1
|
Chen L, Hu H, Yuan Y, Weng S. CSCO guidelines for colorectal cancer version 2024: Updates and discussions. Chin J Cancer Res 2024; 36:233-239. [PMID: 38988483 PMCID: PMC11230882 DOI: 10.21147/j.issn.1000-9604.2024.03.01] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2024] [Accepted: 05/17/2024] [Indexed: 07/12/2024] Open
Affiliation(s)
- Liubo Chen
- Department of Medical Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Hanguang Hu
- Department of Medical Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| | - Ying Yuan
- Department of Medical Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
- Zhejiang Provincial Clinical Research Center for CANCER, Hangzhou 310009, China
- Cancer Center, Zhejiang University, Hangzhou 310058, China
| | - Shanshan Weng
- Department of Medical Oncology (Key Laboratory of Cancer Prevention and Intervention, China National Ministry of Education, Key Laboratory of Molecular Biology in Medical Sciences, Zhejiang Province, China), the Second Affiliated Hospital, Zhejiang University School of Medicine, Hangzhou 310009, China
| |
Collapse
|
2
|
Nusawardhana A, Pale LM, Nicolae CM, Moldovan GL. USP1-dependent nucleolytic expansion of PRIMPOL-generated nascent DNA strand discontinuities during replication stress. Nucleic Acids Res 2024; 52:2340-2354. [PMID: 38180818 PMCID: PMC10954467 DOI: 10.1093/nar/gkad1237] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2023] [Revised: 12/11/2023] [Accepted: 12/15/2023] [Indexed: 01/07/2024] Open
Abstract
DNA replication stress-induced fork arrest represents a significant threat to genomic integrity. One major mechanism of replication restart involves repriming downstream of the arrested fork by PRIMPOL, leaving behind a single-stranded DNA (ssDNA) gap. Accumulation of nascent strand ssDNA gaps has emerged as a possible determinant of the cellular hypersensitivity to genotoxic agents in certain genetic backgrounds such as BRCA deficiency, but how gaps are converted into cytotoxic structures is still unclear. Here, we investigate the processing of PRIMPOL-dependent ssDNA gaps upon replication stress induced by hydroxyurea and cisplatin. We show that gaps generated in PRIMPOL-overexpressing cells are expanded in the 3'-5' direction by the MRE11 exonuclease, and in the 5'-3' direction by the EXO1 exonuclease. This bidirectional exonucleolytic gap expansion ultimately promotes their conversion into DSBs. We moreover identify the de-ubiquitinating enzyme USP1 as a critical regulator of PRIMPOL-generated ssDNA gaps. USP1 promotes gap accumulation during S-phase, and their expansion by the MRE11 and EXO1 nucleases. This activity of USP1 is linked to its role in de-ubiquitinating PCNA, suggesting that PCNA ubiquitination prevents gap accumulation during replication. Finally, we show that USP1 depletion suppresses DSB formation in PRIMPOL-overexpressing cells, highlighting an unexpected role for USP1 in promoting genomic instability under these conditions.
Collapse
Affiliation(s)
- Alexandra Nusawardhana
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Lindsey M Pale
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - Claudia M Nicolae
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| | - George-Lucian Moldovan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University College of Medicine, Hershey, PA 17033, USA
| |
Collapse
|
3
|
Srivatsa A, Schwartz R. Optimizing Design of Genomics Studies for Clonal Evolution Analysis. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.03.14.585055. [PMID: 38559253 PMCID: PMC10980045 DOI: 10.1101/2024.03.14.585055] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2024]
Abstract
Genomic biotechnologies have seen rapid development over the past two decades, allowing for both the inference and modification of genetic and epigenetic information at the single cell level. While these tools present enormous potential for basic research, diagnostics, and treatment, they also raise difficult issues of how to design research studies to deploy these tools most effectively. In designing a study at the population or individual level, a researcher might combine several different sequencing modalities and sampling protocols, each with different utility, costs, and other tradeoffs. The central problem this paper attempts to address is then how one might create an optimal study design for a genomic analysis, with particular focus on studies involving somatic variation, typically for applications in cancer genomics. We pose the study design problem as a stochastic constrained nonlinear optimization problem and introduce a simulation-centered optimization procedure that iteratively optimizes the objective function using surrogate modeling combined with pattern and gradient search. Finally, we demonstrate the use of our procedure on diverse test cases to derive resource and study design allocations optimized for various objectives for the study of somatic cell populations.
Collapse
Affiliation(s)
- Arjun Srivatsa
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh PA 15213, USA
| | - Russell Schwartz
- Ray and Stephanie Lane Computational Biology Department, Carnegie Mellon University, Pittsburgh PA 15213, USA
- Department of Biological Sciences, Carnegie Mellon University, Pittsburgh PA 15213, USA
| |
Collapse
|
4
|
Shimizu D, Ishibashi M, Yamada T, Toda Y, Hosogi S, Ashihara E. POLD1 Is Required for Cell Cycle Progression by Overcoming DNA Damage in Malignant Pleural Mesothelioma. Cancer Genomics Proteomics 2024; 21:158-165. [PMID: 38423601 PMCID: PMC10905272 DOI: 10.21873/cgp.20437] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/13/2023] [Accepted: 12/22/2023] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND/AIM The prognosis of patients with malignant pleural mesothelioma (MPM) remains poor due to lack of effective therapeutic targets. DNA damage caused by long-time exposure to asbestos fibers has been associated with the development of MPM, with mutations at genes encoding DNA damage repair (DDR)-related molecules frequently expressed in patients with MPM. The present study was designed to identify novel therapeutic targets in MPM using large public databases, such as The Cancer Genome Atlas (TCGA) and Genotype Tissue Expression project (GTEx) focused on DDR pathways. MATERIALS AND METHODS The correlations between mRNA expression levels of DDR-related genes and overall survival (OS) were analyzed in mesothelioma patients in TCGA mesothelioma (TCGA-MESO) datasets. The anti-tumor effects of small interfering RNAs (siRNA) against DDR-related genes associated with OS were subsequently tested in MPM cell lines. RESULTS High levels of mRNA encoding DNA polymerase delta 1, catalytic subunit (POLD1) were significantly associated with reduced OS in patients with MPM (p<0.001, Log-rank test). In addition, siRNA targeting POLD1 (siPOLD1) caused cell cycle arrest at the G1/S checkpoint and induced apoptosis involving accumulation of DNA damage in MPM cell lines. CONCLUSION POLD1 plays essential roles in overcoming DNA damage and cell cycle progression at the G1/S checkpoint in MPM cells. These findings suggest that POLD1 may be a novel therapeutic target in MPM.
Collapse
Affiliation(s)
- Daiki Shimizu
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Miku Ishibashi
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Tadaaki Yamada
- Department of Pulmonary Medicine, Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Kyoto, Japan
| | - Yuki Toda
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Shigekuni Hosogi
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan
| | - Eishi Ashihara
- Laboratory of Clinical and Translational Physiology, Kyoto Pharmaceutical University, Kyoto, Japan;
| |
Collapse
|
5
|
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] [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.
Collapse
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.
| |
Collapse
|
6
|
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] [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.
Collapse
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.
| |
Collapse
|
7
|
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.
Collapse
|
8
|
Mur P, Viana-Errasti J, García-Mulero S, Magraner-Pardo L, Muñoz IG, Pons T, Capellá G, Pineda M, Feliubadaló L, Valle L. Recommendations for the classification of germline variants in the exonuclease domain of POLE and POLD1. Genome Med 2023; 15:85. [PMID: 37848928 PMCID: PMC10580551 DOI: 10.1186/s13073-023-01234-y] [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: 04/14/2023] [Accepted: 09/13/2023] [Indexed: 10/19/2023] Open
Abstract
BACKGROUND Germline variants affecting the proofreading activity of polymerases epsilon and delta cause a hereditary cancer and adenomatous polyposis syndrome characterized by tumors with a high mutational burden and a specific mutational spectrum. In addition to the implementation of multiple pieces of evidence for the classification of gene variants, POLE and POLD1 variant classification is particularly challenging given that non-disruptive variants affecting the proofreading activity of the corresponding polymerase are the ones associated with cancer. In response to an evident need in the field, we have developed gene-specific variant classification recommendations, based on the ACMG/AMP (American College of Medical Genetics and Genomics/Association for Molecular Pathology) criteria, for the assessment of non-disruptive variants located in the sequence coding for the exonuclease domain of the polymerases. METHODS A training set of 23 variants considered pathogenic or benign was used to define the usability and strength of the ACMG/AMP criteria. Population frequencies, computational predictions, co-segregation data, phenotypic and tumor data, and functional results, among other features, were considered. RESULTS Gene-specific variant classification recommendations for non-disruptive variants located in the exonuclease domain of POLE and POLD1 were defined. The resulting recommendations were applied to 128 exonuclease domain variants reported in the literature and/or public databases. A total of 17 variants were classified as pathogenic or likely pathogenic, and 17 as benign or likely benign. CONCLUSIONS Our recommendations, with room for improvement in the coming years as more information become available on carrier families, tumor molecular characteristics and functional assays, are intended to serve the clinical and scientific communities and help improve diagnostic performance, avoiding variant misclassifications.
Collapse
Affiliation(s)
- Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
- Department of Health of Catalonia, Catalan Cancer Plan, Barcelona, Spain.
| | - Julen Viana-Errasti
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
| | - Sandra García-Mulero
- Department of Health of Catalonia, Catalan Cancer Plan, Barcelona, Spain
- Unit of Biomarkers and Susceptibility, Oncology Data Analytics Program (ODAP), Catalan Institute of Oncology, Hospitalet de Llobregat, Barcelona, Spain
| | - Lorena Magraner-Pardo
- The CRUK Gene Function Laboratory and The Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research (ICR), London, UK
| | - Inés G Muñoz
- Protein Crystallography Unit, Structural Biology Program, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Tirso Pons
- Department of Immunology and Oncology, National Center for Biotechnology (CNB-CSIC), Spanish National Research Council, Madrid, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Lidia Feliubadaló
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain.
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| |
Collapse
|
9
|
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: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [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.
Collapse
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
| |
Collapse
|
10
|
Xie SM, Lai JX, Liu CQ, Zhang XX, Lin YM, Lan QW, Hong DY, Chen XC, Qiao JD, Mao YL. UBR4 deficiency causes male sterility and testis abnormal in Drosophila. Front Endocrinol (Lausanne) 2023; 14:1165825. [PMID: 37529615 PMCID: PMC10390308 DOI: 10.3389/fendo.2023.1165825] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2023] [Accepted: 06/05/2023] [Indexed: 08/03/2023] Open
Abstract
Introduction It has been established that UBR4 encodes E3 ubiquitin ligase, which determines the specificity of substrate binding during protein ubiquitination and has been associated with various functions of the nervous system but not the reproductive system. Herein, we explored the role of UBR4 on fertility with a Drosophila model. Methods Different Ubr4 knockdown flies were established using the UAS/GAL4 activating sequence system. Fertility, hatchability, and testis morphology were studied, and bioinformatics analyses were conducted. Our results indicated that UBR4 deficiency could induce male sterility and influent egg hatchability in Drosophila. Results We found that Ubr4 deficiency affected the testis during morphological analysis. Proteomics analysis indicated 188 upregulated proteins and 175 downregulated proteins in the testis of Ubr4 knockdown flies. Gene Ontology analysis revealed significant upregulation of CG11598 and Sfp65A, and downregulation of Pelota in Ubr4 knockdown flies. These proteins were involved in the biometabolic or reproductive process in Drosophila. These regulated proteins are important in testis generation and sperm storage promotion. Bioinformatics analysis verified that UBR4 was low expressed in cryptorchidism patients, which further supported the important role of UBR4 in male fertility. Discussion Overall, our findings suggest that UBR4 deficiency could promote male infertility and may be involved in the protein modification of UBR4 by upregulating Sfp65A and CG11598, whereas downregulating Pelota protein expression.
