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Kamio T, Kono Y, Hirosuna K, Ozato T, Yamamoto H, Hirasawa A, Ennishi D, Tomida S, Toyooka S, Otsuka M. Genomic Differences and Distinct TP53 Mutation Site-Linked Chemosensitivity in Early- and Late-Onset Gastric Cancer. Cancer Med 2025; 14:e70793. [PMID: 40249206 PMCID: PMC12007182 DOI: 10.1002/cam4.70793] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2024] [Revised: 01/16/2025] [Accepted: 03/08/2025] [Indexed: 04/19/2025] Open
Abstract
BACKGROUND Gastric cancer (GC) in younger patients often exhibits aggressive behavior and a poorer prognosis than that in older patients. Although the clinical differences may stem from oncogenic gene variations, it is unclear whether genetic differences exist between these groups. This study compared the genetic profiles of early- and late-onset GC and evaluated their impact on treatment outcomes. METHODS We analyzed genetic data from 1284 patients with GC in the Japanese nationwide Center for Cancer Genomics and Advanced Therapeutics (C-CAT) database, comparing early-onset (≤ 39 years; n = 143) and late-onset (≥ 65 years; n = 1141) groups. The influence of TP53 mutations on the time to treatment failure (TTF) with platinum-based chemotherapy and the sensitivity of cancer cells with different TP53 mutation sites to oxaliplatin were assessed in vitro. RESULTS Early- and late-onset GC showed distinct genetic profiles, with fewer neoantigen-associated genetic changes observed in early-onset cases. In particular, TP53 has distinct mutation sites; R175H and R273 mutations are more frequent in early- and late-onset GC, respectively. The R175H mutation showed higher sensitivity to oxaliplatin in vitro, consistent with the longer TTF in early-onset patients (17.3 vs. 7.0 months, p = 0.013) when focusing on the patients with TP53 mutations. CONCLUSION Genomic differences, particularly in TP53 mutation sites, between early- and late-onset GC support the need for age-specific treatment strategies.
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Affiliation(s)
- Tomohiro Kamio
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Dentistry and Pharmaceutical SciencesOkayama UniversityOkayamaJapan
| | - Yoshiyasu Kono
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Dentistry and Pharmaceutical SciencesOkayama UniversityOkayamaJapan
| | - Kensuke Hirosuna
- Department of Regenerative ScienceOkayama University Graduate School of Medicine, Dentistry and Pharmaceutical SciencesOkayamaJapan
| | - Toshiki Ozato
- Department of GastroenterologyOkayama University HospitalOkayamaJapan
| | - Hideki Yamamoto
- Department of Clinical Genomic MedicineOkayama University HospitalOkayamaJapan
| | - Akira Hirasawa
- Department of Clinical Genomic MedicineOkayama University HospitalOkayamaJapan
| | - Daisuke Ennishi
- Center for Comprehensive Genomic MedicineOkayama University HospitalOkayamaJapan
| | - Shuta Tomida
- Center for Comprehensive Genomic MedicineOkayama University HospitalOkayamaJapan
| | - Shinichi Toyooka
- Center for Comprehensive Genomic MedicineOkayama University HospitalOkayamaJapan
- Department of General Thoracic Surgery, Breast and Endocrinological SurgeryFaculty of Medicine, Dentistry and Pharmaceutical SciencesOkayamaJapan
| | - Motoyuki Otsuka
- Department of Gastroenterology and Hepatology, Faculty of Medicine, Dentistry and Pharmaceutical SciencesOkayama UniversityOkayamaJapan
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Kögl J, Pan TL, Marth C, Zeimet AG. The game-changing impact of POLE mutations in oncology-a review from a gynecologic oncology perspective. Front Oncol 2024; 14:1369189. [PMID: 39239272 PMCID: PMC11374733 DOI: 10.3389/fonc.2024.1369189] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Accepted: 07/31/2024] [Indexed: 09/07/2024] Open
Abstract
Somatic mutations within the exonuclease proofreading domain (EDM) of the DNA polymerase Pol ϵ (POLE) gene are increasingly being discovered in ovarian, colorectal, urological, and, especially, endometrial carcinoma (EC), where these are found in up to 10% of the cases. In EC, there are five confirmed pathogenic somatic POLE-EDM mutations that are located at codons 286, 411, 297, 456, and 459, and these are called "hotspot" mutations. POLE mutant tumors are ultramutated entities with a frequency of base substitution mutations that is among the highest in human tumors. Interestingly, these mutations are associated with excellent clinical outcome in EC. An additional six "non-hotspot" POLE-EDM EC mutations are also considered pathogenic, and they also confer a favorable prognosis. Currently, de-escalation of adjuvant treatment is recommended for patients with EC with stage I-II tumors involving any of these 11 EDM mutations, even in patients with other clinicopathological risk factors. The high tumor mutational burden and the consequent increased infiltration of immune cells due to the overexpression of different neoantigens are probably responsible for the improved prognosis. Ongoing studies are examining POLE hotspot mutations among many non-gynecologic tumors, although the impact of such mutations on clinical outcomes is still a topic of debate. Therapeutic modalities for these hypermutated tumors are also an important consideration, including the need for or de-escalation of adjuvant treatments and the response to immune therapy. This review addresses the critical role of POLE mutations in gynecologic oncology and oncology in general, focusing on definitions, variants, underlying pathogenic mechanisms, upcoming developments in the field, and the clinic behavior associated with such mutations.
