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Pancsa T, Vasas B, Melegh Z, Tóth E, Torday L, Sejben A. POLE-Mutant Colon Adenocarcinoma-Case Presentation and Histopathological Evaluation. J Gastrointest Cancer 2024; 55:961-964. [PMID: 38175383 DOI: 10.1007/s12029-023-01004-4] [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] [Accepted: 12/20/2023] [Indexed: 01/05/2024]
Abstract
INTRODUCTION POLE mutant phenotype in colon adenocarcinomas represents a rare molecular subtype. These tumours are generally responsive to immune-checkpoint inhibition therapy and, therefore, are currently considered as a subtype with good prognosis. We hereby present the first detailed case presentation of a POLE mutant colon adenocarcinoma with useful microscopic features. CASE REPORT A 53-year-old male patient's colon adenocarcinoma histologically showed wide variety of growth patterns and massive intra- and peritumoural lymphocytic infiltrate. The majority of the tumour consisted of a high-grade component resembling medullary carcinoma of the colon, while approximately one-third of the tumour was composed of conventional areas exhibiting a tubular pattern. A minority of the tumour was constituted by poorly cohesive rhabdoid cells. Immunohistochemistry was performed, and colorectal origin was proven with CDX-2 and SATB2. Furthermore, proficiency in mismatch repair proteins and SMARCB1 deficiency was observed. The unusually high-grade colon adenocarcinoma, with areas mimicking medullary carcinoma, and generally aggressive morphology raised suspicion of microsatellite instability. The diverse morphology and the SMARCB1 deficiency also raised suspicion of ultramutation caused by POLE alteration. Next-generation sequencing panel confirmed a pathogenetic mutation in POLE exon 9: p.Pro286Arg, c.857C > G. DISCUSSION The diverse, high-grade morphology and increased intratumoural lymphoid infiltration should raise suspicion for POLE-mutated adenocarcinoma during everyday histopathological practice. Mismatch repair proficiency results on immunohistochemistry should not determine the final diagnosis, as only a minor percentage of these tumours are MSI. In every case suspicious for POLE-mutated adenocarcinoma, a 500-cancer gene panel should be carried out.
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Affiliation(s)
- Tamás Pancsa
- Department of Pathology, University of Szeged, Állomás U. 1, Szeged, 6725, Hungary
| | - Béla Vasas
- Department of Pathology, University of Szeged, Állomás U. 1, Szeged, 6725, Hungary
| | - Zsombor Melegh
- Center of Tumor Pathology, Department of Surgical and Molecular Pathology, National Institute of Oncology Hungary, Ráth György U. 7-9, Budapest, 1122, Hungary
| | - Erika Tóth
- Center of Tumor Pathology, Department of Surgical and Molecular Pathology, National Institute of Oncology Hungary, Ráth György U. 7-9, Budapest, 1122, Hungary
| | - László Torday
- Department of Oncotherapy, University of Szeged, Korányi fasor 12, Szeged, 6720, Hungary
| | - Anita Sejben
- Department of Pathology, University of Szeged, Állomás U. 1, Szeged, 6725, Hungary.
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Ostroverkhova D, Tyryshkin K, Beach AK, Moore EA, Masoudi-Sobhanzadeh Y, Barbari SR, Rogozin IB, Shaitan KV, Panchenko AR, Shcherbakova PV. DNA polymerase ε and δ variants drive mutagenesis in polypurine tracts in human tumors. Cell Rep 2024; 43:113655. [PMID: 38219146 PMCID: PMC10830898 DOI: 10.1016/j.celrep.2023.113655] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2023] [Revised: 11/07/2023] [Accepted: 12/19/2023] [Indexed: 01/16/2024] Open
Abstract
Alterations in the exonuclease domain of DNA polymerase ε cause ultramutated cancers. These cancers accumulate AGA>ATA transversions; however, their genomic features beyond the trinucleotide motifs are obscure. We analyze the extended DNA context of ultramutation using whole-exome sequencing data from 524 endometrial and 395 colorectal tumors. We find that G>T transversions in POLE-mutant tumors predominantly affect sequences containing at least six consecutive purines, with a striking preference for certain positions within polypurine tracts. Using this signature, we develop a machine-learning classifier to identify tumors with hitherto unknown POLE drivers and validate two drivers, POLE-E978G and POLE-S461L, by functional assays in yeast. Unlike other pathogenic variants, the E978G substitution affects the polymerase domain of Pol ε. We further show that tumors with POLD1 drivers share the extended signature of POLE ultramutation. These findings expand the understanding of ultramutation mechanisms and highlight peculiar mutagenic properties of polypurine tracts in the human genome.