Collapse
Affiliation(s)
- Shi-Ming Xie
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- The First Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Jia-Xuan Lai
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
- The First Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Chu-Qiao Liu
- The Second Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Xi-Xing Zhang
- The Second Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Yong-Miao Lin
- The Second Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Qi-Wen Lan
- The Second Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - De-Yao Hong
- The First Clinical Medicine School of Guangzhou Medical University, Guangzhou, China
| | - Xiao-Chuan Chen
- Department of Obstetrics and Gynecology, The Sixth Affiliated Hospital, Sun Yat-sen University, Guangzhou, China
| | - Jing-Da Qiao
- Department of Neurology, Institute of Neuroscience, Key Laboratory of Neurogenetics and Channelopathies of Guangdong Province and the Ministry of Education of China, The Second Affiliated Hospital, Guangzhou Medical University, Guangzhou, China
| | - Yu-Ling Mao
- Department of Obstetrics and Gynecology, Center for Reproductive Medicine, Guangdong Provincial Key Laboratory of Major Obstetric Diseases, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
- Key Laboratory for Reproductive Medicine of Guangdong Province, The Third Affiliated Hospital of Guangzhou Medical University, Guangzhou, China
| |
Collapse
|
11
|
Gu S, Szymanski ES, Rangadurai AK, Shi H, Liu B, Manghrani A, Al-Hashimi HM. Dynamic basis for dA•dGTP and dA•d8OGTP misincorporation via Hoogsteen base pairs. Nat Chem Biol 2023; 19:900-910. [PMID: 37095237 DOI: 10.1038/s41589-023-01306-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 03/08/2023] [Indexed: 04/26/2023]
Abstract
Replicative errors contribute to the genetic diversity needed for evolution but in high frequency can lead to genomic instability. Here, we show that DNA dynamics determine the frequency of misincorporating the A•G mismatch, and altered dynamics explain the high frequency of 8-oxoguanine (8OG) A•8OG misincorporation. NMR measurements revealed that Aanti•Ganti (population (pop.) of >91%) transiently forms sparsely populated and short-lived Aanti+•Gsyn (pop. of ~2% and kex = kforward + kreverse of ~137 s-1) and Asyn•Ganti (pop. of ~6% and kex of ~2,200 s-1) Hoogsteen conformations. 8OG redistributed the ensemble, rendering Aanti•8OGsyn the dominant state. A kinetic model in which Aanti+•Gsyn is misincorporated quantitatively predicted the dA•dGTP misincorporation kinetics by human polymerase β, the pH dependence of misincorporation and the impact of the 8OG lesion. Thus, 8OG increases replicative errors relative to G because oxidation of guanine redistributes the ensemble in favor of the mutagenic Aanti•8OGsyn Hoogsteen state, which exists transiently and in low abundance in the A•G mismatch.
Collapse
Affiliation(s)
- Stephanie Gu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Eric S Szymanski
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Base4, Durham, NC, USA
| | - Atul K Rangadurai
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Hospital for Sick Children, Toronto, Ontario, Canada
| | - Honglue Shi
- Department of Chemistry, Duke University, Durham, NC, USA
- Innovative Genomics Institute, University of California, Berkeley, CA, USA
| | - Bei Liu
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
- Department of Chemistry, University of Chicago, Chicago, IL, USA
| | - Akanksha Manghrani
- Department of Biochemistry, Duke University School of Medicine, Durham, NC, USA
| | - Hashim M Al-Hashimi
- Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA.
| |
Collapse
|
12
|
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: 0] [Impact Index Per Article: 0] [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.
Collapse
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
| |
Collapse
|
13
|
Demidova EV, Serebriiskii IG, Vlasenkova R, Kelow S, Andrake MD, Hartman TR, Kent T, Virtucio J, Rosen GL, Pomerantz RT, Dunbrack RL, Golemis EA, Hall MJ, Chen DYT, Daly MB, Arora S. Candidate variants in DNA replication and repair genes in early-onset renal cell carcinoma patients referred for germline testing. BMC Genomics 2023; 24:212. [PMID: 37095444 PMCID: PMC10123997 DOI: 10.1186/s12864-023-09310-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Accepted: 04/13/2023] [Indexed: 04/26/2023] Open
Abstract
BACKGROUND Early-onset renal cell carcinoma (eoRCC) is typically associated with pathogenic germline variants (PGVs) in RCC familial syndrome genes. However, most eoRCC patients lack PGVs in familial RCC genes and their genetic risk remains undefined. METHODS Here, we analyzed biospecimens from 22 eoRCC patients that were seen at our institution for genetic counseling and tested negative for PGVs in RCC familial syndrome genes. RESULTS Analysis of whole-exome sequencing (WES) data found enrichment of candidate pathogenic germline variants in DNA repair and replication genes, including multiple DNA polymerases. Induction of DNA damage in peripheral blood monocytes (PBMCs) significantly elevated numbers of [Formula: see text]H2AX foci, a marker of double-stranded breaks, in PBMCs from eoRCC patients versus PBMCs from matched cancer-free controls. Knockdown of candidate variant genes in Caki RCC cells increased [Formula: see text]H2AX foci. Immortalized patient-derived B cell lines bearing the candidate variants in DNA polymerase genes (POLD1, POLH, POLE, POLK) had DNA replication defects compared to control cells. Renal tumors carrying these DNA polymerase variants were microsatellite stable but had a high mutational burden. Direct biochemical analysis of the variant Pol δ and Pol η polymerases revealed defective enzymatic activities. CONCLUSIONS Together, these results suggest that constitutional defects in DNA repair underlie a subset of eoRCC cases. Screening patient lymphocytes to identify these defects may provide insight into mechanisms of carcinogenesis in a subset of genetically undefined eoRCCs. Evaluation of DNA repair defects may also provide insight into the cancer initiation mechanisms for subsets of eoRCCs and lay the foundation for targeting DNA repair vulnerabilities in eoRCC.
Collapse
Affiliation(s)
- Elena V Demidova
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
- Kazan Federal University, Kazan, 420008, Russia
| | - Ilya G Serebriiskii
- Kazan Federal University, Kazan, 420008, Russia
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Ramilia Vlasenkova
- Kazan Federal University, Kazan, 420008, Russia
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Simon Kelow
- Department of Biochemistry and Molecular Biophysics, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Mark D Andrake
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Tiffiney R Hartman
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
- Arcadia University, Glenside, PA, USA
| | - Tatiana Kent
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - James Virtucio
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Gail L Rosen
- Ecological and Evolutionary Signal-Processing and Informatics Laboratory, Department of Electrical and Computer Engineering, College of Engineering, Drexel University, Philadelphia, PA, 19104, USA
| | - Richard T Pomerantz
- Department of Biochemistry & Molecular Biology, Sidney Kimmel Cancer Center, Thomas Jefferson University, Philadelphia, PA, 19107, USA
| | - Roland L Dunbrack
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Erica A Golemis
- Program in Cancer Signaling and Microenvironment, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
- Department of Cancer and Cellular Biology, Lewis Katz School of Medicine, Philadelphia, PA, 19140, USA
| | - Michael J Hall
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
- Department of Clinical Genetics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA
| | - David Y T Chen
- Department of Surgical Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA
| | - Mary B Daly
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
- Department of Clinical Genetics, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
| | - Sanjeevani Arora
- Cancer Prevention and Control Program, Fox Chase Cancer Center, 333 Cottman Avenue, Philadelphia, PA, 19111, USA.
- Department of Radiation Oncology, Fox Chase Cancer Center, Philadelphia, PA, 19111, USA.
| |
Collapse
|
14
|
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: 10] [Impact Index Per Article: 10.0] [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.
Collapse
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.
| |
Collapse
|
15
|
Han Z, Andrš M, Madhavan BK, Kaymak S, Sulaj A, Kender Z, Kopf S, Kihm L, Pepperkok R, Janscak P, Nawroth P, Kumar V. The importance of nuclear RAGE-Mcm2 axis in diabetes or cancer-associated replication stress. Nucleic Acids Res 2023; 51:2298-2318. [PMID: 36807739 PMCID: PMC10018352 DOI: 10.1093/nar/gkad085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Revised: 01/18/2023] [Accepted: 01/26/2023] [Indexed: 02/23/2023] Open
Abstract
An elevated frequency of DNA replication defects is associated with diabetes and cancer. However, data linking these nuclear perturbations to the onset or progression of organ complications remained unexplored. Here, we report that RAGE (Receptor for Advanced Glycated Endproducts), previously believed to be an extracellular receptor, upon metabolic stress localizes to the damaged forks. There it interacts and stabilizes the minichromosome-maintenance (Mcm2-7) complex. Accordingly, RAGE deficiency leads to slowed fork progression, premature fork collapse, hypersensitivity to replication stress agents and reduction of viability, which was reversed by the reconstitution of RAGE. This was marked by the 53BP1/OPT-domain expression and the presence of micronuclei, premature loss-of-ciliated zones, increased incidences of tubular-karyomegaly, and finally, interstitial fibrosis. More importantly, the RAGE-Mcm2 axis was selectively compromised in cells expressing micronuclei in human biopsies and mouse models of diabetic nephropathy and cancer. Thus, the functional RAGE-Mcm2/7 axis is critical in handling replication stress in vitro and human disease.