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Affiliation(s)
- Johanna Kögl
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Teresa L Pan
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Christian Marth
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria
| | - Alain G Zeimet
- Department of Obstetrics and Gynecology, Medical University of Innsbruck, Innsbruck, Austria
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3
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Yao X, Feng M, Wang W. The Clinical and Pathological Characteristics of POLE-Mutated Endometrial Cancer: A Comprehensive Review. Cancer Manag Res 2024; 16:117-125. [PMID: 38463556 PMCID: PMC10921942 DOI: 10.2147/cmar.s445055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2023] [Accepted: 02/08/2024] [Indexed: 03/12/2024] Open
Abstract
Endometrial cancer shows high histological and molecular heterogeneity. The POLE mutation is a significant molecular alteration in endometrial cancer, leading to the identification of a specific subtype known as POLE-mutated endometrial cancer. This subtype exhibits a high tumor mutation burden, abundant lymphocyte infiltration, and a favorable prognosis, making it a promising candidate for immune checkpoint inhibitor therapy. This paper presents a comprehensive review of the clinical and pathological characteristics, outcomes, treatment advancements, pathogenic POLE gene detection, and alternative testing methods for POLE-mutated endometrial cancer.
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Affiliation(s)
- Xiaohong Yao
- Department of Pathology, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, People’s Republic of China
| | - Min Feng
- Department of Pathology, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
| | - Wei Wang
- Department of Pathology, West China Second University Hospital, Sichuan University, Sichuan, Chengdu, People’s Republic of China
- Key Laboratory of Birth Defects and Related Diseases of Women and Children (Sichuan University), Ministry of Education, Chengdu, Sichuan, People's Republic of China
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4
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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] [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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Strauss JD, Pursell ZF. Replication DNA polymerases, genome instability and cancer therapies. NAR Cancer 2023; 5:zcad033. [PMID: 37388540 PMCID: PMC10304742 DOI: 10.1093/narcan/zcad033] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2023] [Revised: 05/24/2023] [Accepted: 06/25/2023] [Indexed: 07/01/2023] Open
Abstract
It has been over a decade since the initial identification of exonuclease domain mutations in the genes encoding the catalytic subunits of replication DNA polymerases ϵ and δ (POLE and POLD1) in tumors from highly mutated endometrial and colorectal cancers. Interest in studying POLE and POLD1 has increased significantly since then. Prior to those landmark cancer genome sequencing studies, it was well documented that mutations in replication DNA polymerases that reduced their DNA synthesis accuracy, their exonuclease activity or their interactions with other factors could lead to increased mutagenesis, DNA damage and even tumorigenesis in mice. There are several recent, well-written reviews of replication DNA polymerases. The aim of this review is to gather and review in some detail recent studies of DNA polymerases ϵ and δ as they pertain to genome instability, cancer and potential therapeutic treatments. The focus here is primarily on recent informative studies on the significance of mutations in genes encoding their catalytic subunits (POLE and POLD1), mutational signatures, mutations in associated genes, model organisms, and the utility of chemotherapy and immune checkpoint inhibition in polymerase mutant tumors.