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Affiliation(s)
- Daria Ostroverkhova
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Kathrin Tyryshkin
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Annette K Beach
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Elizabeth A Moore
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Yosef Masoudi-Sobhanzadeh
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada
| | - Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Anna R Panchenko
- Department of Pathology and Molecular Medicine, School of Medicine, Queen's University, Kingston, ON, Canada.
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, NE, USA.
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Selves J, de Castro E Gloria H, Brunac AC, Saffi J, Guimbaud R, Brousset P, Hoffmann JS. Exploring the basis of heterogeneity of cancer aggressiveness among the mutated POLE variants. Life Sci Alliance 2024; 7:e202302290. [PMID: 37891003 PMCID: PMC10610022 DOI: 10.26508/lsa.202302290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Revised: 10/04/2023] [Accepted: 10/18/2023] [Indexed: 10/29/2023] Open
Abstract
Germline pathogenic variants in the exonuclease domain of the replicative DNA polymerase Pol ε encoded by the POLE gene, predispose essentially to colorectal and endometrial tumors by inducing an ultramutator phenotype. It is still unclear whether all the POLE alterations influence similar strength tumorigenesis, immune microenvironment, and treatment response. In this review, we summarize the current understanding of the mechanisms and consequences of POLE mutations in human malignancies; we highlight the heterogeneity of mutation rate and cancer aggressiveness among POLE variants, propose some mechanistic basis underlining such heterogeneity, and discuss novel considerations for the choice and efficacy of therapies of POLE tumors.
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Affiliation(s)
- Janick Selves
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
| | - Helena de Castro E Gloria
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Anne-Cécile Brunac
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Jenifer Saffi
- Laboratory of Genetic Toxicology, Federal University of Health Sciences of Porto Alegre, Porto Alegre, Brazil
| | - Rosine Guimbaud
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
- Department of Digestive Oncology, Centre Hospitalier Universitaire (CHU), Toulouse, France
- Department of Digestive Surgery, Centre Hospitalier Universitaire (CHU), Toulouse, France
| | - Pierre Brousset
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Université Fédérale Toulouse Midi-Pyrénées, Université Toulouse III Paul Sabatier, INSERM, CRCT, Toulouse, France
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Toulouse, France
| | - Jean-Sébastien Hoffmann
- Department of Pathology, Institut Universitaire du Cancer-Oncopole de Toulouse; Centre Hospitalier Universitaire (CHU), Toulouse, France
- Laboratoire d'Excellence Toulouse Cancer (TOUCAN), Toulouse, France
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Bilyalov A, Danishevich A, Nikolaev S, Vorobyov N, Abramov I, Pismennaya E, Terehova S, Kosilova Y, Primak A, Stanoevich U, Lisica T, Shipulin G, Gamayunov S, Kolesnikova E, Khatkov I, Gusev O, Bodunova N. Novel Pathogenic Variants in Hereditary Cancer Syndromes in a Highly Heterogeneous Cohort of Patients: Insights from Multigene Analysis. Cancers (Basel) 2023; 16:85. [PMID: 38201513 PMCID: PMC10778304 DOI: 10.3390/cancers16010085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Revised: 12/21/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
Cancer is a major global public health challenge, affecting both quality of life and mortality. Recent advances in genetic research have uncovered hereditary cancer syndromes (HCS) that predispose individuals to malignant neoplasms. While traditional single-gene testing has focused on high-penetrance genes, the past decade has seen a shift toward multigene panels, which facilitate the analysis of multiple genes associated with specific HCS. This approach reveals variants in less-studied gene regions and improves our understanding of cancer predisposition. In a study composed of Russian patients with clinical signs of HCS, we used a multigene hereditary cancer panel and revealed 21.6% individuals with pathogenic or likely pathogenic genetic variants. BRCA1/BRCA2 mutations predominated, followed by the CHEK2 and ATM variants. Of note, 16 previously undescribed variants were identified in the MUTYH, GALNT12, MSH2, MLH1, MLH3, EPCAM, and POLE genes. The implications of the study extend to personalized cancer prevention and treatment strategies, especially in populations lacking extensive epidemiological data, such as Russia. Overall, our research provides valuable genetic insights that give the way for further investigation and advances in the understanding and management of hereditary cancer syndromes.