Collapse
Affiliation(s)
- Zhe Han
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Martin Andrš
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ-14300 Prague, Czech Republic
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Bindhu K Madhavan
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Serap Kaymak
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Alba Sulaj
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
- German Center of Diabetes Research (DZD), Neuherberg, Germany
| | - Zoltan Kender
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
- German Center of Diabetes Research (DZD), Neuherberg, Germany
| | - Stefan Kopf
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
- German Center of Diabetes Research (DZD), Neuherberg, Germany
| | - Lars Kihm
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
| | - Rainer Pepperkok
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
| | - Pavel Janscak
- Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, CZ-14300 Prague, Czech Republic
- Institute of Molecular Cancer Research, University of Zurich, 8057 Zurich, Switzerland
| | - Peter Nawroth
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
- Institute for Immunology, University Hospital of Heidelberg, INF 305, Heidelberg, Germany
- German Center of Diabetes Research (DZD), Neuherberg, Germany
| | - Varun Kumar
- Department of Medicine I and Clinical Chemistry, University Hospital of Heidelberg, INF 410, Heidelberg, Germany
- Institute for Immunology, University Hospital of Heidelberg, INF 305, Heidelberg, Germany
- European Molecular Biology Laboratory, Advanced Light Microscopy Facility, Heidelberg, Germany
- German Center of Diabetes Research (DZD), Neuherberg, Germany
| |
Collapse
|
16
|
Berger MB, Cisneros GA. Distal Mutations in the β-Clamp of DNA Polymerase III* Disrupt DNA Orientation and Affect Exonuclease Activity. J Am Chem Soc 2023; 145:3478-3490. [PMID: 36745735 PMCID: PMC10237177 DOI: 10.1021/jacs.2c11713] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
DNA polymerases are responsible for the replication and repair of DNA found in all DNA-based organisms. DNA Polymerase III is the main replicative polymerase of E. coli and is composed of over 10 proteins. A subset of these proteins (Pol III*) includes the polymerase (α), exonuclease (ϵ), clamp (β), and accessory protein (θ). Mutations of residues in, or around the active site of the catalytic subunits (α and ϵ), can have a significant impact on catalysis. However, the effects of distal mutations in noncatalytic subunits on the activity of catalytic subunits are less well-characterized. Here, we investigate the effects of two Pol III* variants, β-L82E/L82'E and β-L82D/L82'D, on the proofreading reaction catalyzed by ϵ. MD simulations reveal major changes in the dynamics of Pol III*, which extend throughout the complex. These changes are mostly induced by a shift in the position of the DNA substrate inside the β-clamp, although no major structural changes are observed in the protein complex. Quantum mechanics/molecular mechanics (QM/MM) calculations indicate that the β-L82D/L82'D variant has reduced catalytic proficiency due to highly endoergic reaction energies resulting from structural changes in the active site and differences in the electric field at the active site arising from the protein and substrate. Conversely, the β-L82E/L82'E variant is predicted to maintain proofreading activity, exhibiting a similar reaction barrier for nucleotide excision compared with the WT system. However, significant differences in the reaction mechanism are obtained due to the changes induced by the mutations on the β-clamp.
Collapse
Affiliation(s)
- Madison B Berger
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
| | - G Andrés Cisneros
- Department of Chemistry and Biochemistry, University of Texas at Dallas, Richardson, Texas 75080, United States
- Department of Physics, University of Texas at Dallas, Richardson, Texas 75080, United States
| |
Collapse
|
17
|
Gallitto M, Zhang Z. The evolving tale of Pol2 function. Genes Dev 2023; 37:72-73. [PMID: 36813532 PMCID: PMC10069447 DOI: 10.1101/gad.350527.123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/24/2023]
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.
Collapse
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
| |
Collapse
|
18
|
Tavano F, Gioffreda D, Fontana A, Palmieri O, Gentile A, Latiano T, Latiano A, Latiano TP, Scaramuzzi M, Maiello E, Bazzocchi F, Perri F. Evaluation of inherited germline mutations in cancer susceptibility genes among pancreatic cancer patients: a single-center study. Mol Med 2023; 29:14. [PMID: 36717774 PMCID: PMC9885574 DOI: 10.1186/s10020-023-00600-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 01/04/2023] [Indexed: 01/31/2023] Open
Abstract
BACKGROUND Germline mutations in cancer susceptibility genes were identified in pancreatic cancer (PanC) patients with a sporadic disease and in those unselected for family cancer history. METHODS With the aim to determine the prevalence of germline predisposition genes mutations in PanC, and to evaluate whether they were associated with the presence of PanC, we profiled a custom AmpliSeq panel of 27 cancer susceptibility genes in 47 PanC patients and 51 control subjects by using the Ion Torrent PGM system. RESULTS Multigene panel testing identified a total of 31 variants in 27 PanC (57.4%), including variants with pathogenic/likely pathogenic effect, those of uncertain significance, and variants whose clinical significance remains currently undefined. Five patients carried more than one variant in the same gene or in different genes. Eight patients (17.0%) had at least one pathogenic/likely pathogenic variant in four main genes: CFTR (10.6%), BRCA2 (8.5%), ATM and CHEK2 (2.1%). Pathogenic/likely pathogenic mutation were identified in patients with positive PanC family history (20%) or in patients without first-degree relatives affected by PanC (13.6%). All the BRCA2 mutation carriers were unselected PanC patients. The presence of mutations in BRCA2 was significantly associated with an increased occurrence of PanC and with positive family history for endometrial cancer (p = 0.018). CONCLUSIONS This study confirmed the potential remarkable contribution of BRCA2 in assessing the presence of PanC. Overall our findings supported the recommendation of offering the germline testing to all the PanC patients with the intent to reduce the number of underdiagnosed carriers of mutations in predisposition genes, and not to preclude their relatives from the opportunity to benefit from surveillance programs.
Collapse
Affiliation(s)
- Francesca Tavano
- grid.413503.00000 0004 1757 9135Division of Gastroenterology, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| | - Domenica Gioffreda
- grid.413503.00000 0004 1757 9135Division of Gastroenterology, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| | - Andrea Fontana
- grid.413503.00000 0004 1757 9135Unit of Biostatistics, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| | - Orazio Palmieri
- grid.413503.00000 0004 1757 9135Division of Gastroenterology, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| | - Annamaria Gentile
- grid.413503.00000 0004 1757 9135Division of Gastroenterology, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| | - Tiziana Latiano
- grid.413503.00000 0004 1757 9135Division of Gastroenterology, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| | - Anna Latiano
- grid.413503.00000 0004 1757 9135Division of Gastroenterology, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| | - Tiziana Pia Latiano
- grid.413503.00000 0004 1757 9135Department of Oncology, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| | - Matteo Scaramuzzi
- grid.413503.00000 0004 1757 9135Department of Surgery, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| | - Evaristo Maiello
- grid.413503.00000 0004 1757 9135Department of Oncology, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| | - Francesca Bazzocchi
- grid.413503.00000 0004 1757 9135Department of Surgery, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| | - Francesco Perri
- grid.413503.00000 0004 1757 9135Division of Gastroenterology, Fondazione “Casa Sollievo della Sofferenza” IRCCS Hospital, Viale Cappuccini 1, FG 71013 San Giovanni Rotondo, Italy
| |
Collapse
|
19
|
Bonjoch L, Soares de Lima Y, Díaz-Gay M, Dotti I, Muñoz J, Moreira L, Carballal S, Ocaña T, Cuatrecasas M, Ortiz O, Castells A, Pellisé M, Balaguer F, Salas A, Alexandrov LB, Castellví-Bel S. Unraveling the impact of a germline heterozygous POLD1 frameshift variant in serrated polyposis syndrome. Front Mol Biosci 2023; 10:1119900. [PMID: 36756361 PMCID: PMC9900627 DOI: 10.3389/fmolb.2023.1119900] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 01/10/2023] [Indexed: 01/24/2023] Open
Abstract
Serrated polyposis syndrome (SPS) is one of the most frequent polyposis syndromes characterized by an increased risk for developing colorectal cancer (CRC). Although SPS etiology has been mainly associated with environmental factors, germline predisposition to SPS could also be relevant for cases with familial aggregation or a family history of SPS/CRC. After whole-exome sequencing of 39 SPS patients from 16 families, we identified a heterozygous germline frameshift variant in the POLD1 gene (c.1941delG, p.(Lys648fs*46)) in a patient with SPS and CRC. Tumor presented an ultra-hypermutated phenotype and microsatellite instability. The POLD1 germline variant segregated in three additional SPS-affected family members. We attempted to create yeast and cellular models for this variant but were no viable. Alternatively, we generated patient-derived organoids (PDOs) from healthy rectal tissue of the index case, as well as from a control donor. Then, we challenged PDOs with a DNA-damaging agent to induce replication stress. No significant differences were observed in the DNA damage response between control and POLD1-Lys648fs PDOs, nor specific mutational signatures were observed. Our results do not support the pathogenicity of the analyzed POLD1 frameshift variant. One possible explanation is that haplosufficiency of the wild-type allele may be compensating for the absence of expression of the frameshift allele. Overall, future work is required to elucidate if functional consequences could be derived from POLD1 alterations different from missense variants in their proofreading domain. To our knowledge, our study presents the first organoid model for germline POLD1 variants and establishes the basis for its use as a model for disease in SPS, CRC and other malignancies.
Collapse
Affiliation(s)
- Laia Bonjoch
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Yasmin Soares de Lima
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Marcos Díaz-Gay
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, UC San Diego, La Jolla, CA, United States
| | - Isabella Dotti
- Inflammatory Bowel Disease Unit, Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Leticia Moreira
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Sabela Carballal
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Miriam Cuatrecasas
- Pathology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd) and Tumor Bank-Biobank, Hospital Clínic, Barcelona, Spain
| | - Oswaldo Ortiz
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Antoni Castells
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Maria Pellisé
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Azucena Salas
- Inflammatory Bowel Disease Unit, Gastroenterology Department, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS) Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| | - Ludmil B. Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, UC San Diego, La Jolla, CA, United States
| | - Sergi Castellví-Bel
- Gastroenterology Department, Institut d’Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBERehd), Hospital Clínic, Barcelona, Spain
| |
Collapse
|
20
|
Barbari SR, Beach AK, Markgren JG, Parkash V, Moore EA, Johansson E, Shcherbakova PV. Enhanced polymerase activity permits efficient synthesis by cancer-associated DNA polymerase ϵ variants at low dNTP levels. Nucleic Acids Res 2022; 50:8023-8040. [PMID: 35822874 PMCID: PMC9371911 DOI: 10.1093/nar/gkac602] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 06/13/2022] [Accepted: 06/29/2022] [Indexed: 11/28/2022] Open
Abstract
Amino acid substitutions in the exonuclease domain of DNA polymerase ϵ (Polϵ) cause ultramutated tumors. Studies in model organisms suggested pathogenic mechanisms distinct from a simple loss of exonuclease. These mechanisms remain unclear for most recurrent Polϵ mutations. Particularly, the highly prevalent V411L variant remained a long-standing puzzle with no detectable mutator effect in yeast despite the unequivocal association with ultramutation in cancers. Using purified four-subunit yeast Polϵ, we assessed the consequences of substitutions mimicking human V411L, S459F, F367S, L424V and D275V. While the effects on exonuclease activity vary widely, all common cancer-associated variants have increased DNA polymerase activity. Notably, the analog of Polϵ-V411L is among the strongest polymerases, and structural analysis suggests defective polymerase-to-exonuclease site switching. We further show that the V411L analog produces a robust mutator phenotype in strains that lack mismatch repair, indicating a high rate of replication errors. Lastly, unlike wild-type and exonuclease-dead Polϵ, hyperactive variants efficiently synthesize DNA at low dNTP concentrations. We propose that this characteristic could promote cancer cell survival and preferential participation of mutator polymerases in replication during metabolic stress. Our results support the notion that polymerase fitness, rather than low fidelity alone, is an important determinant of variant pathogenicity.