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Affiliation(s)
- Juliet D Strauss
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70118 LA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, 70118 LA, USA
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, 70118 LA, USA
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Poulsgaard GA, Sørensen SG, Juul RI, Nielsen MM, Pedersen JS. Sequence dependencies and mutation rates of localized mutational processes in cancer. Genome Med 2023; 15:63. [PMID: 37592287 PMCID: PMC10436389 DOI: 10.1186/s13073-023-01217-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2023] [Accepted: 08/02/2023] [Indexed: 08/19/2023] Open
Abstract
BACKGROUND Cancer mutations accumulate through replication errors and DNA damage coupled with incomplete repair. Individual mutational processes often show nucleotide sequence and functional region preferences. As a result, some sequence contexts mutate at much higher rates than others, with additional variation found between functional regions. Mutational hotspots, with recurrent mutations across cancer samples, represent genomic positions with elevated mutation rates, often caused by highly localized mutational processes. METHODS We count the 11-mer genomic sequences across the genome, and using the PCAWG set of 2583 pan-cancer whole genomes, we associate 11-mers with mutational signatures, hotspots of single nucleotide variants, and specific genomic regions. We evaluate the mutation rates of individual and combined sets of 11-mers and derive mutational sequence motifs. RESULTS We show that hotspots generally identify highly mutable sequence contexts. Using these, we show that some mutational signatures are enriched in hotspot sequence contexts, corresponding to well-defined sequence preferences for the underlying localized mutational processes. This includes signature 17b (of unknown etiology) and signatures 62 (POLE deficiency), 7a (UV), and 72 (linked to lymphomas). In some cases, the mutation rate and sequence preference increase further when focusing on certain genomic regions, such as signature 62 in transcribed regions, where the mutation rate is increased up to 9-folds over cancer type and mutational signature average. CONCLUSIONS We summarize our findings in a catalog of localized mutational processes, their sequence preferences, and their estimated mutation rates.
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Affiliation(s)
- Gustav Alexander Poulsgaard
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Simon Grund Sørensen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Randi Istrup Juul
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Morten Muhlig Nielsen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark
| | - Jakob Skou Pedersen
- Department of Clinical Medicine, Aarhus University, Palle Juul-Jensens Boulevard 82, 8200, Aarhus N, Denmark.
- Department of Molecular Medicine (MOMA), Aarhus University Hospital, Palle Juul-Jensens Boulevard 99, 8200, Aarhus N, Denmark.
- Bioinformatics Research Centre (BiRC), Aarhus University, University City 81, Building 1872, 3Rd Floor, 8000, Aarhus C, Denmark.
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7
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Labrousse G, Vande Perre P, Parra G, Jaffrelot M, Leroy L, Chibon F, Escudie F, Selves J, Hoffmann JS, Guimbaud R, Lutzmann M. The hereditary N363K POLE exonuclease mutant extends PPAP tumor spectrum to glioblastomas by causing DNA damage and aneuploidy in addition to increased mismatch mutagenicity. NAR Cancer 2023; 5:zcad011. [PMID: 36915289 PMCID: PMC10006997 DOI: 10.1093/narcan/zcad011] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Revised: 01/27/2023] [Accepted: 02/22/2023] [Indexed: 03/13/2023] Open
Abstract
The exonuclease domain of DNA polymerases epsilon's catalytic subunit (POLE) removes misincorporated nucleotides, called proofreading. POLE-exonuclease mutations cause colorectal- and endometrial cancers with an extreme burden of single nucleotide substitutions. We recently reported that particularly the hereditary POLE exonuclease mutation N363K predisposes in addition to aggressive giant cell glioblastomas. We knocked-in this mutation homozygously into human cell lines and compared its properties to knock-ins of the likewise hereditary POLE L424V mutation and to a complete proofreading-inactivating mutation (exo-null). We found that N363K cells have higher mutation rates as both L424V- or exo-null mutant cells. In contrast to L424V cells, N363K cells expose a growth defect, replication stress and DNA damage. In non-transformed cells, these burdens lead to aneuploidy but macroscopically normal nuclei. In contrast, transformed N363K cells phenocopy the enlarged and disorganized nuclei of giant cell glioblastomas. Taken together, our data characterize a POLE exonuclease domain mutant that not only causes single nucleotide hypermutation, but in addition DNA damage and chromosome instability, leading to an extended tumor spectrum. Our results expand the understanding of the polymerase exonuclease domain and suggest that an assessment of both the mutational potential and the genetic instability might refine classification and treatment of POLE-mutated tumors.
