ines
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Charles I White
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France
| | - Steven E Jacobsen
- Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, Los Angeles, CA, 90095, USA
- Howard Hughes Medical Institute, University of California, Los Angeles, Los Angeles, CA, 90095, USA
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay (IPS2), CNRS, INRA, University Paris-Sud, University of Evry, University Paris-Diderot, Sorbonne Paris-Cite, University of Paris-Saclay, Batiment, 630, 91405, Orsay, France
| | - Olivier Mathieu
- Institute of Genetics Reproduction and Development (iGReD), Université Clermont Auvergne, CNRS, Inserm, F-63000, Clermont-Ferrand, France.
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Kolehmainen A, Pasanen A, Tuomi T, Koivisto-Korander R, Bützow R, Loukovaara M. Clinical factors as prognostic variables among molecular subgroups of endometrial cancer. PLoS One 2020; 15:e0242733. [PMID: 33232359 PMCID: PMC7685425 DOI: 10.1371/journal.pone.0242733] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2020] [Accepted: 11/06/2020] [Indexed: 11/18/2022] Open
Abstract
Background Clinical factors may influence endometrial cancer survival outcomes. We examined the prognostic significance of age, body mass index (BMI), and type 2 diabetes among molecular subgroups of endometrial cancer. Methods This was a single institution retrospective study of patients who underwent surgery for endometrial carcinoma between January 2007 and December 2012. Tumors were classified into four molecular subgroups by immunohistochemistry of mismatch repair (MMR) proteins and p53, and sequencing of polymerase-ϵ (POLE). Overall, cancer-related, and non-cancer-related mortality were estimated using univariable and multivariable survival analyses. Results Age >65 years was associated with increased mortality rates in the whole cohort (n = 515) and in the “no specific molecular profile” (NSMP) (n = 218) and MMR deficient (MMR-D) (n = 191) subgroups during a median follow-up time of 81 months (range 1‒136). However, hazard ratios for cancer-related mortality were non-significant for NSMP and MMR-D. Diabetes was associated with increased overall and non-cancer-related mortality in the whole cohort and MMR-D subgroup. Overweight/obesity had no effect on outcomes in the whole cohort, but was associated with decreased overall and cancer-related mortality in the NSMP subgroup, and increased overall and non-cancer-related mortality in the MMR-D subgroup. Overweight/obesity effect on cancer-related mortality in the NSMP subgroup remained unchanged after controlling for confounders. High-risk uterine factors were more common, and estrogen and progesterone receptor expression less common in NSMP subtype cancers of normal-weight patients compared with overweight/obese patients. No clinical factors were associated with outcomes in p53 aberrant (n = 69) and POLE mutant (n = 37) subgroups. No cancer-related deaths occurred in the POLE mutant subgroup. Conclusions The prognostic effects of age, BMI, and type 2 diabetes do not appear to be uniform for the molecular subgroups of endometrial cancer. Our data support further evaluation of BMI combined with genomics-based risk-assessment.
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Affiliation(s)
- Anne Kolehmainen
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Annukka Pasanen
- Department of Pathology, Helsinki University Hospital and Research Program in Applied Tumor Genomics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Taru Tuomi
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Riitta Koivisto-Korander
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Ralf Bützow
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- Department of Pathology, Helsinki University Hospital and Research Program in Applied Tumor Genomics, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Mikko Loukovaara
- Department of Obstetrics and Gynecology, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
- * E-mail:
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Sviderskiy VO, Blumenberg L, Gorodetsky E, Karakousi TR, Hirsh N, Alvarez SW, Terzi EM, Kaparos E, Whiten GC, Ssebyala S, Tonzi P, Mir H, Neel BG, Huang TT, Adams S, Ruggles KV, Possemato R. Hyperactive CDK2 Activity in Basal-like Breast Cancer Imposes a Genome Integrity Liability that Can Be Exploited by Targeting DNA Polymerase ε. Mol Cell 2020; 80:682-698.e7. [PMID: 33152268 PMCID: PMC7687292 DOI: 10.1016/j.molcel.2020.10.016] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 08/12/2020] [Accepted: 10/09/2020] [Indexed: 02/06/2023]
Abstract
Knowledge of fundamental differences between breast cancer subtypes has driven therapeutic advances; however, basal-like breast cancer (BLBC) remains clinically intractable. Because BLBC exhibits alterations in DNA repair enzymes and cell-cycle checkpoints, elucidation of factors enabling the genomic instability present in this subtype has the potential to reveal novel anti-cancer strategies. Here, we demonstrate that BLBC is especially sensitive to suppression of iron-sulfur cluster (ISC) biosynthesis and identify DNA polymerase epsilon (POLE) as an ISC-containing protein that underlies this phenotype. In BLBC cells, POLE suppression leads to replication fork stalling, DNA damage, and a senescence-like state or cell death. In contrast, luminal breast cancer and non-transformed mammary cells maintain viability upon POLE suppression but become dependent upon an ATR/CHK1/CDC25A/CDK2 DNA damage response axis. We find that CDK1/2 targets exhibit hyperphosphorylation selectively in BLBC tumors, indicating that CDK2 hyperactivity is a genome integrity vulnerability exploitable by targeting POLE.
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Affiliation(s)
- Vladislav O Sviderskiy
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Lili Blumenberg
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Elizabeth Gorodetsky
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Triantafyllia R Karakousi
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Nicole Hirsh
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Samantha W Alvarez
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Erdem M Terzi
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Efiyenia Kaparos
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Gabrielle C Whiten
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Shakirah Ssebyala
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Peter Tonzi
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Hannan Mir
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Benjamin G Neel
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Tony T Huang
- Department of Biochemistry and Molecular Pharmacology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Sylvia Adams
- Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Kelly V Ruggles
- Department of Medicine, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA
| | - Richard Possemato
- Department of Pathology, New York University School of Medicine, New York, NY 10016, USA; Laura & Isaac Perlmutter Cancer Center, New York University School of Medicine, New York, NY 10016, USA.