Collapse
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, NE 68198, USA
| | - Annette K Beach
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Joel G Markgren
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Vimal Parkash
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Elizabeth A Moore
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Erik Johansson
- Department of Medical Biochemistry and Biophysics, Umeå University, SE-90187 Umeå, Sweden
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
21
|
Functional landscapes of POLE and POLD1 mutations in checkpoint blockade-dependent antitumor immunity. Nat Genet 2022; 54:996-1012. [PMID: 35817971 PMCID: PMC10181095 DOI: 10.1038/s41588-022-01108-w] [Citation(s) in RCA: 31] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Accepted: 05/26/2022] [Indexed: 12/13/2022]
Abstract
Defects in pathways governing genomic fidelity have been linked to improved response to immune checkpoint blockade therapy (ICB). Pathogenic POLE/POLD1 mutations can cause hypermutation, yet how diverse mutations in POLE/POLD1 influence antitumor immunity following ICB is unclear. Here, we comprehensively determined the effect of POLE/POLD1 mutations in ICB and elucidated the mechanistic impact of these mutations on tumor immunity. Murine syngeneic tumors harboring Pole/Pold1 functional mutations displayed enhanced antitumor immunity and were sensitive to ICB. Patients with POLE/POLD1 mutated tumors harboring telltale mutational signatures respond better to ICB than patients harboring wild-type or signature-negative tumors. A mutant POLE/D1 function-associated signature-based model outperformed several traditional approaches for identifying POLE/POLD1 mutated patients that benefit from ICB. Strikingly, the spectrum of mutational signatures correlates with the biochemical features of neoantigens. Alterations that cause POLE/POLD1 function-associated signatures generate T cell receptor (TCR)-contact residues with increased hydrophobicity, potentially facilitating T cell recognition. Altogether, the functional landscapes of POLE/POLD1 mutations shape immunotherapy efficacy.
Collapse
|
22
|
Efficient discrimination against RNA-containing primers by human DNA polymerase ε. Sci Rep 2022; 12:10163. [PMID: 35715491 PMCID: PMC9205888 DOI: 10.1038/s41598-022-14602-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Accepted: 06/09/2022] [Indexed: 01/13/2023] Open
Abstract
DNA polymerase ε (Polε) performs bulk synthesis of DNA on the leading strand during genome replication. Polε binds two substrates, a template:primer and dNTP, and catalyzes a covalent attachment of dNMP to the 3' end of the primer. Previous studies have shown that Polε easily inserts and extends ribonucleotides, which may promote mutagenesis and genome instability. In this work, we analyzed the mechanisms of discrimination against RNA-containing primers by human Polε (hPolε), performing binding and kinetic studies at near-physiological salt concentration. Pre-steady-state kinetic studies revealed that hPolεCD extends RNA primers with approximately 3300-fold lower efficiency in comparison to DNA, and addition of one dNMP to the 3' end of an RNA primer increases activity 36-fold. Likewise, addition of one rNMP to the 3' end of a DNA primer reduces activity 38-fold. The binding studies conducted in the presence of 0.15 M NaCl revealed that human hPolεCD has low affinity to DNA (KD of 1.5 µM). Strikingly, a change of salt concentration from 0.1 M to 0.15 M reduces the stability of the hPolεCD/DNA complex by 25-fold. Upon template:primer binding, the incoming dNTP and magnesium ions make hPolε discriminative against RNA and chimeric RNA-DNA primers. In summary, our studies revealed that hPolε discrimination against RNA-containing primers is based on the following factors: incoming dNTP, magnesium ions, a steric gate for the primer 2'OH, and the rigid template:primer binding pocket near the catalytic site. In addition, we showed the importance of conducting functional studies at near-physiological salt concentration.
Collapse
|
23
|
Wang D, Zhang Y, li R, Li J, Zhang R. Consistency and reproducibility of large panel next-generation sequencing: Multi-laboratory assessment of somatic mutation detection on reference materials with mismatch repair and proofreading deficiency. J Adv Res 2022; 44:161-172. [PMID: 36725187 PMCID: PMC9937796 DOI: 10.1016/j.jare.2022.03.016] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2021] [Revised: 03/16/2022] [Accepted: 03/27/2022] [Indexed: 02/04/2023] Open
Abstract
INTRODUCTION Clinical precision oncology increasingly relies on accurate genome-wide profiling using large panel next generation sequencing; however, difficulties in accurate and consistent detection of somatic mutation from individual platforms and pipelines remain an open question. OBJECTIVES To obtain paired tumor-normal reference materials that can be effectively constructed and interchangeable with clinical samples, and evaluate the performance of 56 panels under routine testing conditions based on the reference samples. METHODS Genes involved in mismatch repair and DNA proofreading were knocked down using the CRISPR-Cas9 technology to accumulate somatic mutations in a defined GM12878 cell line. They were used as reference materials to comprehensively evaluate the reproducibility and accuracy of detection results of oncopanels and explore the potential influencing factors. RESULTS In total, 14 paired tumor-normal reference DNA samples from engineered cell lines were prepared, and a reference dataset comprising 168 somatic mutations in a high-confidence region of 1.8 Mb were generated. For mutations with an allele frequency (AF) of more than 5% in reference samples, 56 panels collectively reported 1306 errors, including 729 false negatives (FNs), 179 false positives (FPs) and 398 reproducibility errors. The performance metric varied among panels with precision and recall ranging from 0.773 to 1 and 0.683 to 1, respectively. Incorrect and inadequate filtering accounted for a large proportion of false discovery (including FNs and FPs), while low-quality detection, cross-contamination and other sequencing errors during the wet bench process were other sources of FNs and FPs. In addition, low AF (<5%) considerably influenced the reproducibility and comparability among panels. CONCLUSIONS This study provided an integrated practice for developing reference standard to assess oncopanels in detecting somatic mutations and quantitatively revealed the source of detection errors. It will promote optimization, validation, and quality control among laboratories with potential applicability in clinical use.
Collapse
Affiliation(s)
- Duo Wang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Yuanfeng Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Rui li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China,Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China,Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China
| | - Jinming Li
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
| | - Rui Zhang
- National Center for Clinical Laboratories, Institute of Geriatric Medicine, Chinese Academy of Medical Sciences, Beijing Hospital/National Center of Gerontology, P. R. China; Graduate School of Peking Union Medical College, Chinese Academy of Medical Sciences, Beijing, P. R. China; Beijing Engineering Research Center of Laboratory Medicine, Beijing Hospital, Beijing, P. R. China.
| |
Collapse
|
24
|
Global genomic instability caused by reduced expression of DNA polymerase ε in yeast. Proc Natl Acad Sci U S A 2022; 119:e2119588119. [PMID: 35290114 PMCID: PMC8944251 DOI: 10.1073/pnas.2119588119] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
SignificanceAlthough most studies of the genetic regulation of genome stability involve an analysis of mutations within the coding sequences of genes required for DNA replication or DNA repair, recent studies in yeast show that reduced levels of wild-type enzymes can also produce a mutator phenotype. By whole-genome sequencing and other methods, we find that reduced levels of the wild-type DNA polymerase ε in yeast greatly increase the rates of mitotic recombination, aneuploidy, and single-base mutations. The observed pattern of genome instability is different from those observed in yeast strains with reduced levels of the other replicative DNA polymerases, Pol α and Pol δ. These observations are relevant to our understanding of cancer and other diseases associated with genetic instability.
Collapse
|
25
|
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: 0.5] [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.
Collapse
|
26
|
Probing altered enzyme activity in the biochemical characterization of cancer. Biosci Rep 2022; 42:230680. [PMID: 35048115 PMCID: PMC8819661 DOI: 10.1042/bsr20212002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 01/10/2022] [Accepted: 01/19/2022] [Indexed: 11/30/2022] Open
Abstract
Enzymes have evolved to catalyze their precise reactions at the necessary rates, locations, and time to facilitate our development, to respond to a variety of insults and challenges, and to maintain a healthy, balanced state. Enzymes achieve this extraordinary feat through their unique kinetic parameters, myriad regulatory strategies, and their sensitivity to their surroundings, including substrate concentration and pH. The Cancer Genome Atlas (TCGA) highlights the extraordinary number of ways in which the finely tuned activities of enzymes can be disrupted, contributing to cancer development and progression often due to somatic and/or inherited genetic alterations. Rather than being limited to the domain of enzymologists, kinetic constants such as kcat, Km, and kcat/Km are highly informative parameters that can impact a cancer patient in tangible ways—these parameters can be used to sort tumor driver mutations from passenger mutations, to establish the pathways that cancer cells rely on to drive patients’ tumors, to evaluate the selectivity and efficacy of anti-cancer drugs, to identify mechanisms of resistance to treatment, and more. In this review, we will discuss how changes in enzyme activity, primarily through somatic mutation, can lead to altered kinetic parameters, new activities, or changes in conformation and oligomerization. We will also address how changes in the tumor microenvironment can affect enzymatic activity, and briefly describe how enzymology, when combined with additional powerful tools, and can provide us with tremendous insight into the chemical and molecular mechanisms of cancer.
Collapse
|
27
|
Sehested A, Meade J, Scheie D, Østrup O, Bertelsen B, Misiakou MA, Sarosiek T, Kessler E, Melchior LC, Munch-Petersen HF, Pai RK, Schmuth M, Gottschling H, Zschocke J, Gallon R, Wimmer K. Constitutional POLE variants causing a phenotype reminiscent of constitutional mismatch repair deficiency. Hum Mutat 2022; 43:85-96. [PMID: 34816535 DOI: 10.1002/humu.24299] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2021] [Revised: 10/28/2021] [Accepted: 11/03/2021] [Indexed: 12/20/2022]
Abstract
Heterozygous POLE or POLD1 germline pathogenic variants (PVs) cause polymerase proofreading associated polyposis (PPAP), a constitutional polymerase proofreading deficiency that typically presents with colorectal adenomas and carcinomas in adulthood. Constitutional mismatch-repair deficiency (CMMRD), caused by germline bi-allelic PVs affecting one of four MMR genes, results in a high propensity for the hematological, brain, intestinal tract, and other malignancies in childhood. Nonmalignant clinical features, such as skin pigmentation alterations, are found in nearly all CMMRD patients and are important diagnostic markers. Here, we excluded CMMRD in three cancer patients with highly suspect clinical phenotypes but identified in each a constitutional heterozygous POLE PV. These, and two additional POLE PVs identified in published CMMRD-like patients, have not previously been reported as germline PVs despite all being well-known somatic mutations in hyper-mutated tumors. Together, these five cases show that specific POLE PVs may have a stronger "mutator" effect than known PPAP-associated POLE PVs and may cause a CMMRD-like phenotype distinct from PPAP. The common underlying mechanism, that is, a constitutional replication error repair defect, and a similar tumor spectrum provide a good rationale for monitoring these patients with a severe constitutional polymerase proofreading deficiency according to protocols proposed for CMMRD.