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Affiliation(s)
- Guillaume Labrousse
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
| | - Pierre Vande Perre
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
- Oncogenetics Department, Institute Claudius Regaud, IUCT-Oncopole, Toulouse, France
| | - Genis Parra
- Center for Genomic Analysis, CNAG, Carrer de Baldiri Reixac 4, Barcelona, Spain
| | - Marion Jaffrelot
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
- Oncogenetics Department, Institute Claudius Regaud, IUCT-Oncopole, Toulouse, France
- Department of Digestive Oncology, IUCT Rangueil-Larrey, CHU de Toulouse, Toulouse, France
| | - Laura Leroy
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
| | - Frederic Chibon
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
| | - Frederic Escudie
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irene-Joliot-Curie, 31059Toulouse, France
| | - Janick Selves
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irene-Joliot-Curie, 31059Toulouse, France
| | - Jean-Sebastien Hoffmann
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irene-Joliot-Curie, 31059Toulouse, France
| | - Rosine Guimbaud
- Oncogenetics Department, Institute Claudius Regaud, IUCT-Oncopole, Toulouse, France
- Department of Digestive Oncology, IUCT Rangueil-Larrey, CHU de Toulouse, Toulouse, France
| | - Malik Lutzmann
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
- Institute of Human Genetics, IGH, UMR 9002, Centre National de la Recherche Scientifique, University of Montpellier, 34396Montpellier, France
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Ostroverkhova D, Przytycka TM, Panchenko AR. Cancer driver mutations: predictions and reality. Trends Mol Med 2023:S1471-4914(23)00067-9. [PMID: 37076339 DOI: 10.1016/j.molmed.2023.03.007] [Citation(s) in RCA: 61] [Impact Index Per Article: 30.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 03/17/2023] [Accepted: 03/23/2023] [Indexed: 04/21/2023]
Abstract
Cancer cells accumulate many genetic alterations throughout their lifetime, but only a few of them drive cancer progression, termed driver mutations. Driver mutations may vary between cancer types and patients, can remain latent for a long time and become drivers at particular cancer stages, or may drive oncogenesis only in conjunction with other mutations. The high mutational, biochemical, and histological tumor heterogeneity makes driver mutation identification very challenging. In this review we summarize recent efforts to identify driver mutations in cancer and annotate their effects. We underline the success of computational methods to predict driver mutations in finding novel cancer biomarkers, including in circulating tumor DNA (ctDNA). We also report on the boundaries of their applicability in clinical research.
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Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada
| | - Teresa M Przytycka
- National Library of Medicine, National Institutes of Health (NIH), Bethesda, MD, USA.
| | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, Queen's University, Kingston, ON, Canada; Department of Biology and Molecular Sciences, Queen's University, Kingston, ON, Canada; School of Computing, Queen's University, Kingston, ON, Canada; Ontario Institute of Cancer Research, Toronto, ON, Canada.
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9
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Polymerase Epsilon-Associated Ultramutagenesis in Cancer. Cancers (Basel) 2022; 14:cancers14061467. [PMID: 35326618 PMCID: PMC8946778 DOI: 10.3390/cancers14061467] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Revised: 03/09/2022] [Accepted: 03/09/2022] [Indexed: 01/27/2023] Open
Abstract
With advances in next generation sequencing (NGS) technologies, efforts have been made to develop personalized medicine, targeting the specific genetic makeup of an individual. Somatic or germline DNA Polymerase epsilon (PolE) mutations cause ultramutated (>100 mutations/Mb) cancer. In contrast to mismatch repair-deficient hypermutated (>10 mutations/Mb) cancer, PolE-associated cancer is primarily microsatellite stable (MSS) In this article, we provide a comprehensive review of this PolE-associated ultramutated tumor. We describe its molecular characteristics, including the mutation sites and mutation signature of this type of tumor and the mechanism of its ultramutagenesis. We discuss its good clinical prognosis and elucidate the mechanism for enhanced immunogenicity with a high tumor mutation burden, increased neoantigen load, and enriched tumor-infiltrating lymphocytes. We also provide the rationale for immune checkpoint inhibitors in PolE-mutated tumors.