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Yuan Z, Li H. Molecular mechanisms of eukaryotic origin initiation, replication fork progression, and chromatin maintenance. Biochem J 2020; 477:3499-3525. [PMID: 32970141 PMCID: PMC7574821 DOI: 10.1042/bcj20200065] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Revised: 08/29/2020] [Accepted: 09/04/2020] [Indexed: 12/13/2022]
Abstract
Eukaryotic DNA replication is a highly dynamic and tightly regulated process. Replication involves several dozens of replication proteins, including the initiators ORC and Cdc6, replicative CMG helicase, DNA polymerase α-primase, leading-strand DNA polymerase ε, and lagging-strand DNA polymerase δ. These proteins work together in a spatially and temporally controlled manner to synthesize new DNA from the parental DNA templates. During DNA replication, epigenetic information imprinted on DNA and histone proteins is also copied to the daughter DNA to maintain the chromatin status. DNA methyltransferase 1 is primarily responsible for copying the parental DNA methylation pattern into the nascent DNA. Epigenetic information encoded in histones is transferred via a more complex and less well-understood process termed replication-couple nucleosome assembly. Here, we summarize the most recent structural and biochemical insights into DNA replication initiation, replication fork elongation, chromatin assembly and maintenance, and related regulatory mechanisms.
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Affiliation(s)
- Zuanning Yuan
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, U.S.A
| | - Huilin Li
- Structural Biology Program, Van Andel Institute, Grand Rapids, Michigan, U.S.A
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35
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Hodel KP, Sun MJS, Ungerleider N, Park VS, Williams LG, Bauer DL, Immethun VE, Wang J, Suo Z, Lu H, McLachlan JB, Pursell ZF. POLE Mutation Spectra Are Shaped by the Mutant Allele Identity, Its Abundance, and Mismatch Repair Status. Mol Cell 2020; 78:1166-1177.e6. [PMID: 32497495 PMCID: PMC8177757 DOI: 10.1016/j.molcel.2020.05.012] [Citation(s) in RCA: 30] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2019] [Revised: 04/10/2020] [Accepted: 05/11/2020] [Indexed: 12/11/2022]
Abstract
Human tumors with exonuclease domain mutations in the gene encoding DNA polymerase ε (POLE) have incredibly high mutation burdens. These errors arise in four unique mutation signatures occurring in different relative amounts, the etiologies of which remain poorly understood. We used CRISPR-Cas9 to engineer human cell lines expressing POLE tumor variants, with and without mismatch repair (MMR). Whole-exome sequencing of these cells after defined numbers of population doublings permitted analysis of nascent mutation accumulation. Unlike an exonuclease active site mutant that we previously characterized, POLE cancer mutants readily drive signature mutagenesis in the presence of functional MMR. Comparison of cell line and human patient data suggests that the relative abundance of mutation signatures partitions POLE tumors into distinct subgroups dependent on the nature of the POLE allele, its expression level, and MMR status. These results suggest that different POLE mutants have previously unappreciated differences in replication fidelity and mutagenesis.
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Affiliation(s)
- Karl P Hodel
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Meijuan J S Sun
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Nathan Ungerleider
- Department of Pathology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Leonard G Williams
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; BioInnovation Program, Tulane University, New Orleans, LA 70112, USA
| | - David L Bauer
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Victoria E Immethun
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Jieqiong Wang
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - Zucai Suo
- Department of Biomedical Sciences, Florida State University, Tallahassee, FL 32306, USA
| | - Hua Lu
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA
| | - James B McLachlan
- Department of Microbiology and Immunology, Tulane University School of Medicine, New Orleans, LA 70112, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA 70112, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA 70112, USA.
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Siamishi I, Iwanami N, Clapes T, Trompouki E, O'Meara CP, Boehm T. Lymphocyte-Specific Function of the DNA Polymerase Epsilon Subunit Pole3 Revealed by Neomorphic Alleles. Cell Rep 2020; 31:107756. [PMID: 32553171 DOI: 10.1016/j.celrep.2020.107756] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2019] [Revised: 04/06/2020] [Accepted: 05/20/2020] [Indexed: 11/17/2022] Open
Abstract
Immunodeficiencies are typically caused by loss-of-function mutations in lymphocyte-specific genes. Occasionally, mutations in ubiquitous general-purpose factors, including those affecting essential components of the DNA polymerase epsilon (POLE) holoenzyme, have cell-type-specific consequences. POLE3, one of the four components of the POLE holoenzyme, features a histone fold domain and a unique acidic C terminus, making it a particularly attractive candidate mediating cell type-specific activities of POLE. Mice lacking Pole3 survive up to late embryonic stages, indicating that this subunit is dispensable for DNA replication. The phenotypes of viable hypomorphic and neomorphic alleles are surprisingly tissue restricted and reveal a stage-specific function of the histone fold domain of Pole3 during T and B cell development. Gradual introduction of positively charged residues into the acidic C terminus leads to peripheral lymphopenia of increasing severity. Our findings serve as a paradigm to understand the molecular basis of cell-type-specific non-replicative functions of the ubiquitous POLE complex.
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Affiliation(s)
- Iliana Siamishi
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany; Faculty of Biology, University of Freiburg, 79108 Freiburg, Germany
| | - Norimasa Iwanami
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Clapes
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Eirini Trompouki
- Department of Cellular and Molecular Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Connor P O'Meara
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany
| | - Thomas Boehm
- Department of Developmental Immunology, Max Planck Institute of Immunobiology and Epigenetics, 79108 Freiburg, Germany.