Collapse
Affiliation(s)
- Astrid Sehested
- Department of Pediatrics and Adolescent Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Julia Meade
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - David Scheie
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Olga Østrup
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Birgitte Bertelsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Maria Anna Misiakou
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Elena Kessler
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, Pennsylvania, USA
| | - Linea C Melchior
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | | | - Reetesh K Pai
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Matthias Schmuth
- Department of Dermatology, Venereology and Allergy, Medical University of Innsbruck, Innsbruck, Austria
| | - Hendrik Gottschling
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Johannes Zschocke
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| | - Richard Gallon
- Faculty of Medical Sciences, Newcastle University, Newcastle upon Tyne, UK
| | - Katharina Wimmer
- Institute of Human Genetics, Medical University of Innsbruck, Innsbruck, Austria
| |
Collapse
|
28
|
Zhou ZX, Lujan SA, Burkholder AB, St. Charles J, Dahl J, Farrell CE, Williams JS, Kunkel TA. How asymmetric DNA replication achieves symmetrical fidelity. Nat Struct Mol Biol 2021; 28:1020-1028. [PMID: 34887558 PMCID: PMC8815454 DOI: 10.1038/s41594-021-00691-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 10/22/2021] [Indexed: 11/09/2022]
Abstract
Accurate DNA replication of an undamaged template depends on polymerase selectivity for matched nucleotides, exonucleolytic proofreading of mismatches, and removal of remaining mismatches via DNA mismatch repair (MMR). DNA polymerases (Pols) δ and ε have 3'-5' exonucleases into which mismatches are partitioned for excision in cis (intrinsic proofreading). Here we provide strong evidence that Pol δ can extrinsically proofread mismatches made by itself and those made by Pol ε, independently of both Pol δ's polymerization activity and MMR. Extrinsic proofreading across the genome is remarkably efficient. We report, with unprecedented accuracy, in vivo contributions of nucleotide selectivity, proofreading, and MMR to the fidelity of DNA replication in Saccharomyces cerevisiae. We show that extrinsic proofreading by Pol δ improves and balances the fidelity of the two DNA strands. Together, we depict a comprehensive picture of how nucleotide selectivity, proofreading, and MMR cooperate to achieve high and symmetrical fidelity on the two strands.
Collapse
Affiliation(s)
- Zhi-Xiong Zhou
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Scott A. Lujan
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Adam B. Burkholder
- Integrative Bioinformatics Support Group, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Jordan St. Charles
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Joseph Dahl
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Corinne E. Farrell
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Jessica S. Williams
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| | - Thomas A. Kunkel
- Genome Integrity & Structural Biology Laboratory, NIH/NIEHS, DHHS, Research Triangle Park, North Carolina, USA
| |
Collapse
|
29
|
Lee SY, Kim JJ, Miller KM. Bromodomain proteins: protectors against endogenous DNA damage and facilitators of genome integrity. Exp Mol Med 2021; 53:1268-1277. [PMID: 34548613 PMCID: PMC8492697 DOI: 10.1038/s12276-021-00673-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 07/13/2021] [Indexed: 12/11/2022] Open
Abstract
Endogenous DNA damage is a major contributor to mutations, which are drivers of cancer development. Bromodomain (BRD) proteins are well-established participants in chromatin-based DNA damage response (DDR) pathways, which maintain genome integrity from cell-intrinsic and extrinsic DNA-damaging sources. BRD proteins are most well-studied as regulators of transcription, but emerging evidence has revealed their importance in other DNA-templated processes, including DNA repair and replication. How BRD proteins mechanistically protect cells from endogenous DNA damage through their participation in these pathways remains an active area of investigation. Here, we review several recent studies establishing BRD proteins as key influencers of endogenous DNA damage, including DNA–RNA hybrid (R-loops) formation during transcription and participation in replication stress responses. As endogenous DNA damage is known to contribute to several human diseases, including neurodegeneration, immunodeficiencies, cancer, and aging, the ability of BRD proteins to suppress DNA damage and mutations is likely to provide new insights into the involvement of BRD proteins in these diseases. Although many studies have focused on BRD proteins in transcription, evidence indicates that BRD proteins have emergent functions in DNA repair and genome stability and are participants in the etiology and treatment of diseases involving endogenous DNA damage. Bromodomain (BRD) proteins, known to regulate gene expression, switching particular genes on and off, also play key roles in repairing DNA damage, and studying them may help identify treatments for various diseases, including cancer. DNA damage can occur during normal cellular metabolism, for example, during copying DNA and gene expression. DNA damage is implicated in tumor formation as well as in neurodegeneration, immunodeficiency, and aging. Seo Yun Lee and colleagues at The University of Texas at Austin, USA, have reviewed new results showing how BRD proteins function in repairing DNA damage. They report that when DNA is damaged during copying in BRD-deficient cells, tumors can result. They also report that defects in BRD proteins are often present in cancers. Studying how BRD proteins function in both healthy and diseased cells could help to identify new therapies.
Collapse
Affiliation(s)
- Seo Yun Lee
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Jae Jin Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA. .,Department of Life Science and Multidisciplinary Genome Institute, Hallym University, Chuncheon, Korea.
| | - Kyle M Miller
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA. .,Livestrong Cancer Institutes, Dell Medical School, The University of Texas at Austin, Austin, TX, USA.
| |
Collapse
|
30
|
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] [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.
Collapse
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
| | | |
Collapse
|
31
|
Stepchenkova EI, Zhuk AS, Cui J, Tarakhovskaya ER, Barbari SR, Shcherbakova PV, Polev DE, Fedorov R, Poliakov E, Rogozin IB, Lada AG, Pavlov YI. Compensation for the absence of the catalytically active half of DNA polymerase ε in yeast by positively selected mutations in CDC28. Genetics 2021; 218:6222163. [PMID: 33844024 DOI: 10.1093/genetics/iyab060] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2020] [Accepted: 04/02/2021] [Indexed: 11/14/2022] Open
Abstract
Current eukaryotic replication models postulate that leading and lagging DNA strands are replicated predominantly by dedicated DNA polymerases. The catalytic subunit of the leading strand DNA polymerase ε, Pol2, consists of two halves made of two different ancestral B-family DNA polymerases. Counterintuitively, the catalytically active N-terminal half is dispensable, while the inactive C-terminal part is required for viability. Despite extensive studies of yeast Saccharomyces cerevisiae strains lacking the active N-terminal half, it is still unclear how these strains survive and recover. We designed a robust method for constructing mutants with only the C-terminal part of Pol2. Strains without the active polymerase part show severe growth defects, sensitivity to replication inhibitors, chromosomal instability, and elevated spontaneous mutagenesis. Intriguingly, the slow-growing mutant strains rapidly accumulate fast-growing clones. Analysis of genomic DNA sequences of these clones revealed that the adaptation to the loss of the catalytic N-terminal part of Pol2 occurs by a positive selection of mutants with improved growth. Elevated mutation rates help generate sufficient numbers of these variants. Single nucleotide changes in the cell cycle-dependent kinase gene, CDC28, improve the growth of strains lacking the N-terminal part of Pol2, and rescue their sensitivity to replication inhibitors and, in parallel, lower mutation rates. Our study predicts that changes in mammalian homologs of cyclin-dependent kinases may contribute to cellular responses to the leading strand polymerase defects.
Collapse
Affiliation(s)
- Elena I Stepchenkova
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, Saint-Petersburg 199034, Russia.,Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg 199034, Russia.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Anna S Zhuk
- ITMO University, Saint-Petersburg 191002, Russia
| | - Jian Cui
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Elena R Tarakhovskaya
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, Saint-Petersburg 199034, Russia.,Department of Plant Physiology and Biochemistry, Saint-Petersburg State University, Saint-Petersburg 199034, Russia
| | - Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Dmitrii E Polev
- Research Resource Center "Biobank," Research Park, Saint-Petersburg State University, Saint-Petersburg 198504, Russia
| | - Roman Fedorov
- Department of Mathematics, University of Pittsburgh, PA 15213, USA
| | - Eugenia Poliakov
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Artem G Lada
- Department of Microbiology and Molecular Genetics, University of California Davis, Davis, CA 92697, USA
| | - Youri I Pavlov
- Department of Genetics and Biotechnology, Saint-Petersburg State University, Saint-Petersburg 199034, Russia.,Eppley Institute for Research in Cancer and Allied Diseases, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Biochemistry and Molecular Biology, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Microbiology and Pathology, University of Nebraska Medical Center, Omaha, NE 68198, USA.,Department of Genetics Cell Biology and Anatomy, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
32
|
Shia J. The diversity of tumours with microsatellite instability: molecular mechanisms and impact upon microsatellite instability testing and mismatch repair protein immunohistochemistry. Histopathology 2021; 78:485-497. [PMID: 33010064 DOI: 10.1111/his.14271] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2020] [Revised: 08/31/2020] [Accepted: 09/28/2020] [Indexed: 12/21/2022]
Abstract
Microsatellite instability (MSI) as a distinct molecular phenotype in human neoplasms was first recognised in 1993. Since then there has been tremendous progress in our understanding of this phenotype, including its genomic drivers and functional consequences. Currently, the multiple lines of investigation on MSI seem to have converged upon one important facet: its diversity, both genotypically and phenotypically, and both within and across tumour types. This review article offers a pathologist's perspective on our current understanding of this diversity, and highlights its potentially significant impact on the effective use of our current MSI detection tools: PCR- or sequencing-based MSI testing and mismatch repair protein immunohistochemistry.
Collapse
Affiliation(s)
- Jinru Shia
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| |
Collapse
|
33
|
Fuchs J, Cheblal A, Gasser SM. Underappreciated Roles of DNA Polymerase δ in Replication Stress Survival. Trends Genet 2021; 37:476-487. [PMID: 33608117 DOI: 10.1016/j.tig.2020.12.003] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2020] [Revised: 12/11/2020] [Accepted: 12/14/2020] [Indexed: 01/06/2023]
Abstract
Recent structural analysis of Fe-S centers in replication proteins and insights into the structure and function of DNA polymerase δ (DNA Pol δ) subunits have shed light on the key role played by this polymerase at replication forks under stress. The sequencing of cancer genomes reveals multiple point mutations that compromise the activity of POLD1, the DNA Pol δ catalytic subunit, whereas the loci encoding the accessory subunits POLD2 and POLD3 are amplified in a very high proportion of human tumors. Consistently, DNA Pol δ is key for the survival of replication stress and is involved in multiple long-patch repair pathways. Synthetic lethality arises from compromising the function and availability of the noncatalytic subunits of DNA Pol δ under conditions of replication stress, opening the door to novel therapies.