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10
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Park VS, Sun MJS, Frey WD, Williams LG, Hodel KP, Strauss JD, Wellens SJ, Jackson JG, Pursell ZF. Mouse model and human patient data reveal critical roles for Pten and p53 in suppressing POLE mutant tumor development. NAR Cancer 2022; 4:zcac004. [PMID: 35252866 PMCID: PMC8892059 DOI: 10.1093/narcan/zcac004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 01/17/2022] [Accepted: 02/17/2022] [Indexed: 12/24/2022] Open
Abstract
Mutations in the exonuclease domain of POLE are associated with tumors harboring very high mutation burdens. The mechanisms linking this significant mutation accumulation and tumor development remain poorly understood. Pole+/P286R;Trp53+/– mice showed accelerated cancer mortality compared to Pole+/P286R;Trp53+/+ mice. Cells from Pole+/P286R mice showed increased p53 activation, and subsequent loss of p53 permitted rapid growth, implicating canonical p53 loss of heterozygosity in POLE mutant tumor growth. However, p53 status had no effect on tumor mutation burden or single base substitution signatures in POLE mutant tumors from mice or humans. Pten has important roles in maintaining genome stability. We find that PTEN mutations are highly enriched in human POLE mutant tumors, including many in POLE signature contexts. One such signature mutation, PTEN-F341V, was previously shown in a mouse model to specifically decrease nuclear Pten and lead to increased DNA damage. We found tumors in Pole+/P286R mice that spontaneously acquired PtenF341V mutations and were associated with significantly reduced nuclear Pten and elevated DNA damage. Re-analysis of human TCGA (The Cancer Genome Atlas) data showed that all PTEN-F341V mutations occurred in tumors with mutations in POLE. Taken together with recent published work, our results support the idea that development of POLE mutant tumors may involve disabling surveillance of nuclear DNA damage in addition to POLE-mediated hypermutagenesis.
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Affiliation(s)
- Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Meijuan J S Sun
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Wesley D Frey
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Leonard G Williams
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Karl P Hodel
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Juliet D Strauss
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Sydney J Wellens
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - James G Jackson
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
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11
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Garmezy B, Gheeya J, Lin HY, Huang Y, Kim T, Jiang X, Thein KZ, Pilié PG, Zeineddine F, Wang W, Shaw KR, Rodon J, Shen JP, Yuan Y, Meric-Bernstam F, Chen K, Yap TA. Clinical and Molecular Characterization of POLE Mutations as Predictive Biomarkers of Response to Immune Checkpoint Inhibitors in Advanced Cancers. JCO Precis Oncol 2022; 6:e2100267. [PMID: 35108036 PMCID: PMC8820927 DOI: 10.1200/po.21.00267] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 11/16/2021] [Accepted: 12/28/2021] [Indexed: 12/12/2022] Open
Abstract
PURPOSE DNA polymerase epsilon is critical to DNA proofreading and replication. Mutations in POLE have been associated with hypermutated tumors and antitumor response to immune checkpoint inhibitor (ICI) therapy. We present a clinicopathologic analysis of patients with advanced cancers harboring POLE mutations, the pattern of co-occurring mutations, and their response to ICI therapy within the context of mutation pathogenicity. METHODS We conducted a retrospective analysis of next-generation sequencing data at MD Anderson Cancer Center to identify patient tumors with POLE mutations and their co-occurring mutations. The pathogenicity of each mutation was annotated using InterVar and ClinVar. Differences in therapeutic response to ICI, survival, and co-occurring mutations were reported by POLE pathogenicity status. RESULTS Four hundred fifty-eight patient tumors with POLE mutations were identified from 14,229 next-generation sequencing reports; 15.0% of POLE mutations were pathogenic, 15.9% benign, and 69.1% variant of unknown significance. Eighty-two patients received either programmed death 1 or programmed death ligand-1 inhibitors as monotherapy or in combination with cytotoxic T-cell lymphocyte-4 inhibitors. Patients with pathogenic POLE mutations had improved clinical benefit rate (82.4% v 30.0%; P = .013), median progression-free survival (15.1 v 2.2 months; P < .001), overall survival (29.5 v 6.8 months; P < .001), and longer treatment duration (median 15.5 v 2.5 months; P < .001) compared to those with benign variants. Progression-free survival and overall survival remained superior when adjusting for number of co-occurring mutations (≥ 10 v < 10) and/or microsatellite instability status (proficient mismatch repair v deficient mismatch repair). The number of comutations was not associated with response to ICI (clinical benefit v progressive disease: median 13 v 11 comutations; P = .18). CONCLUSION Pathogenic POLE mutations were associated with clinical benefit to ICI therapy. Further studies are warranted to validate POLE mutation as a predictive biomarker of ICI therapy.