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Qiu C, Jin H, Vvedenskaya I, Llenas JA, Zhao T, Malik I, Visbisky AM, Schwartz SL, Cui P, Čabart P, Han KH, Lai WKM, Metz RP, Johnson CD, Sze SH, Pugh BF, Nickels BE, Kaplan CD. Universal promoter scanning by Pol II during transcription initiation in Saccharomyces cerevisiae. Genome Biol 2020; 21:132. [PMID: 32487207 PMCID: PMC7265651 DOI: 10.1186/s13059-020-02040-0] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2019] [Accepted: 05/08/2020] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND The majority of eukaryotic promoters utilize multiple transcription start sites (TSSs). How multiple TSSs are specified at individual promoters across eukaryotes is not understood for most species. In Saccharomyces cerevisiae, a pre-initiation complex (PIC) comprised of Pol II and conserved general transcription factors (GTFs) assembles and opens DNA upstream of TSSs. Evidence from model promoters indicates that the PIC scans from upstream to downstream to identify TSSs. Prior results suggest that TSS distributions at promoters where scanning occurs shift in a polar fashion upon alteration in Pol II catalytic activity or GTF function. RESULTS To determine the extent of promoter scanning across promoter classes in S. cerevisiae, we perturb Pol II catalytic activity and GTF function and analyze their effects on TSS usage genome-wide. We find that alterations to Pol II, TFIIB, or TFIIF function widely alter the initiation landscape consistent with promoter scanning operating at all yeast promoters, regardless of promoter class. Promoter architecture, however, can determine the extent of promoter sensitivity to altered Pol II activity in ways that are predicted by a scanning model. CONCLUSIONS Our observations coupled with previous data validate key predictions of the scanning model for Pol II initiation in yeast, which we term the shooting gallery. In this model, Pol II catalytic activity and the rate and processivity of Pol II scanning together with promoter sequence determine the distribution of TSSs and their usage.
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Affiliation(s)
- Chenxi Qiu
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: Department of Medicine, Division of Translational Therapeutics, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, 02215, USA
| | - Huiyan Jin
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
| | - Irina Vvedenskaya
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Jordi Abante Llenas
- Department of Electrical and Computer Engineering, Texas A&M University, College Station, TX, 77843-3128, USA
- Present Address: Whitaker Biomedical Engineering Institute, Johns Hopkins University, Baltimore, MD, 21218, USA
| | - Tingting Zhao
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Indranil Malik
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: Department of Neurology, University of Michigan, Ann Arbor, MI, 48109, USA
| | - Alex M Visbisky
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA
| | - Scott L Schwartz
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Ping Cui
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
| | - Pavel Čabart
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Present Address: First Faculty of Medicine, Charles University, BIOCEV, 252 42, Vestec, Czech Republic
| | - Kang Hoo Han
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
| | - William K M Lai
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
- Present Address: Department of Molecular Biology and Genetics, 458 Biotechnology, Cornell University, New York, 14853, USA
| | - Richard P Metz
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Charles D Johnson
- Genomics and Bioinformatics Service, Texas A&M AgriLife, College Station, TX, 77845, USA
| | - Sing-Hoi Sze
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX, 77843-2128, USA
- Department of Computer Science and Engineering, Texas A&M University, College Station, TX, 77843-3127, USA
| | - B Franklin Pugh
- Department of Biochemistry and Molecular Biology, Penn State University, University Park, PA, 16802, USA
- Present Address: Department of Molecular Biology and Genetics, 458 Biotechnology, Cornell University, New York, 14853, USA
| | - Bryce E Nickels
- Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, 08854, USA
- Department of Genetics, Rutgers University, Piscataway, NJ, 08854, USA
| | - Craig D Kaplan
- Department of Biological Sciences, University of Pittsburgh, Pittsburgh, PA, 15260, USA.
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Hsieh THS, Cattoglio C, Slobodyanyuk E, Hansen AS, Rando OJ, Tjian R, Darzacq X. Resolving the 3D Landscape of Transcription-Linked Mammalian Chromatin Folding. Mol Cell 2020; 78:539-553.e8. [PMID: 32213323 PMCID: PMC7703524 DOI: 10.1016/j.molcel.2020.03.002] [Citation(s) in RCA: 272] [Impact Index Per Article: 68.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 01/28/2020] [Accepted: 03/02/2020] [Indexed: 01/31/2023]
Abstract
Whereas folding of genomes at the large scale of epigenomic compartments and topologically associating domains (TADs) is now relatively well understood, how chromatin is folded at finer scales remains largely unexplored in mammals. Here, we overcome some limitations of conventional 3C-based methods by using high-resolution Micro-C to probe links between 3D genome organization and transcriptional regulation in mouse stem cells. Combinatorial binding of transcription factors, cofactors, and chromatin modifiers spatially segregates TAD regions into various finer-scale structures with distinct regulatory features including stripes, dots, and domains linking promoters-to-promoters (P-P) or enhancers-to-promoters (E-P) and bundle contacts between Polycomb regions. E-P stripes extending from the edge of domains predominantly link co-expressed loci, often in the absence of CTCF and cohesin occupancy. Acute inhibition of transcription disrupts these gene-related folding features without altering higher-order chromatin structures. Our study uncovers previously obscured finer-scale genome organization, establishing functional links between chromatin folding and gene regulation.
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Affiliation(s)
- Tsung-Han S Hsieh
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Claudia Cattoglio
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Elena Slobodyanyuk
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA
| | - Anders S Hansen
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA; Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA 02142, USA
| | - Oliver J Rando
- Department of Biochemistry and Molecular Pharmacology, University of Massachusetts Medical School, Worcester, MA 01605, USA
| | - Robert Tjian
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Howard Hughes Medical Institute, University of California, Berkeley, Berkeley, CA 94720, USA.
| | - Xavier Darzacq
- Department of Molecular and Cell Biology, University of California, Berkeley, Berkeley, CA 94720, USA; Li Ka Shing Center for Biomedical and Health Sciences, University of California, Berkeley, Berkeley, CA 94720, USA; CIRM Center of Excellence, University of California, Berkeley, Berkeley, CA 94720, USA; Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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Rogers RF, Walton MI, Cherry DL, Collins I, Clarke PA, Garrett MD, Workman P. CHK1 Inhibition Is Synthetically Lethal with Loss of B-Family DNA Polymerase Function in Human Lung and Colorectal Cancer Cells. Cancer Res 2020; 80:1735-1747. [PMID: 32161100 PMCID: PMC7611445 DOI: 10.1158/0008-5472.can-19-1372] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 01/10/2020] [Accepted: 02/20/2020] [Indexed: 02/07/2023]
Abstract
Checkpoint kinase 1 (CHK1) is a key mediator of the DNA damage response that regulates cell-cycle progression, DNA damage repair, and DNA replication. Small-molecule CHK1 inhibitors sensitize cancer cells to genotoxic agents and have shown single-agent preclinical activity in cancers with high levels of replication stress. However, the underlying genetic determinants of CHK1 inhibitor sensitivity remain unclear. We used the developmental clinical drug SRA737 in an unbiased large-scale siRNA screen to identify novel mediators of CHK1 inhibitor sensitivity and uncover potential combination therapies and biomarkers for patient selection. We identified subunits of the B-family of DNA polymerases (POLA1, POLE, and POLE2) whose silencing sensitized the human A549 non-small cell lung cancer (NSCLC) and SW620 colorectal cancer cell lines to SRA737. B-family polymerases were validated using multiple siRNAs in a panel of NSCLC and colorectal cancer cell lines. Replication stress, DNA damage, and apoptosis were increased in human cancer cells following depletion of the B-family DNA polymerases combined with SRA737 treatment. Moreover, pharmacologic blockade of B-family DNA polymerases using aphidicolin or CD437 combined with CHK1 inhibitors led to synergistic inhibition of cancer cell proliferation. Furthermore, low levels of POLA1, POLE, and POLE2 protein expression in NSCLC and colorectal cancer cells correlated with single-agent CHK1 inhibitor sensitivity and may constitute biomarkers of this phenotype. These findings provide a potential basis for combining CHK1 and B-family polymerase inhibitors in cancer therapy. SIGNIFICANCE: These findings demonstrate how the therapeutic benefit of CHK1 inhibitors may potentially be enhanced and could have implications for patient selection and future development of new combination therapies.