Collapse
Affiliation(s)
- Jeannette Fuchs
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland
| | - Anais Cheblal
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Sciences, University of Basel, Klingelbergstrasse 90, CH-4056 Basel, Switzerland
| | - Susan M Gasser
- Friedrich Miescher Institute for Biomedical Research, Maulbeerstrasse 66, CH-4058 Basel, Switzerland; Faculty of Sciences, University of Basel, Klingelbergstrasse 90, CH-4056 Basel, Switzerland.
| |
Collapse
|
34
|
Alvarado-Cruz I, Meas R, Paluri SLA, Carufe KEW, Khan M, Sweasy JB. The double-edged sword of cancer mutations: exploiting neoepitopes for the fight against cancer. Mutagenesis 2021; 35:69-78. [PMID: 31880305 DOI: 10.1093/mutage/gez049] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022] Open
Abstract
Defects in DNA repair have been linked to the accumulation of somatic mutations in tumours. These mutations can promote oncogenesis; however, recent developments have indicated that they may also lead to a targeted immune response against the tumour. This response is initiated by the development of new antigenic epitopes (neoepitopes) arising from mutations in protein-coding genes that are processed and then presented on the surface of tumour cells. These neoepitopes are unique to the tumour, thus enabling lymphocytes to launch an immune response against the cancer cells. Immunotherapies, such as checkpoint inhibitors (CPIs) and tumour-derived vaccines, have been shown to enhance the immunogenic response to cancers and have led to complete remission in some cancer patients. There are tumours that are not responsive to immunotherapy or conventional tumour therapeutics; therefore, there is a push for new treatments to combat these unresponsive cancers. Recently, combinatorial treatments have been developed to further utilise the immune system in the fight against cancer. These treatments have the potential to exploit the defects in DNA repair by inducing more DNA damage and mutations. This can potentially lead to the expression of high levels of neoepitopes on the surface of tumour cells that will stimulate an immunological response. Overall, exploiting DNA repair defects in tumours may provide an edge in this long fight against cancer.
Collapse
Affiliation(s)
| | - Rithy Meas
- Department of Therapeutic Radiology, Yale University, New Haven, CT, USA
| | | | | | - Mohammed Khan
- Department of Cellular and Molecular Medicine, UA College of Medicine, Tucson, AZ, USA
| | | |
Collapse
|
35
|
Rate volatility and asymmetric segregation diversify mutation burden in cells with mutator alleles. Commun Biol 2021; 4:21. [PMID: 33398111 PMCID: PMC7782790 DOI: 10.1038/s42003-020-01544-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2020] [Accepted: 12/01/2020] [Indexed: 11/15/2022] Open
Abstract
Mutations that compromise mismatch repair (MMR) or DNA polymerase ε or δ exonuclease domains produce mutator phenotypes capable of fueling cancer evolution. Here, we investigate how combined defects in these pathways expands genetic heterogeneity in cells of the budding yeast, Saccharomyces cerevisiae, using a single-cell resolution approach that tallies all mutations arising from individual divisions. The distribution of replication errors present in mother cells after the initial S-phase was broader than expected for a single uniform mutation rate across all cell divisions, consistent with volatility of the mutator phenotype. The number of mismatches that then segregated to the mother and daughter cells co-varied, suggesting that each division is governed by a different underlying genome-wide mutation rate. The distribution of mutations that individual cells inherit after the second S-phase is further broadened by the sequential actions of semiconservative replication and mitotic segregation of chromosomes. Modeling suggests that this asymmetric segregation may diversify mutation burden in mutator-driven tumors. Dowsett et al use a single-cell resolution approach to analyse the distribution of mutations across several divisions in yeast diploid strains mutated in mismatch repair and polymerase delta proofreading. They find that the underlying mutation rate varies from one division to another, and that new mutations segregate unequally between sister chromatids at each division, expanding genetic heterogeneity in the population.
Collapse
|
36
|
Galati MA, Hodel KP, Gams MS, Sudhaman S, Bridge T, Zahurancik WJ, Ungerleider NA, Park VS, Ercan AB, Joksimovic L, Siddiqui I, Siddaway R, Edwards M, de Borja R, Elshaer D, Chung J, Forster VJ, Nunes NM, Aronson M, Wang X, Ramdas J, Seeley A, Sarosiek T, Dunn GP, Byrd JN, Mordechai O, Durno C, Martin A, Shlien A, Bouffet E, Suo Z, Jackson JG, Hawkins CE, Guidos CJ, Pursell ZF, Tabori U. Cancers from Novel Pole-Mutant Mouse Models Provide Insights into Polymerase-Mediated Hypermutagenesis and Immune Checkpoint Blockade. Cancer Res 2020; 80:5606-5618. [PMID: 32938641 PMCID: PMC8218238 DOI: 10.1158/0008-5472.can-20-0624] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 06/25/2020] [Accepted: 09/11/2020] [Indexed: 12/31/2022]
Abstract
POLE mutations are a major cause of hypermutant cancers, yet questions remain regarding mechanisms of tumorigenesis, genotype-phenotype correlation, and therapeutic considerations. In this study, we establish mouse models harboring cancer-associated POLE mutations P286R and S459F, which cause rapid albeit distinct time to cancer initiation in vivo, independent of their exonuclease activity. Mouse and human correlates enabled novel stratification of POLE mutations into three groups based on clinical phenotype and mutagenicity. Cancers driven by these mutations displayed striking resemblance to the human ultrahypermutation and specific signatures. Furthermore, Pole-driven cancers exhibited a continuous and stochastic mutagenesis mechanism, resulting in intertumoral and intratumoral heterogeneity. Checkpoint blockade did not prevent Pole lymphomas, but rather likely promoted lymphomagenesis as observed in humans. These observations provide insights into the carcinogenesis of POLE-driven tumors and valuable information for genetic counseling, surveillance, and immunotherapy for patients. SIGNIFICANCE: Two mouse models of polymerase exonuclease deficiency shed light on mechanisms of mutation accumulation and considerations for immunotherapy.See related commentary by Wisdom and Kirsch p. 5459.
Collapse
Affiliation(s)
- Melissa A Galati
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Karl P Hodel
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana
| | - Miki S Gams
- Program in Developmental and Stem Cell Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Sumedha Sudhaman
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Taylor Bridge
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Cell Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Walter J Zahurancik
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio
| | - Nathan A Ungerleider
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana
| | - Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana
| | - Ayse B Ercan
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Lazar Joksimovic
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Iram Siddiqui
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Robert Siddaway
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Cell Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melissa Edwards
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Richard de Borja
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Dana Elshaer
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Jiil Chung
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Victoria J Forster
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nuno M Nunes
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Melyssa Aronson
- The Familial Gastrointestinal Cancer Registry at the Zane Cohen Centre for Digestive Disease, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Xia Wang
- H Lee Moffitt Cancer Centre and Research Institute, Tampa, Florida
| | - Jagadeesh Ramdas
- Department of Pediatrics, Geisinger Medical Center, Danville, Pennsylvania
| | - Andrea Seeley
- Department of Pediatrics, Geisinger Medical Center, Danville, Pennsylvania
| | | | - Gavin P Dunn
- Department of Neurological Surgery, Andrew M. and Jane M. Bursky Center for Human Immunology and Immunotherapy Programs, Washington University School of Medicine, St. Louis, Missouri
| | - Jonathan N Byrd
- Department of Neurology, Washington University School of Medicine, St. Louis, Missouri
| | - Oz Mordechai
- Department of Pediatric Hematology Oncology, Rambam Health Care Campus, Haifa, Israel
| | - Carol Durno
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Paediatrics, University of Toronto, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Alberto Martin
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Eric Bouffet
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Zucai Suo
- The Ohio State Biochemistry Program, The Ohio State University, Columbus, Ohio
- Department of Biomedical Sciences, College of Medicine, Florida State University, Tallahassee, Florida
| | - James G Jackson
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana
| | - Cynthia E Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Program in Cell Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatric Laboratory Medicine, Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Cynthia J Guidos
- Program in Developmental and Stem Cell Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Immunology, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, Louisiana
- Tulane Cancer Center, Tulane University School of Medicine, New Orleans, Louisiana
| | - Uri Tabori
- Program in Genetics and Genome Biology, The Peter Gilgan Centre for Research and Learning, The Hospital for Sick Children, Toronto, Ontario, Canada.
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
- Institute of Medical Science, Faculty of Medicine, University of Toronto, Toronto, Ontario, Canada
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| |
Collapse
|
37
|
Reha-Krantz LJ, Goodman MF. John W. (Jan) Drake: A Biochemical View of a Geneticist Par Excellence. Genetics 2020; 216:827-836. [PMID: 33268388 PMCID: PMC7768258 DOI: 10.1534/genetics.120.303813] [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: 09/07/2020] [Accepted: 10/22/2020] [Indexed: 11/18/2022] Open
Abstract
John W. Drake died 02-02-2020, a mathematical palindrome, which he would have enjoyed, given his love of "word play and logic," as stated in his obituary and echoed by his family, friends, students, and colleagues. Many aspects of Jan's career have been reviewed previously, including his early years as a Caltech graduate student, and when he was editor-in-chief, with the devoted assistance of his wife Pam, of this journal for 15 impactful years. During his editorship, he raised the profile of GENETICS as the flagship journal of the Genetics Society of America and inspired and contributed to the creation of the Perspectives column, coedited by Jim Crow and William Dove. At the same time, Jan was building from scratch the Laboratory of Molecular Genetics on the newly established Research Triangle Park campus of the National Institute of Environmental Health Science, which he headed for 30 years. This commentary offers a unique perspective on Jan's legacy; we showcase Jan's 1969 benchmark discovery of antimutagenic T4 DNA polymerases and the research by three generations (and counting) of scientists whose research stems from that groundbreaking discovery. This is followed by a brief discussion of Jan's passion: his overriding interest in analyzing mutation rates across species. Several anecdotal stories are included to bring alive one of Jan's favorite phrases, "to think like a geneticist." We feature Jan's genetical approach to mutation studies, along with the biochemistry of DNA polymerase function, our area of expertise. But in the end, we acknowledge, as Jan did, that genetics, also known as in vivo biochemistry, prevails.
Collapse
Affiliation(s)
- Linda J Reha-Krantz
- Department of Biological Sciences, University of Alberta, Edmonton, Alberta T6G 2E9, Canada
| | - Myron F Goodman
- Department of Biological Sciences, University of Southern California, Los Angeles, California 90089
| |
Collapse
|
38
|
Pavlov YI, Zhuk AS, Stepchenkova EI. DNA Polymerases at the Eukaryotic Replication Fork Thirty Years after: Connection to Cancer. Cancers (Basel) 2020; 12:E3489. [PMID: 33255191 PMCID: PMC7760166 DOI: 10.3390/cancers12123489] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 11/13/2020] [Accepted: 11/13/2020] [Indexed: 12/13/2022] Open
Abstract
Recent studies on tumor genomes revealed that mutations in genes of replicative DNA polymerases cause a predisposition for cancer by increasing genome instability. The past 10 years have uncovered exciting details about the structure and function of replicative DNA polymerases and the replication fork organization. The principal idea of participation of different polymerases in specific transactions at the fork proposed by Morrison and coauthors 30 years ago and later named "division of labor," remains standing, with an amendment of the broader role of polymerase δ in the replication of both the lagging and leading DNA strands. However, cancer-associated mutations predominantly affect the catalytic subunit of polymerase ε that participates in leading strand DNA synthesis. We analyze how new findings in the DNA replication field help elucidate the polymerase variants' effects on cancer.