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Affiliation(s)
- Benjamin Garmezy
- Division of Cancer Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jinesh Gheeya
- The University of Texas Health Science Center at Houston, Houston, TX
| | - Heather Y. Lin
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Yuefan Huang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Taebeom Kim
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Xianli Jiang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kyaw Z. Thein
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Patrick G. Pilié
- Department of Genitourinary Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Fadl Zeineddine
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Wanlin Wang
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Kenna R. Shaw
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Jordi Rodon
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
| | - John Paul Shen
- Department of Gastrointestinal Medical Oncology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ying Yuan
- Department of Biostatistics, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Funda Meric-Bernstam
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Ken Chen
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Timothy A. Yap
- Department of Investigational Cancer Therapeutics (Phase I Clinical Trials Program), The University of Texas MD Anderson Cancer Center, Houston, TX
- Khalifa Institute for Personalized Cancer Therapy, The University of Texas MD Anderson Cancer Center, Houston, TX
- The Institute for Applied Cancer Science, The University of Texas MD Anderson Cancer Center, Houston, TX
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12
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Fang H, Zhu X, Yang H, Oh J, Barbour JA, Wong JWH. Deficiency of replication-independent DNA mismatch repair drives a 5-methylcytosine deamination mutational signature in cancer. SCIENCE ADVANCES 2021; 7:eabg4398. [PMID: 34730999 PMCID: PMC8565909 DOI: 10.1126/sciadv.abg4398] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Multiple mutational signatures have been associated with DNA mismatch repair (MMR)–deficient cancers, but the mechanisms underlying their origin remain unclear. Here, using mutation data from cancer genomes, we identify a previously unknown function of MMR that is able to protect genomes from 5-methylcytosine (5mC) deamination–induced somatic mutations in a replication-independent manner. Cancers with deficiency of MMR proteins MSH2/MSH6 (MutSα) exhibit mutational signature contributions distinct from those that are deficient in MLH1/PMS2 (MutLα). This disparity arises from unrepaired 5mC deamination–induced mismatches rather than replicative DNA polymerase errors. In cancers with biallelic loss of MBD4 DNA glycosylase, repair of 5mC deamination damage is strongly associated with H3K36me3 chromatin, implicating MutSα as the essential factor in its repair. We thus uncover a noncanonical role of MMR in the protection against 5mC deamination–induced mutation in human cancers.
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13
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Gilad G, Leiserson MDM, Sharan R. A data-driven approach for constructing mutation categories for mutational signature analysis. PLoS Comput Biol 2021; 17:e1009542. [PMID: 34665813 PMCID: PMC8555780 DOI: 10.1371/journal.pcbi.1009542] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2021] [Revised: 10/29/2021] [Accepted: 10/06/2021] [Indexed: 11/29/2022] Open
Abstract
Mutational processes shape the genomes of cancer patients and their understanding has important applications in diagnosis and treatment. Current modeling of mutational processes by identifying their characteristic signatures views each base substitution in a limited context of a single flanking base on each side. This context definition gives rise to 96 categories of mutations that have become the standard in the field, even though wider contexts have been shown to be informative in specific cases. Here we propose a data-driven approach for constructing a mutation categorization for mutational signature analysis. Our approach is based on the assumption that tumor cells that are exposed to similar mutational processes, show similar expression levels of DNA damage repair genes that are involved in these processes. We attempt to find a categorization that maximizes the agreement between mutation and gene expression data, and show that it outperforms the standard categorization over multiple quality measures. Moreover, we show that the categorization we identify generalizes to unseen data from different cancer types, suggesting that mutation context patterns extend beyond the immediate flanking bases. Cancer is a group of genetic diseases that occur as a result of an accumulation of somatic mutations in genes that regulate cellular growth and differentiation. These mutations arise from mutagenic processes such as exposure to environmental mutagens and defective DNA damage repair pathways. Each of these processes results in a characteristic pattern of mutations, referred to as a mutational signature. These signatures reveal the mutagenic mechanisms that have influenced the development of a specific tumor, and thus provide new insights into its causes and potential treatments. Originally, a mutational signature has been defined using 96 mutation categories that take into account solely the information from the mutated base and its flanking bases. Here, we aim to challenge this arbitrary categorization, which is widely used in mutational signature analysis. We have developed a novel framework for the construction of mutation categories that is based on the assumption that the activities of DNA damage repair genes are correlated with the mutational processes that are active in a given tumor. We show that using this approach we are able to identify an alternative mutation categorization that outperforms the standard categorization with respect to multiple metrics. This categorization includes categories that account for bases that extend beyond the immediate flanking bases, suggesting that mutational signatures should be studied in broader sequence contexts.