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Affiliation(s)
- Rebecca F Rogers
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Michael I Walton
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Daniel L Cherry
- School of Biosciences, Stacey Building, University of Kent, Canterbury, Kent, United Kingdom
| | - Ian Collins
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Paul A Clarke
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, United Kingdom
| | - Michelle D Garrett
- School of Biosciences, Stacey Building, University of Kent, Canterbury, Kent, United Kingdom.
| | - Paul Workman
- Cancer Research UK Cancer Therapeutics Unit, The Institute of Cancer Research, London, United Kingdom.
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Fang H, Barbour JA, Poulos RC, Katainen R, Aaltonen LA, Wong JWH. Mutational processes of distinct POLE exonuclease domain mutants drive an enrichment of a specific TP53 mutation in colorectal cancer. PLoS Genet 2020; 16:e1008572. [PMID: 32012149 PMCID: PMC7018097 DOI: 10.1371/journal.pgen.1008572] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2019] [Revised: 02/13/2020] [Accepted: 12/17/2019] [Indexed: 01/16/2023] Open
Abstract
Cancer genomes with mutations in the exonuclease domain of Polymerase Epsilon (POLE) present with an extraordinarily high somatic mutation burden. In vitro studies have shown that distinct POLE mutants exhibit different polymerase activity. Yet, genome-wide mutation patterns and driver mutation formation arising from different POLE mutants remains unclear. Here, we curated somatic mutation calls from 7,345 colorectal cancer samples from published studies and publicly available databases. These include 44 POLE mutant samples including 9 with whole genome sequencing data available. The POLE mutant samples were categorized based on the specific POLE mutation present. Mutation spectrum, associations of somatic mutations with epigenomics features and co-occurrence with specific driver mutations were examined across different POLE mutants. We found that different POLE mutants exhibit distinct mutation spectrum with significantly higher relative frequency of C>T mutations in POLE V411L mutants. Our analysis showed that this increase frequency in C>T mutations is not dependent on DNA methylation and not associated with other genomic features and is thus specifically due to DNA sequence context alone. Notably, we found strong association of the TP53 R213* mutation specifically with POLE P286R mutants. This truncation mutation occurs within the TT[C>T]GA context. For C>T mutations, this sequence context is significantly more likely to be mutated in POLE P286R mutants compared with other POLE exonuclease domain mutants. This study refines our understanding of DNA polymerase fidelity and underscores genome-wide mutation spectrum and specific cancer driver mutation formation observed in POLE mutant cancers. Cancer arises through the accumulation of somatic mutations. The way that these somatic mutations form can vary greatly in different cancers. One of the most mutagenic processes that have been identified is caused by mutations within a replicative DNA polymerase known as Polymerase Epsilon (POLE). Cancers with such mutations present with hundreds of thousands of somatic mutations in their genome. Previous cancer genomics studies have identified a number of mutation hotspots in POLE, however how these different POLE mutants behave in affecting mutation distribution has not been studied. Here, we describe the genome-wide mutation profiles of distinct POLE mutant cancers. We find that different mutants indeed result in different mutation profiles and that this can be explained by the different fidelities of these mutants in replicating specific DNA sequences. Significantly, these differences have important implications in cancer formation as we found that a POLE mutation is strongly associated with a specific truncation of the TP53 cancer driver gene. This study furthers our understanding of the POLE mutagenic process in cancer and provide important insights into carcinogenesis in cancers with such mutations.
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Affiliation(s)
- Hu Fang
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
| | - Jayne A. Barbour
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
- Prince of Wales Clinical School, UNSW Medicine, UNSW Sydney, New South Wales, Australia
| | - Rebecca C. Poulos
- Children’s Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, New South Wales, Australia
| | - Riku Katainen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Lauri A. Aaltonen
- Applied Tumor Genomics Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Medical and Clinical Genetics, Medicum, University of Helsinki, Helsinki, Finland
| | - Jason W. H. Wong
- School of Biomedical Sciences, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Hong Kong Special Administrative Region
- Prince of Wales Clinical School, UNSW Medicine, UNSW Sydney, New South Wales, Australia
- * E-mail:
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41
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Stasenko M, Tunnage I, Ashley CW, Rubinstein MM, Latham AJ, Da Cruz Paula A, Mueller JJ, Leitao MM, Friedman CF, Makker V, Soslow RA, DeLair DF, Hyman DM, Zamarin D, Alektiar KM, Aghajanian CA, Abu-Rustum NR, Weigelt B, Cadoo KA. Clinical outcomes of patients with POLE mutated endometrioid endometrial cancer. Gynecol Oncol 2019; 156:194-202. [PMID: 31757464 DOI: 10.1016/j.ygyno.2019.10.028] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Revised: 10/23/2019] [Accepted: 10/25/2019] [Indexed: 12/11/2022]
Abstract
OBJECTIVES Assess outcomes of a clinical cohort of patients with endometrioid endometrial cancer (EEC) harboring somatic POLE exonuclease domain mutations (EDMs). METHODS Patients were consented to a protocol of tumor-normal massively parallel sequencing of 410-468 cancer related genes. EECs subjected to sequencing from 2014 to 2018 were reviewed. Tumors with somatic POLE EDMs were identified. EECs were assessed for microsatellite instability (MSI) using MSIsensor and immunohistochemical analysis for mismatch repair (MMR) proteins. RESULTS Of the 451 EECs sequenced, 23 had a POLE EDM (5%): 20 primary and 3 recurrent tumors sequenced. Nineteen cases (83%) were stage I/II and 4 (17%) were stages III/IV. Thirteen EECs (57%) were of FIGO grades 1/2, 10 (43%) grade 3. All patients were treated with surgery and 17 (89%) received adjuvant therapy. Five (22%) demonstrated loss of DNA MMR protein expression, none were due to Lynch syndrome. MSIsensor scores were conclusive for 21 samples: 19 were microsatellite stable and 2 MSI-high. After median follow-up of 30 months, 4/23 (17%) developed recurrences: 3 with initial grade 3 stage I and 1 with grade 1 stage III disease. One patient with grade 2 stage IV EEC had progressive disease after treatment. CONCLUSIONS Patients with POLE EDM EEC have been shown to have a favorable prognosis. In this real-world cohort of patients, de novo metastatic disease and recurrences in initially uterine-confined cases were observed. Further research is warranted before incorporating the presence of POLE EDM into decision-making regarding adjuvant therapy.