Collapse
Affiliation(s)
- Youri I. Pavlov
- Eppley Institute for Research in Cancer and Allied Diseases and Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia;
| | - Anna S. Zhuk
- International Laboratory of Computer Technologies, ITMO University, 197101 Saint Petersburg, Russia;
| | - Elena I. Stepchenkova
- Department of Genetics and Biotechnology, Saint-Petersburg State University, 199034 Saint Petersburg, Russia;
- Laboratory of Mutagenesis and Genetic Toxicology, Vavilov Institute of General Genetics, Saint-Petersburg Branch, Russian Academy of Sciences, 199034 Saint Petersburg, Russia
| |
Collapse
|
39
|
Haratipour P, Minard C, Nakhjiri M, Negahbani A, Chamberlain BT, Osuna J, Upton TG, Zhao M, Kashemirov BA, McKenna CE. Completing the β,γ-CXY-dNTP Stereochemical Probe Toolkit: Synthetic Access to the dCTP Diastereomers and 31P and 19F NMR Correlations with Absolute Configurations. J Org Chem 2020; 85:14592-14609. [PMID: 33125847 DOI: 10.1021/acs.joc.0c01204] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Nucleoside 5'-triphosphate (dNTP) analogues in which the β,γ-oxygen is mimicked by a CXY group (β,γ-CXY-dNTPs) have provided information about DNA polymerase catalysis and fidelity. Definition of CXY stereochemistry is important to elucidate precise binding modes. We previously reported the (R)- and (S)-β,γ-CHX-dGTP diastereomers (X = F, Cl), prepared via P,C-dimorpholinamide CHCl (6a, 6b) and CHF (7a, 7b) bisphosphonates (BPs) equipped with an (R)-mandelic acid as a chiral auxiliary, with final deprotection using H2/Pd. This method also affords the β,γ-CHCl-dTTP (11a, 11b), β,γ-CHF (12a, 12b), and β,γ-CHCl (13a, 13b) dATP diastereomers as documented here, but the reductive deprotection step is not compatible with dCTP or the bromo substituent in β,γ-CHBr-dNTP analogues. To complete assembly of the toolkit, we describe an alternative synthetic strategy featuring ethylbenzylamine or phenylglycine-derived chiral BP synthons incorporating a photolabile protecting group. After acid-catalyzed removal of the (R)-(+)-α-ethylbenzylamine auxiliary, coupling with activated dCMP and photochemical deprotection, the individual diastereomers of β,γ-CHBr- (33a, 33b), β,γ-CHCl- (34a, 34b), β,γ-CHF-dCTP (35a, 35b) were obtained. The β,γ-CH(CH3)-dATPs (44a, 44b) were obtained using a methyl (R)-(-)-phenylglycinate auxiliary. 31P and 19F NMR Δδ values are correlated with CXY stereochemistry and pKa2-4 values for 13 CXY-bisphosphonic acids and imidodiphosphonic acid are tabulated.
Collapse
Affiliation(s)
- Pouya Haratipour
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Corinne Minard
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Maryam Nakhjiri
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Amirsoheil Negahbani
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Brian T Chamberlain
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Jorge Osuna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Thomas G Upton
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Michelle Zhao
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Boris A Kashemirov
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| | - Charles E McKenna
- Department of Chemistry, Dana and David Dornsife College of Letters, Arts and Sciences, University of Southern California, University Park Campus, Los Angeles, California 90089, United States
| |
Collapse
|
40
|
Bulock CR, Xing X, Shcherbakova PV. Mismatch repair and DNA polymerase δ proofreading prevent catastrophic accumulation of leading strand errors in cells expressing a cancer-associated DNA polymerase ϵ variant. Nucleic Acids Res 2020; 48:9124-9134. [PMID: 32756902 PMCID: PMC7498342 DOI: 10.1093/nar/gkaa633] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2020] [Revised: 07/13/2020] [Accepted: 07/27/2020] [Indexed: 12/15/2022] Open
Abstract
Substitutions in the exonuclease domain of DNA polymerase ϵ cause ultramutated human tumors. Yeast and mouse mimics of the most common variant, P286R, produce mutator effects far exceeding the effect of Polϵ exonuclease deficiency. Yeast Polϵ-P301R has increased DNA polymerase activity, which could underlie its high mutagenicity. We aimed to understand the impact of this increased activity on the strand-specific role of Polϵ in DNA replication and the action of extrinsic correction systems that remove Polϵ errors. Using mutagenesis reporters spanning a well-defined replicon, we show that both exonuclease-deficient Polϵ (Polϵ-exo−) and Polϵ-P301R generate mutations in a strictly strand-specific manner, yet Polϵ-P301R is at least ten times more mutagenic than Polϵ-exo− at each location analyzed. Thus, the cancer variant remains a dedicated leading-strand polymerase with markedly low accuracy. We further show that P301R substitution is lethal in strains lacking Polδ proofreading or mismatch repair (MMR). Heterozygosity for pol2-P301R is compatible with either defect but causes strong synergistic increases in the mutation rate, indicating that Polϵ-P301R errors are corrected by Polδ proofreading and MMR. These data reveal the unexpected ease with which polymerase exchange occurs in vivo, allowing Polδ exonuclease to prevent catastrophic accumulation of Polϵ-P301R-generated errors on the leading strand.
Collapse
Affiliation(s)
- Chelsea R Bulock
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Xuanxuan Xing
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE 68198, USA
| |
Collapse
|
41
|
Rosa RCA, Yurchenko AA, Chahud F, Ribeiro-Silva A, Brunaldi MO, Silva WA, Kannouche PL, Nikolaev S, Ferraz VEDF. First description of ultramutated endometrial cancer caused by germline loss-of-function and somatic exonuclease domain mutations in POLE gene. Genet Mol Biol 2020; 43:e20200100. [PMID: 33001133 PMCID: PMC7521106 DOI: 10.1590/1678-4685-gmb-2020-0100] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Accepted: 07/08/2020] [Indexed: 11/22/2022] Open
Abstract
Endometrial cancer (EC) harboring heterozygous POLE proofreading inactivating mutations (POLE-exo*) is associated with an increased number of somatic mutations that result in a distinctive anti-tumor immune response. However, the consequences of such POLE mutations in the context of the missing wild-type allele have not yet been described in endometrial tumors. A 72-year-old woman harboring a germline monoallelic frameshift mutation (p.Pro269fsTer26) in POLE was diagnosed with an EC having a somatic heterozygous mutation in the exonuclease domain of POLE (S459F). Targeted gene sequencing revealed an ultramutated phenotype (381 mutations/Mb) in the tumor and a 2-fold excess of mutations on the DNA leading strand. Additionally, we observed a mutational signature similar to the COSMIC signature 10, a higher mutation rate in this tumor than in endometrial tumors with heterozygous POLE-exo*, and an increased number of T lymphocytes. This is the first report of an ultramutated EC harboring a somatic POLE-exo* mutation in association with a germline loss-of-function mutation in this gene. The absence of a wild type POLE allele led to a particularly high mutational burden.
Collapse
Affiliation(s)
- Reginaldo Cruz Alves Rosa
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Andrey A. Yurchenko
- Université Paris Saclay, Inserm U981, Gustave Roussy Cancer
Campus, Villejuif, France
| | - Fernando Chahud
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Patologia e Medicina Legal, Ribeirão Preto, SP,
Brazil
| | - Alfredo Ribeiro-Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Patologia e Medicina Legal, Ribeirão Preto, SP,
Brazil
| | - Mariângela Ottoboni Brunaldi
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Patologia e Medicina Legal, Ribeirão Preto, SP,
Brazil
| | - Wilson Araújo Silva
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
| | - Patricia L. Kannouche
- Paris-Sud University, CNRS-UMR 8200, Equipe labellisée Ligue
Contre le Cancer, Gustave Roussy Cancer Campus, Villejuif, France
| | - Sergey Nikolaev
- Université Paris Saclay, Inserm U981, Gustave Roussy Cancer
Campus, Villejuif, France
| | - Victor Evangelista de Faria Ferraz
- Universidade de São Paulo, Faculdade de Medicina de Ribeirão
Preto, Departamento de Genética, Ribeirão Preto, SP, Brazil
- Universidade de São Paulo, Centro de Genômica Médica, Hospital
das Clínicas, Faculdade de Medicina de Ribeirão Preto, Ribeirão Preto, SP,
Brazil
| |
Collapse
|
42
|
Guilliam TA, Yeeles JTP. An updated perspective on the polymerase division of labor during eukaryotic DNA replication. Crit Rev Biochem Mol Biol 2020; 55:469-481. [PMID: 32883112 DOI: 10.1080/10409238.2020.1811630] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
In eukaryotes three DNA polymerases (Pols), α, δ, and ε, are tasked with bulk DNA synthesis of nascent strands during genome duplication. Most evidence supports a model where Pol α initiates DNA synthesis before Pol ε and Pol δ replicate the leading and lagging strands, respectively. However, a number of recent reports, enabled by advances in biochemical and genetic techniques, have highlighted emerging roles for Pol δ in all stages of leading-strand synthesis; initiation, elongation, and termination, as well as fork restart. By focusing on these studies, this review provides an updated perspective on the division of labor between the replicative polymerases during DNA replication.
Collapse
Affiliation(s)
- Thomas A Guilliam
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| | - Joseph T P Yeeles
- Division of Protein and Nucleic Acid Chemistry, Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
| |
Collapse
|
43
|
Cerritelli SM, Iranzo J, Sharma S, Chabes A, Crouch RJ, Tollervey D, El Hage A. High density of unrepaired genomic ribonucleotides leads to Topoisomerase 1-mediated severe growth defects in absence of ribonucleotide reductase. Nucleic Acids Res 2020; 48:4274-4297. [PMID: 32187369 PMCID: PMC7192613 DOI: 10.1093/nar/gkaa103] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Revised: 02/05/2020] [Accepted: 02/07/2020] [Indexed: 12/12/2022] Open
Abstract
Cellular levels of ribonucleoside triphosphates (rNTPs) are much higher than those of deoxyribonucleoside triphosphates (dNTPs), thereby influencing the frequency of incorporation of ribonucleoside monophosphates (rNMPs) by DNA polymerases (Pol) into DNA. RNase H2-initiated ribonucleotide excision repair (RER) efficiently removes single rNMPs in genomic DNA. However, processing of rNMPs by Topoisomerase 1 (Top1) in absence of RER induces mutations and genome instability. Here, we greatly increased the abundance of genomic rNMPs in Saccharomyces cerevisiae by depleting Rnr1, the major subunit of ribonucleotide reductase, which converts ribonucleotides to deoxyribonucleotides. We found that in strains that are depleted of Rnr1, RER-deficient, and harbor an rNTP-permissive replicative Pol mutant, excessive accumulation of single genomic rNMPs severely compromised growth, but this was reversed in absence of Top1. Thus, under Rnr1 depletion, limited dNTP pools slow DNA synthesis by replicative Pols and provoke the incorporation of high levels of rNMPs in genomic DNA. If a threshold of single genomic rNMPs is exceeded in absence of RER and presence of limited dNTP pools, Top1-mediated genome instability leads to severe growth defects. Finally, we provide evidence showing that accumulation of RNA/DNA hybrids in absence of RNase H1 and RNase H2 leads to cell lethality under Rnr1 depletion.