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Affiliation(s)
- Gal Gilad
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Mark D. M. Leiserson
- Department of Computer Science and Center for Bioinformatics and Computational Biology, University of Maryland, College Park, Maryland, United States of America
| | - Roded Sharan
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
- * E-mail:
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14
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POLE, POLD1, and NTHL1: the last but not the least hereditary cancer-predisposing genes. Oncogene 2021; 40:5893-5901. [PMID: 34363023 DOI: 10.1038/s41388-021-01984-2] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2021] [Revised: 07/20/2021] [Accepted: 07/23/2021] [Indexed: 02/06/2023]
Abstract
POLE, POLD1, and NTHL1 are involved in DNA replication and have recently been recognized as hereditary cancer-predisposing genes, because their alterations are associated with colorectal cancer and other tumors. POLE/POLD1-associated syndrome shows an autosomal dominant inheritance, whereas NTHL1-associated syndrome follows an autosomal recessive pattern. Although the prevalence of germline monoallelic POLE/POLD1 and biallelic NTHL1 pathogenic variants is low, they determine different phenotypes with a broad tumor spectrum overlapping that of other hereditary conditions like Lynch Syndrome or Familial Adenomatous Polyposis. Endometrial and breast cancers, and probably ovarian and brain tumors are also associated with POLE/POLD1 alterations, while breast cancer and other unusual tumors are correlated with NTHL1 pathogenic variants. POLE-mutated colorectal and endometrial cancers are associated with better prognosis and may show favorable responses to immunotherapy. Since POLE/POLD1-mutated tumors show a high tumor mutational burden producing an increase in neoantigens, the identification of POLE/POLD1 alterations could help select patients suitable for immunotherapy treatment. In this review, we will investigate the role of POLE, POLD1, and NTHL1 genetic variants in cancer predisposition, discussing the potential future therapeutic applications and assessing the utility of performing a routine genetic testing for these genes, in order to implement prevention and surveillance strategies in mutation carriers.
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15
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Seplyarskiy VB, Sunyaev S. The origin of human mutation in light of genomic data. Nat Rev Genet 2021; 22:672-686. [PMID: 34163020 DOI: 10.1038/s41576-021-00376-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/06/2021] [Indexed: 02/05/2023]
Abstract
Despite years of active research into the role of DNA repair and replication in mutagenesis, surprisingly little is known about the origin of spontaneous human mutation in the germ line. With the advent of high-throughput sequencing, genome-scale data have revealed statistical properties of mutagenesis in humans. These properties include variation of the mutation rate and spectrum along the genome at different scales in relation to epigenomic features and dependency on parental age. Moreover, mutations originated in mothers are less frequent than mutations originated in fathers and have a distinct genomic distribution. Statistical analyses that interpret these patterns in the context of known biochemistry can provide mechanistic models of mutagenesis in humans.
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Affiliation(s)
- Vladimir B Seplyarskiy
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA
| | - Shamil Sunyaev
- Division of Genetics, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA. .,Department of Biomedical Informatics, Harvard Medical School, Boston, MA, USA.
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16
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Morledge-Hampton B, Wyrick JJ. Mutperiod: Analysis of periodic mutation rates in nucleosomes. Comput Struct Biotechnol J 2021; 19:4177-4183. [PMID: 34527191 PMCID: PMC8349767 DOI: 10.1016/j.csbj.2021.07.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 07/21/2021] [Accepted: 07/23/2021] [Indexed: 11/19/2022] Open
Abstract
Nucleosomes modulate DNA damage and repair, resulting in periodic mutation rates in nucleosomal DNA. Previous research has characterized these patterns in many sequenced tumor genomes; however, computational tools to identify and quantify these periodicities have not been developed for the broader scientific community. Here, we describe mutperiod, a Python and R based toolset that quantifies nucleosome mutational periodicities and compares them across different genetic and cellular backgrounds. We use mutperiod to demonstrate that DNA mismatch repair contributes to the nucleosome mutational periodicity observed in esophageal adenocarcinomas, and that the strength of this mutational periodicity varies in different chromatin states.
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Affiliation(s)
- Benjamin Morledge-Hampton
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
- Corresponding authors at: School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA (B. Morledge-Hampton and J.J. Wyrick).
| | - John J. Wyrick
- School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA
- Center for Reproductive Biology, Washington State University, Pullman, WA 99164, USA
- Corresponding authors at: School of Molecular Biosciences, Washington State University, Pullman, WA 99164, USA (B. Morledge-Hampton and J.J. Wyrick).