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Affiliation(s)
- Marina Stasenko
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Irina Tunnage
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Charles W Ashley
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Maria M Rubinstein
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Alicia J Latham
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA
| | - Arnaud Da Cruz Paula
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Jennifer J Mueller
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA
| | - Mario M Leitao
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA
| | - Claire F Friedman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA
| | - Vicky Makker
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA
| | - Robert A Soslow
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA
| | - Deborah F DeLair
- Department of Pathology, NYU Langone Medical Center, New York, NY, USA
| | - David M Hyman
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA
| | - Dimitriy Zamarin
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA
| | - Kaled M Alektiar
- Weill Medical College of Cornell University, New York, NY, USA; Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Carol A Aghajanian
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA
| | - Nadeem R Abu-Rustum
- Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA
| | - Britta Weigelt
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA
| | - Karen A Cadoo
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA; Weill Medical College of Cornell University, New York, NY, USA.
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Affiliation(s)
- Stephen Branden Van Oss
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
| | - Anne-Ruxandra Carvunis
- Department of Computational and Systems Biology, Pittsburgh Center for Evolutionary Biology and Medicine, School of Medicine, University of Pittsburgh, Pittsburgh, PA, United States of America
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Ishikawa M, Nakayama K, Nakamura K, Ono R, Yamashita H, Ishibashi T, Minamoto T, Iida K, Razia S, Ishikawa N, Kyo S. High frequency of POLE mutations in synchronous endometrial and ovarian carcinoma. Hum Pathol 2018; 85:92-100. [PMID: 30448219 DOI: 10.1016/j.humpath.2018.11.001] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Revised: 11/01/2018] [Accepted: 11/04/2018] [Indexed: 11/20/2022]
Abstract
Synchronous endometrial and ovarian carcinomas) represent 5% to 10% of endometrial or ovarian carcinomas. We assessed genetic alterations (in PTEN, CTNNB1, POLE, etc) and evaluated correlations with patient outcomes to determine the utility of clonality analyses for differentiating between metastases and concurrent primary tumors and for determining whether genetic alterations in synchronous tumors are predictive of biological behavior. Genomic DNA was isolated from formalin-fixed, paraffin-embedded tissues and frozen tissues from patients with synchronous endometrial and ovarian carcinomas. Samples were obtained from the Department of Obstetrics and Gynecology at the Shimane University School of Medicine between 2003 and 2017. Sanger sequencing was used to analyze the mutational status of the coding exons in TP53, PTEN, POLE, PIK3CA, KRAS, and CTNNB1 using previously published primers. All patients lived, and 3 had disease recurrence. The frequencies of somatic mutations in TP53, PTEN, CTNNB1, KRAS, and POLE were 3 (37.5%), 2 (25.0%), 3 (37.5%), 0 (0.0%), and 5 (62.5%) of 8 cases in ovarian tumors and 3 (37.5%), 2 (25.0%), 3 (37.5%), 1 (12.5%), and 5 (62.5%) of 8 cases in endometrial tumors, respectively. The frequencies of POLE and CTNNB1 mutations were higher than those in previous reports. A clonal relationship was determined by genomic analyses in 3 of 6 cases that were initially diagnosed as primary independent tumors. We confirmed that these 3 cases were indicated metastatic tumors because the lesion of mutation was the same. This information, provided by the sequencing-based strategy, could be useful for hypothesizing a patient's prognosis and deciding on treatment.
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Affiliation(s)
- Masako Ishikawa
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, 6938501 Izumo, Japan
| | - Kentaro Nakayama
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, 6938501 Izumo, Japan; Cancer Genomic Medicine Center, Shimane University Hospital, 6938501 Izumo, Japan.