Collapse
Affiliation(s)
- Susana M Cerritelli
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - Jaime Iranzo
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
| | - Sushma Sharma
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå SE-901 87, Sweden
| | - Andrei Chabes
- Department of Medical Biochemistry and Biophysics, Umeå University, Umeå SE-901 87, Sweden
| | - Robert J Crouch
- SFR, Division of Intramural Research, Eunice Kennedy Shriver National Institute of Child Health and Human Development, National Institutes of Health, Bethesda, MD, USA
| | - David Tollervey
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| | - Aziz El Hage
- The Wellcome Centre for Cell Biology, University of Edinburgh, Edinburgh, UK
| |
Collapse
|
44
|
Li HD, Lu C, Zhang H, Hu Q, Zhang J, Cuevas IC, Sahoo SS, Aguilar M, Maurais EG, Zhang S, Wang X, Akbay EA, Li GM, Li B, Koduru P, Ly P, Fu YX, Castrillon DH. A PoleP286R mouse model of endometrial cancer recapitulates high mutational burden and immunotherapy response. JCI Insight 2020; 5:138829. [PMID: 32699191 DOI: 10.1172/jci.insight.138829] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 06/10/2020] [Indexed: 12/18/2022] Open
Abstract
Cancer is instigated by mutator phenotypes, including deficient mismatch repair and p53-associated chromosomal instability. More recently, a distinct class of cancers was identified with unusually high mutational loads due to heterozygous amino acid substitutions (most commonly P286R) in the proofreading domain of DNA polymerase ε, the leading strand replicase encoded by POLE. Immunotherapy has revolutionized cancer treatment, but new model systems are needed to recapitulate high mutational burdens characterizing human cancers and permit study of mechanisms underlying clinical responses. Here, we show that activation of a conditional LSL-PoleP286R allele in endometrium is sufficient to elicit in all animals endometrial cancers closely resembling their human counterparts, including very high mutational burden. Diverse investigations uncovered potentially novel aspects of Pole-driven tumorigenesis, including secondary p53 mutations associated with tetraploidy, and cooperation with defective mismatch repair through inactivation of Msh2. Most significantly, there were robust antitumor immune responses with increased T cell infiltrates, accelerated tumor growth following T cell depletion, and unfailing clinical regression following immune checkpoint therapy. This model predicts that human POLE-driven cancers will prove consistently responsive to immune checkpoint blockade. Furthermore, this is a robust and efficient approach to recapitulate in mice the high mutational burdens and immune responses characterizing human cancers.
Collapse
Affiliation(s)
| | | | - He Zhang
- Quantitative Biomedical Research Center, Department of Population and Data Sciences
| | | | | | | | | | | | | | | | | | - Esra A Akbay
- Department of Pathology.,Simmons Comprehensive Cancer Center
| | - Guo-Min Li
- Department of Radiation Oncology.,Advanced Imaging Research Center
| | - Bo Li
- Simmons Comprehensive Cancer Center.,Lyda Hill Department of Bioinformatics.,Department of Immunology
| | | | - Peter Ly
- Department of Pathology.,Simmons Comprehensive Cancer Center.,Department of Cell Biology, and
| | - Yang-Xin Fu
- Department of Pathology.,Simmons Comprehensive Cancer Center.,Department of Immunology
| | - Diego H Castrillon
- Department of Pathology.,Simmons Comprehensive Cancer Center.,Department of Obstetrics & Gynecology, UT Southwestern Medical Center, Dallas, Texas, USA
| |
Collapse
|
45
|
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: 31] [Impact Index Per Article: 7.8] [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.
Collapse
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.
| |
Collapse
|
46
|
Hühns M, Nürnberg S, Kandashwamy KK, Maletzki C, Bauer P, Prall F. High mutational burden in colorectal carcinomas with monoallelic POLE mutations: absence of allelic loss and gene promoter methylation. Mod Pathol 2020; 33:1220-1231. [PMID: 31857678 DOI: 10.1038/s41379-019-0430-6] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2019] [Revised: 10/28/2019] [Accepted: 11/11/2019] [Indexed: 01/09/2023]
Abstract
Hypermutator-type colorectal carcinomas are microsatellite-stable and have point mutations of the exonuclease domain of the DNA polymerase ε or δ genes (POLE and POLD1, respectively), and an ultrahigh tumor mutational burden (TMB). These tumors may be associated with enhanced antitumor immunity and preferentially afflict younger patients, but this notion awaits validation by accrual of further cases for detailed correlative phenotypic and molecular study. We performed POLE and POLD1 exonuclease domain Sanger sequencing of 271 unselected colorectal carcinomas. We identified two microsatellite-stable tumors with somatic POLE p.P286R variants, both with ultrahigh TMBs as demonstrated by whole exome sequencing. A POLE p.V411L was found in another two microsatellite-stable tumors with ultrahigh TMBs. Two of these four tumors were from young patients (<50 years old, nonsyndromic), and there was seen a prominent T-cell infiltration in three of them. Furthermore, a somatic POLE p.A465T was found in a Lynch-associated tumor, which, hypothetically, might have enhanced TMB (which was the highest of all). In two tumors, a somatic POLE p.V411L and a POLD1 p.E279K, respectively, were found only focally, and TMBs were low. It is commonly assumed that compromise of one allele is sufficient, but this has not been specifically addressed. Therefore, resequencing of the POLE or POLD1 mutations was done with DNA from tumor cells isolated by laser-capture microdissection. This demonstrated that the mutations were monoallelic, and there was no evidence of a "second hit", neither by allelic loss (allelotyping with polymorphic microsatellite markers), nor by promoter methylation (Pyromark CpG assays). Taken together, including at least the more common DNA polymerase mutations in NGS panels allows for straightforward identification of hypermutator-type colorectal carcinomas which often may be "immunoreactive". This is important at least in young patients or when a metastasizing stage of disease has been reached and immune-checkpoint therapy enters deliberation.
Collapse
Affiliation(s)
- Maja Hühns
- Institute of Pathology, University Medicine of Rostock, Strempelstraße 14, 18057, Rostock, Germany
| | | | | | - Claudia Maletzki
- Clinic for Hematology, Oncology and Palliative Care, University Medical Center Rostock, University of Rostock, Ernst-Heydemann-Strasse 6, 18057, Rostock, Germany
| | - Peter Bauer
- Centogene AG, Am Strande 7, 18055, Rostock, Germany
| | - Friedrich Prall
- Institute of Pathology, University Medicine of Rostock, Strempelstraße 14, 18057, Rostock, Germany.
| |
Collapse
|
47
|
Cervelli T, Lodovichi S, Bellè F, Galli A. Yeast-based assays for the functional characterization of cancer-associated variants of human DNA repair genes. MICROBIAL CELL 2020; 7:162-174. [PMID: 32656256 PMCID: PMC7328678 DOI: 10.15698/mic2020.07.721] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
Technological advances are continuously revealing new genetic variants that are often difficult to interpret. As one of the most genetically tractable model organisms, yeast can have a central role in determining the consequences of human genetic variation. DNA repair gene mutations are associated with many types of cancers, therefore the evaluation of the functional impact of these mutations is crucial for risk assessment and for determining therapeutic strategies. Owing to the evolutionary conservation of DNA repair pathways between human cells and the yeast Saccharomyces cerevisiae, several functional assays have been developed. Here, we describe assays for variants of human genes belonging to the major DNA repair pathways divided in functional assays for human genes with yeast orthologues and human genes lacking a yeast orthologue. Human genes with orthologues can be studied by introducing the correspondent human mutations directly in the yeast gene or expressing the human gene carrying the mutations; while the only possible approach for human genes without a yeast orthologue is the heterologous expression. The common principle of these approaches is that the mutated gene determines a phenotypic alteration that can vary according to the gene studied and the domain of the protein. Here, we show how the versatility of yeast can help in classifying cancer-associated variants.
Collapse
Affiliation(s)
- Tiziana Cervelli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
| | - Samuele Lodovichi
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
| | - Francesca Bellè
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
| | - Alvaro Galli
- Yeast Genetics and Genomics Group, Laboratory of Functional Genetics and Genomics, Institute of Clinical Physiology CNR, Via Moruzzi 1, 56125 Pisa, Italy
| |
Collapse
|
48
|
DNA polymerase ε relies on a unique domain for efficient replisome assembly and strand synthesis. Nat Commun 2020; 11:2437. [PMID: 32415104 PMCID: PMC7228970 DOI: 10.1038/s41467-020-16095-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2019] [Accepted: 04/14/2020] [Indexed: 12/21/2022] Open
Abstract
DNA polymerase epsilon (Pol ε) is required for genome duplication and tumor suppression. It supports both replisome assembly and leading strand synthesis; however, the underlying mechanisms remain to be elucidated. Here we report that a conserved domain within the Pol ε catalytic core influences both of these replication steps in budding yeast. Modeling cancer-associated mutations in this domain reveals its unexpected effect on incorporating Pol ε into the four-member pre-loading complex during replisome assembly. In addition, genetic and biochemical data suggest that the examined domain supports Pol ε catalytic activity and symmetric movement of replication forks. Contrary to previously characterized Pol ε cancer variants, the examined mutants cause genome hyper-rearrangement rather than hyper-mutation. Our work thus suggests a role of the Pol ε catalytic core in replisome formation, a reliance of Pol ε strand synthesis on a unique domain, and a potential tumor-suppressive effect of Pol ε in curbing genome re-arrangements.
Collapse
|
49
|
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: 37] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [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.
Collapse
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.
| |
Collapse
|
50
|
Acharya N, Khandagale P, Thakur S, Sahu JK, Utkalaja BG. Quaternary structural diversity in eukaryotic DNA polymerases: monomeric to multimeric form. Curr Genet 2020; 66:635-655. [PMID: 32236653 DOI: 10.1007/s00294-020-01071-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 03/13/2020] [Accepted: 03/24/2020] [Indexed: 12/14/2022]
Abstract
Sixteen eukaryotic DNA polymerases have been identified and studied so far. Based on the sequence similarity of the catalytic subunits of DNA polymerases, these have been classified into four A, B, X and Y families except PrimPol, which belongs to the AEP family. The quaternary structure of these polymerases also varies depending upon whether they are composed of one or more subunits. Therefore, in this review, we used a quaternary structure-based classification approach to group DNA polymerases as either monomeric or multimeric and highlighted functional significance of their accessory subunits. Additionally, we have briefly summarized various DNA polymerase discoveries from a historical perspective, emphasized unique catalytic mechanism of each DNA polymerase and highlighted recent advances in understanding their cellular functions.
Collapse
Affiliation(s)
- Narottam Acharya
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India.
| | - Prashant Khandagale
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Shweta Thakur
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Jugal Kishor Sahu
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| | - Bhabasha Gyanadeep Utkalaja
- Laboratory of Genomic Instability and Diseases, Department of Infectious Disease Biology, Institute of Life Sciences, Bhubaneswar, 751023, India
| |
Collapse
|