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17
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Huelsman KM, Basil JB, Sisson R, Lipe LR, Mahon B, Draper DJ. Somatic Tumor Profile Analysis in a Patient with Germline PMS2 Mutation and Synchronous Ovarian and Uterine Carcinomas. J Pers Med 2021; 11:jpm11070634. [PMID: 34357101 PMCID: PMC8307264 DOI: 10.3390/jpm11070634] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 04/25/2021] [Accepted: 07/01/2021] [Indexed: 11/23/2022] Open
Abstract
Lynch syndrome patients with synchronous endometrial and ovarian cancer (SEOC) are rare. When these cases occur, they are most often endometrioid histology and early grade. Early-grade tumors are not often sent for somatic tumor profiling. We present a 39 year old SEOC patient with germline PMS2 Lynch syndrome and clinical tumor analysis leading to insight regarding the origin and cause of these tumors, with potential therapy options. PMS2-related SEOC is less common due to lower risks for these cancers associated with germline PMS2 mutation compared to other Lynch genes. While synchronous cancers are not common, they are more likely to occur with Lynch syndrome. Tumor profiling with next-generation sequencing of 648 genes identified sixteen shared somatic actionable and biologically relevant mutations. This case is a rare example of a patient with PMS2 germline Lynch syndrome with shared somatic variants that demonstrate clonality of the two tumors arising from one common site.
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Affiliation(s)
- Karen M. Huelsman
- TriHealth Cancer Institute, Cincinnati, OH 45220, USA; (J.B.B.); (D.J.D.)
- Correspondence: ; Tel.: +1-513-862-2759; Fax: +1-513-852-3169
| | - Jack B. Basil
- TriHealth Cancer Institute, Cincinnati, OH 45220, USA; (J.B.B.); (D.J.D.)
| | - Rebecca Sisson
- Cincinnati Children’s Hospital Medical Center, Cincinnati, OH 45229, USA;
| | | | | | - David J. Draper
- TriHealth Cancer Institute, Cincinnati, OH 45220, USA; (J.B.B.); (D.J.D.)
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18
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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: 0.8] [Reference Citation Analysis] [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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19
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Shilkin ES, Petrova DV, Poltorachenko VA, Boldinova EO, Zharkov DO, Makarova AV. Template Properties of 5-Methyl-2'-Deoxycytidine and 5-Hydroxymethyl-2'-Deoxycytidine in Reactions with Human Translesion and Reparative DNA Polymerases. Mol Biol 2021. [DOI: 10.1134/s0026893321020138] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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20
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Hu H, Cai W, Wu D, Hu W, Dong Wang L, Mao J, Zheng S, Ge W. Ultra-mutated colorectal cancer patients with POLE driver mutations exhibit distinct clinical patterns. Cancer Med 2021; 10:135-142. [PMID: 33125191 PMCID: PMC7826451 DOI: 10.1002/cam4.3579] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2020] [Revised: 10/08/2020] [Accepted: 10/11/2020] [Indexed: 12/15/2022] Open
Abstract
POLE mutations, which lead to an ultramutated phenotype in colorectal cancer (CRC), have been reported as a promising marker in immunotherapy. We performed sequencing of CRC cases in Zhejiang University (ZJU) and extracted obtainable data from recently published results, including The Cancer Genome Atlas (TCGA), Japanese studies and clinical trials, to present clinical patterns of POLE driver-mutated CRC and reveal its heterogeneity. The rate of somatic POLE driver mutations has been reported as 2.60% (ZJU cohort), 1.50% (TCGA cohort), 1.00% (Japan cohort), and 1.00% (Lancet cohort). POLE driver mutations show a clearly increased mutation burden (mean TMB: 217.98 mut/Mb in ZJU; 203.13 mut/Mb in TCGA). Based on pooled data, more than 70.00% of patients with POLE driver mutations were diagnosed before they were 55 years old and at an early disease stage (Stage 0-II >70.00%), and more than 70.00% were male. Among Asian patients, 68.40% developed POLE driver mutations in the left-side colon, whereas 64.00% of non-Asian patients developed them in the right-side colon (p < 0.01). The top three amino acid changes due to POLE driver mutations are P286R, V411L, and S459F. Investigators and physicians should ascertain the heterogeneity and clinical patterns of POLE driver mutations to be better equipped to design clinical trials and analyze the data.
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Affiliation(s)
- Hanguang Hu
- Department of Medical OncologyThe Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
| | - Wen Cai
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education)The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Dehao Wu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education)The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
| | - Wangxiong Hu
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education)The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
| | - Li Dong Wang
- Henan Key Laboratory for Esophageal Cancer Research of the First Affiliated HospitalState Key Laboratory for Esophageal Cancer Prevention & TreatmentZhengzhou UniversityZhengzhouHenanChina
| | - Jianshan Mao
- Department of GastroenterologySecond Affiliated Hospital of Zhejiang University School of MedicineHangzhouChina
| | - Shu Zheng
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education)The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
| | - Weiting Ge
- Cancer Institute (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education)The Second Affiliated HospitalSchool of MedicineZhejiang UniversityHangzhouZhejiangChina
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21
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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: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [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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