| | - Kohei Nakamura
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, 6938501 Izumo, Japan; Cancer Genomic Medicine Center, Shimane University Hospital, 6938501 Izumo, Japan
| | - Ruriko Ono
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, 6938501 Izumo, Japan
| | - Hitomi Yamashita
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, 6938501 Izumo, Japan
| | - Tomoka Ishibashi
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, 6938501 Izumo, Japan
| | - Toshiko Minamoto
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, 6938501 Izumo, Japan
| | - Kouji Iida
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, 6938501 Izumo, Japan
| | - Sultana Razia
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, 6938501 Izumo, Japan
| | - Noriyoshi Ishikawa
- Department of Organ Pathology, Shimane University School of Medicine, 6938501 Izumo, Japan
| | - Satoru Kyo
- Department of Obstetrics and Gynecology, Shimane University School of Medicine, 6938501 Izumo, Japan
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Li HD, Cuevas I, Zhang M, Lu C, Alam MM, Fu YX, You MJ, Akbay EA, Zhang H, Castrillon DH. Polymerase-mediated ultramutagenesis in mice produces diverse cancers with high mutational load. J Clin Invest 2018; 128:4179-4191. [PMID: 30124468 PMCID: PMC6118636 DOI: 10.1172/jci122095] [Citation(s) in RCA: 50] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2018] [Accepted: 07/03/2018] [Indexed: 12/26/2022] Open
Abstract
Mutations underlie all cancers, and their identification and study are the foundation of cancer biology. We describe what we believe to be a novel approach to mutagenesis and cancer studies based on the DNA polymerase ε (POLE) ultramutator phenotype recently described in human cancers, in which a single amino acid substitution (most commonly P286R) in the proofreading domain results in error-prone DNA replication. We engineered a conditional PoleP286R allele in mice. PoleP286R/+ embryonic fibroblasts exhibited a striking mutator phenotype and immortalized more efficiently. PoleP286R/+ mice were born at Mendelian ratios but rapidly developed lethal cancers of diverse lineages, yielding the most cancer-prone monoallelic model described to date, to our knowledge. Comprehensive whole-genome sequencing analyses showed that the cancers were driven by high base substitution rates in the range of human cancers, overcoming a major limitation of previous murine cancer models. These data establish polymerase-mediated ultramutagenesis as an efficient in vivo approach for the generation of diverse animal cancer models that recapitulate the high mutational loads inherent to human cancers.
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Affiliation(s)
- Hao-Dong Li
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Ileana Cuevas
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Musi Zhang
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Changzheng Lu
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Md Maksudul Alam
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - Yang-Xin Fu
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - M. James You
- Department of Hematopathology, Division of Pathology and Laboratory Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas, USA
| | - Esra A. Akbay
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
| | - He Zhang
- Lyda Hill Department of Bioinformatics, UTSW Medical Center, Dallas, Texas, USA
| | - Diego H. Castrillon
- Department of Pathology and Simmons Comprehensive Cancer Center, University of Texas Southwestern (UTSW) Medical Center, Dallas, Texas, USA
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45
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Temko D, Van Gool IC, Rayner E, Glaire M, Makino S, Brown M, Chegwidden L, Palles C, Depreeuw J, Beggs A, Stathopoulou C, Mason J, Baker A, Williams M, Cerundolo V, Rei M, Taylor JC, Schuh A, Ahmed A, Amant F, Lambrechts D, Smit VTHBM, Bosse T, Graham TA, Church DN, Tomlinson I. Somatic POLE exonuclease domain mutations are early events in sporadic endometrial and colorectal carcinogenesis, determining driver mutational landscape, clonal neoantigen burden and immune response. J Pathol 2018; 245:283-296. [PMID: 29604063 PMCID: PMC6032922 DOI: 10.1002/path.5081] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2017] [Revised: 02/05/2018] [Accepted: 03/20/2018] [Indexed: 01/07/2023]
Abstract
Genomic instability, which is a hallmark of cancer, is generally thought to occur in the middle to late stages of tumourigenesis, following the acquisition of permissive molecular aberrations such as TP53 mutation or whole genome doubling. Tumours with somatic POLE exonuclease domain mutations are notable for their extreme genomic instability (their mutation burden is among the highest in human cancer), distinct mutational signature, lymphocytic infiltrate, and excellent prognosis. To what extent these characteristics are determined by the timing of POLE mutations in oncogenesis is unknown. Here, we have shown that pathogenic POLE mutations are detectable in non-malignant precursors of endometrial and colorectal cancer. Using genome and exome sequencing, we found that multiple driver mutations in POLE-mutant cancers show the characteristic POLE mutational signature, including those in genes conventionally regarded as initiators of tumourigenesis. In POLE-mutant cancers, the proportion of monoclonal predicted neoantigens was similar to that in other cancers, but the absolute number was much greater. We also found that the prominent CD8+ T-cell infiltrate present in POLE-mutant cancers was evident in their precursor lesions. Collectively, these data indicate that somatic POLE mutations are early, quite possibly initiating, events in the endometrial and colorectal cancers in which they occur. The resulting early onset of genomic instability may account for the striking immune response and excellent prognosis of these tumours, as well as their early presentation. © 2018 The Authors. The Journal of Pathology published by John Wiley & Sons Ltd on behalf of Pathological Society of Great Britain and Ireland.
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MESH Headings
- Adenocarcinoma/enzymology
- Adenocarcinoma/genetics
- Adenocarcinoma/immunology
- Adenocarcinoma/pathology
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Antigens, Neoplasm/metabolism
- CD8-Positive T-Lymphocytes/immunology
- CD8-Positive T-Lymphocytes/metabolism
- Cell Transformation, Neoplastic/genetics
- Cell Transformation, Neoplastic/immunology
- Cell Transformation, Neoplastic/metabolism
- Cell Transformation, Neoplastic/pathology
- Colorectal Neoplasms/enzymology
- Colorectal Neoplasms/genetics
- Colorectal Neoplasms/immunology
- Colorectal Neoplasms/pathology
- DNA Polymerase II/genetics
- DNA Polymerase II/metabolism
- Databases, Genetic
- Endometrial Neoplasms/enzymology
- Endometrial Neoplasms/genetics
- Endometrial Neoplasms/immunology
- Endometrial Neoplasms/pathology
- Female
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic
- Genetic Predisposition to Disease
- Genomic Instability
- Humans
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Male