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Affiliation(s)
- Airat Bilyalov
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (I.K.)
| | - Anastasiia Danishevich
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (I.K.)
| | - Sergey Nikolaev
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (I.K.)
| | - Nikita Vorobyov
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (I.K.)
| | - Ivan Abramov
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (I.K.)
- The Federal State Budgetary Scientific Institution “Izmerov Research Institute of Occupational Health”, 105275 Moscow, Russia
| | | | - Svetlana Terehova
- Kursk Regional Scientific and Clinical Center Named after G. Y. Ostroverkhov, 305524 Kursk, Russia; (S.T.); (Y.K.); (A.P.)
| | - Yuliya Kosilova
- Kursk Regional Scientific and Clinical Center Named after G. Y. Ostroverkhov, 305524 Kursk, Russia; (S.T.); (Y.K.); (A.P.)
| | - Anastasiia Primak
- Kursk Regional Scientific and Clinical Center Named after G. Y. Ostroverkhov, 305524 Kursk, Russia; (S.T.); (Y.K.); (A.P.)
| | - Uglesha Stanoevich
- Kursk Regional Scientific and Clinical Center Named after G. Y. Ostroverkhov, 305524 Kursk, Russia; (S.T.); (Y.K.); (A.P.)
| | - Tatyana Lisica
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical and Biological Agency, 119435 Moscow, Russia
| | - German Shipulin
- Centre for Strategic Planning and Management of Biomedical Health Risks, Federal Medical and Biological Agency, 119435 Moscow, Russia
| | - Sergey Gamayunov
- Nizhny Novgorod Regional Oncologic Hospital, 603163 Nizhny Novgorod, Russia
| | - Elena Kolesnikova
- Nizhny Novgorod Regional Oncologic Hospital, 603163 Nizhny Novgorod, Russia
| | - Igor Khatkov
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (I.K.)
| | - Oleg Gusev
- Institute of Fundamental Medicine and Biology, Kazan Federal University, 420008 Kazan, Russia
- Life Improvement by Future Technologies (LIFT) Center, 121205 Moscow, Russia
| | - Natalia Bodunova
- SBHI Moscow Clinical Scientific Center Named after Loginov MHD, 111123 Moscow, Russia (I.K.)
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Labrousse G, Vande Perre P, Parra G, Jaffrelot M, Leroy L, Chibon F, Escudie F, Selves J, Hoffmann JS, Guimbaud R, Lutzmann M. The hereditary N363K POLE exonuclease mutant extends PPAP tumor spectrum to glioblastomas by causing DNA damage and aneuploidy in addition to increased mismatch mutagenicity. NAR Cancer 2023; 5:zcad011. [PMID: 36915289 PMCID: PMC10006997 DOI: 10.1093/narcan/zcad011] [Citation(s) in RCA: 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.