- Middle Aged
- Mutation
- Neoplasm Grading
- Neoplasm Staging
- Phenotype
- Poly-ADP-Ribose Binding Proteins/genetics
- Poly-ADP-Ribose Binding Proteins/metabolism
- Tumor Microenvironment
- Whole Genome Sequencing
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Affiliation(s)
- Daniel Temko
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Centre for Maths and Physics in the Life Sciences and Experimental Biology (CoMPLEX)University College LondonLondonUK
- Department of Computer ScienceUniversity College LondonLondonUK
| | - Inge C Van Gool
- Department of PathologyLeiden University Medical CentreLeidenThe Netherlands
| | - Emily Rayner
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Mark Glaire
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Seiko Makino
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Matthew Brown
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Laura Chegwidden
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Claire Palles
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Jeroen Depreeuw
- KU Leuven (University of Leuven), University Hospitals Leuven, Department of Obstetrics and GynaecologyDivision of Gynaecological OncologyLeuvenBelgium
- KU Leuven, Department of Human GeneticsLaboratory for Translational GeneticsLeuvenBelgium
- VIB Centre for Cancer BiologyLaboratory for Translational GeneticsLeuvenBelgium
| | - Andrew Beggs
- Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUK
| | | | - John Mason
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Ann‐Marie Baker
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - Marc Williams
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
- Department of Cell and Developmental BiologyUniversity College LondonLondonUK
| | - Vincenzo Cerundolo
- MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Margarida Rei
- MRC Human Immunology Unit, Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
| | - Jenny C Taylor
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Anna Schuh
- Department of OncologyUniversity of OxfordOxfordUK
| | - Ahmed Ahmed
- Ovarian Cancer Cell Laboratory, Weatherall Institute of Molecular MedicineUniversity of OxfordOxfordUK
- Nuffield Department of Obstetrics & GynaecologyUniversity of OxfordOxfordUK
| | - Frédéric Amant
- Centre for Gynaecological Oncology AmsterdamNetherlands Cancer InstituteAmsterdamThe Netherlands
| | - Diether Lambrechts
- KU Leuven, Department of Human GeneticsLaboratory for Translational GeneticsLeuvenBelgium
- VIB Centre for Cancer BiologyLaboratory for Translational GeneticsLeuvenBelgium
| | - Vincent THBM Smit
- Department of PathologyLeiden University Medical CentreLeidenThe Netherlands
| | - Tjalling Bosse
- Department of PathologyLeiden University Medical CentreLeidenThe Netherlands
| | - Trevor A Graham
- Evolution and Cancer Laboratory, Barts Cancer Institute, Barts and the London School of Medicine and DentistryQueen Mary University of LondonLondonUK
| | - David N Church
- Wellcome Trust Centre for Human GeneticsUniversity of OxfordOxfordUK
| | - Ian Tomlinson
- Institute of Cancer and Genomic SciencesUniversity of BirminghamBirminghamUK
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46
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Chojnacki M, Melendy T. The HPV E2 Transcriptional Transactivation Protein Stimulates Cellular DNA Polymerase Epsilon. Viruses 2018; 10:v10060321. [PMID: 29895728 PMCID: PMC6024689 DOI: 10.3390/v10060321] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2018] [Revised: 06/04/2018] [Accepted: 06/08/2018] [Indexed: 01/28/2023] Open
Abstract
The papillomavirus (PV) protein E2 is one of only two proteins required for viral DNA replication. E2 is the viral transcriptional regulator/activation protein as well as the initiator of viral DNA replication. E2 is known to interact with various cellular DNA replication proteins, including the PV E1 protein, the cellular ssDNA binding complex (RPA), and topoisomerase I. Recently, we observed that cellular DNA polymerase ε (pol ε) interacts with the PV helicase protein, E1. E1 stimulates its activity with a very high degree of specificity, implicating pol ε in PV DNA replication. In this paper, we evaluated whether E2 also shows a functional interaction with pol ε. We found that E2 stimulates the DNA synthesis activity of pol ε, independently of pol ε’ s processivity factors, RFC, PCNA, and RPA, or E1. This appears to be specific for pol ε, as cellular DNA polymerase δ is unaffected by E1. However, unlike other known stimulatory factors of pol ε, E2 does not affect the processivity of pol ε. The domains of E2 were analyzed individually and in combination for their ability to stimulate pol ε. Both the transactivation and hinge domains were found to be important for this stimulation, while the E2 DNA-binding domain was dispensable. These findings support a role for E2 beyond E1 recruitment in viral DNA replication, demonstrate a novel functional interaction in PV DNA replication, and further implicate cellular pol ε in PV DNA replication.
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Affiliation(s)
- Michaelle Chojnacki
- Departments of Microbiology & Immunology and Biochemistry, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA.
| | - Thomas Melendy
- Departments of Microbiology & Immunology and Biochemistry, Jacobs School of Medicine & Biomedical Sciences, University at Buffalo, Buffalo, NY 14214, USA.
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47
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Hatakeyama K, Ohshima K, Nagashima T, Ohnami S, Ohnami S, Serizawa M, Shimoda Y, Maruyama K, Akiyama Y, Urakami K, Kusuhara M, Mochizuki T, Yamaguchi K. Molecular profiling and sequential somatic mutation shift in hypermutator tumours harbouring POLE mutations. Sci Rep 2018; 8:8700. [PMID: 29880869 PMCID: PMC5992218 DOI: 10.1038/s41598-018-26967-4] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 05/23/2018] [Indexed: 01/08/2023] Open
Abstract
Defective DNA polymerase ε (POLE) proofreading leads to extensive somatic mutations that exhibit biased mutational properties; however, the characteristics of POLE-mutated tumours remain unclear. In the present study, we describe a molecular profile using whole exome sequencing based on the transition of somatic mutations in 10 POLE-mutated solid tumours that were obtained from 2,042 Japanese patients. The bias of accumulated variations in these mutants was quantified to follow a pattern of somatic mutations, thereby classifying the sequential mutation shift into three periods. During the period prior to occurrence of the aberrant POLE, bare accumulation of mutations in cancer-related genes was observed, whereas PTEN was highly mutated in conjunction with or subsequent to the event, suggesting that POLE and PTEN mutations were responsible for the development of POLE-mutated tumours. Furthermore, homologous recombination was restored following the occurrence of PTEN mutations. Our strategy for estimation of the footprint of somatic mutations may provide new insight towards the understanding of mutation-driven tumourigenesis.
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Affiliation(s)
- Keiichi Hatakeyama
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan.
| | - Keiichi Ohshima
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Takeshi Nagashima
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
- SRL Inc., Shinjuku-ku, Tokyo, 163-0409, Japan
| | - Shumpei Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Sumiko Ohnami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Masakuni Serizawa
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yuji Shimoda
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
- SRL Inc., Shinjuku-ku, Tokyo, 163-0409, Japan
| | - Koji Maruyama
- Experimental Animal Facility, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Yasuto Akiyama
- Immunotheraphy Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Kenichi Urakami
- Cancer Diagnostics Research Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Masatoshi Kusuhara
- Drug Discovery and Development Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
- Regional Resource Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Tohru Mochizuki
- Medical Genetics Division, Shizuoka Cancer Center Research Institute, Sunto-gun, Shizuoka, 411-8777, Japan
| | - Ken Yamaguchi
- Shizuoka Cancer Center, Sunto-gun, Shizuoka, 411-8777, Japan
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48
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Barbari SR, Kane DP, Moore EA, Shcherbakova PV. Functional Analysis of Cancer-Associated DNA Polymerase ε Variants in Saccharomyces cerevisiae. G3 (Bethesda) 2018; 8:1019-1029. [PMID: 29352080 PMCID: PMC5844290 DOI: 10.1534/g3.118.200042] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/17/2018] [Indexed: 01/17/2023]
Abstract
DNA replication fidelity relies on base selectivity of the replicative DNA polymerases, exonucleolytic proofreading, and postreplicative DNA mismatch repair (MMR). Ultramutated human cancers without MMR defects carry alterations in the exonuclease domain of DNA polymerase ε (Polε). They have been hypothesized to result from defective proofreading. However, modeling of the most common variant, Polε-P286R, in yeast produced an unexpectedly strong mutator effect that exceeded the effect of proofreading deficiency by two orders of magnitude and indicated the involvement of other infidelity factors. The in vivo consequences of many additional Polε mutations reported in cancers remain poorly understood. Here, we genetically characterized 13 cancer-associated Polε variants in the yeast system. Only variants directly altering the DNA binding cleft in the exonuclease domain elevated the mutation rate. Among these, frequently recurring variants were stronger mutators than rare variants, in agreement with the idea that mutator phenotype has a causative role in tumorigenesis. In nearly all cases, the mutator effects exceeded those of an exonuclease-null allele, suggesting that mechanisms distinct from loss of proofreading may drive the genome instability in most ultramutated tumors. All mutator alleles were semidominant, supporting the view that heterozygosity for the polymerase mutations is sufficient for tumor development. In contrast to the DNA binding cleft alterations, peripherally located variants, including a highly recurrent V411L, did not significantly elevate mutagenesis. Finally, the analysis of Polε variants found in MMR-deficient tumors suggested that the majority cause no mutator phenotype alone but some can synergize with MMR deficiency to increase the mutation rate.
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Affiliation(s)
- Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Daniel P Kane
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Elizabeth A Moore
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
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49
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Beringer M, Pisano P, Di Carlo V, Blanco E, Chammas P, Vizán P, Gutiérrez A, Aranda S, Payer B, Wierer M, Di Croce L. EPOP Functionally Links Elongin and Polycomb in Pluripotent Stem Cells. Mol Cell 2017; 64:645-658. [PMID: 27863225 DOI: 10.1016/j.molcel.2016.10.018] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2016] [Revised: 08/30/2016] [Accepted: 10/14/2016] [Indexed: 11/19/2022]
Abstract
The cellular plasticity of pluripotent stem cells is thought to be sustained by genomic regions that display both active and repressive chromatin properties. These regions exhibit low levels of gene expression, yet the mechanisms controlling these levels remain unknown. Here, we describe Elongin BC as a binding factor at the promoters of bivalent sites. Biochemical and genome-wide analyses show that Elongin BC is associated with Polycomb Repressive Complex 2 (PRC2) in pluripotent stem cells. Elongin BC is recruited to chromatin by the PRC2-associated factor EPOP (Elongin BC and Polycomb Repressive Complex 2 Associated Protein, also termed C17orf96, esPRC2p48, E130012A19Rik), a protein expressed in the inner cell mass of the mouse blastocyst. Both EPOP and Elongin BC are required to maintain low levels of expression at PRC2 genomic targets. Our results indicate that keeping the balance between activating and repressive cues is a more general feature of chromatin in pluripotent stem cells than previously appreciated.
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Affiliation(s)
- Malte Beringer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Paola Pisano
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Valerio Di Carlo
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Enrique Blanco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Paul Chammas
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Pedro Vizán
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Arantxa Gutiérrez
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Sergi Aranda
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Bernhard Payer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain
| | - Michael Wierer
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Max Planck Institute for Biochemistry, Am Klopferspitz 18, 82152 Martinsried, Germany
| | - Luciano Di Croce
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain; Universitat Pompeu Fabra (UPF), 08003 Barcelona, Spain; ICREA, Pg. Lluis Companys 23, 08010 Barcelona, Spain.
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50
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Zhou JC, Janska A, Goswami P, Renault L, Abid Ali F, Kotecha A, Diffley JFX, Costa A. CMG-Pol epsilon dynamics suggests a mechanism for the establishment of leading-strand synthesis in the eukaryotic replisome. Proc Natl Acad Sci U S A 2017; 114:4141-4146. [PMID: 28373564 PMCID: PMC5402455 DOI: 10.1073/pnas.1700530114] [Citation(s) in RCA: 80] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
The replisome unwinds and synthesizes DNA for genome duplication. In eukaryotes, the Cdc45-MCM-GINS (CMG) helicase and the leading-strand polymerase, Pol epsilon, form a stable assembly. The mechanism for coupling DNA unwinding with synthesis is starting to be elucidated, however the architecture and dynamics of the replication fork remain only partially understood, preventing a molecular understanding of chromosome replication. To address this issue, we conducted a systematic single-particle EM study on multiple permutations of the reconstituted CMG-Pol epsilon assembly. Pol epsilon contains two flexibly tethered lobes. The noncatalytic lobe is anchored to the motor of the helicase, whereas the polymerization domain extends toward the side of the helicase. We observe two alternate configurations of the DNA synthesis domain in the CMG-bound Pol epsilon. We propose that this conformational switch might control DNA template engagement and release, modulating replisome progression.
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Affiliation(s)
- Jin Chuan Zhou
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Agnieszka Janska
- Chromosome Replication Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Panchali Goswami
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Ludovic Renault
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Ferdos Abid Ali
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Abhay Kotecha
- Division of Structural Biology, Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, OX3 7BN, United Kingdom
| | - John F X Diffley
- Chromosome Replication Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom
| | - Alessandro Costa
- Macromolecular Machines Laboratory, The Francis Crick Institute, London, NW1 1AT, United Kingdom;
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