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Affiliation(s)
- Guillaume Labrousse
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
| | - Pierre Vande Perre
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
- Oncogenetics Department, Institute Claudius Regaud, IUCT-Oncopole, Toulouse, France
| | - Genis Parra
- Center for Genomic Analysis, CNAG, Carrer de Baldiri Reixac 4, Barcelona, Spain
| | - Marion Jaffrelot
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
- Oncogenetics Department, Institute Claudius Regaud, IUCT-Oncopole, Toulouse, France
- Department of Digestive Oncology, IUCT Rangueil-Larrey, CHU de Toulouse, Toulouse, France
| | - Laura Leroy
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
| | - Frederic Chibon
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
| | - Frederic Escudie
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irene-Joliot-Curie, 31059Toulouse, France
| | - Janick Selves
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irene-Joliot-Curie, 31059Toulouse, France
| | - Jean-Sebastien Hoffmann
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
- Laboratoire d’Excellence Toulouse Cancer (TOUCAN), Laboratoire de Pathologie, Institut Universitaire du Cancer-Toulouse, Oncopole, 1 Avenue Irene-Joliot-Curie, 31059Toulouse, France
| | - Rosine Guimbaud
- Oncogenetics Department, Institute Claudius Regaud, IUCT-Oncopole, Toulouse, France
- Department of Digestive Oncology, IUCT Rangueil-Larrey, CHU de Toulouse, Toulouse, France
| | - Malik Lutzmann
- Cancer Research Center of Toulouse, CRCT, 2 Avenue Hubert Curien, 31000Toulouse, France
- Institute of Human Genetics, IGH, UMR 9002, Centre National de la Recherche Scientifique, University of Montpellier, 34396Montpellier, France
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Choi DJ, Armstrong G, Lozzi B, Vijayaraghavan P, Plon SE, Wong TC, Boerwinkle E, Muzny DM, Chen HC, Gibbs RA, Ostrom QT, Melin B, Deneen B, Bondy ML, Bainbridge MN. The genomic landscape of familial glioma. SCIENCE ADVANCES 2023; 9:eade2675. [PMID: 37115922 PMCID: PMC10146888 DOI: 10.1126/sciadv.ade2675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/04/2022] [Accepted: 03/22/2023] [Indexed: 05/03/2023]
Abstract
Glioma is a rare brain tumor with a poor prognosis. Familial glioma is a subset of glioma with a strong genetic predisposition that accounts for approximately 5% of glioma cases. We performed whole-genome sequencing on an exploratory cohort of 203 individuals from 189 families with a history of familial glioma and an additional validation cohort of 122 individuals from 115 families. We found significant enrichment of rare deleterious variants of seven genes in both cohorts, and the most significantly enriched gene was HERC2 (P = 0.0006). Furthermore, we identified rare noncoding variants in both cohorts that were predicted to affect transcription factor binding sites or cause cryptic splicing. Last, we selected a subset of discovered genes for validation by CRISPR knockdown screening and found that DMBT1, HP1BP3, and ZCH7B3 have profound impacts on proliferation. This study performs comprehensive surveillance of the genomic landscape of familial glioma.
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Affiliation(s)
- Dong-Joo Choi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Georgina Armstrong
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - Brittney Lozzi
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | | | - Sharon E. Plon
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
| | - Terence C. Wong
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
| | - Eric Boerwinkle
- The University of Texas Health Science Center School of Public Health, Houston, TX, USA
| | - Donna M. Muzny
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Hsiao-Chi Chen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Richard A. Gibbs
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
| | - Quinn T. Ostrom
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
| | - Beatrice Melin
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Benjamin Deneen
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
| | - Melissa L. Bondy
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - The Gliogene Consortium
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- The University of Texas Health Science Center School of Public Health, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
| | - Genomics England Research Consortium
- Center for Cell and Gene Therapy, Baylor College of Medicine, Houston, TX, USA
- Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
- Rady Children’s Institute for Genomic Medicine, San Diego, CA, USA
- Department of Pediatrics/Hematology-Oncology, Baylor College of Medicine, Houston, TX, USA
- The University of Texas Health Science Center School of Public Health, Houston, TX, USA
- Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX, USA
- Department of Neurosurgery, Duke University School of Medicine, Durham, NC, USA
- Department of Radiation Sciences, Oncology, Umeå University, Umeå, Sweden
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Rocque MJ, Leipart V, Kumar Singh A, Mur P, Olsen MF, Engebretsen LF, Martin-Ramos E, Aligué R, Sætrom P, Valle L, Drabløs F, Otterlei M, Sjursen W. Characterization of POLE c.1373A > T p.(Tyr458Phe), causing high cancer risk. Mol Genet Genomics 2023; 298:555-566. [PMID: 36856825 PMCID: PMC10133059 DOI: 10.1007/s00438-023-02000-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2022] [Accepted: 02/15/2023] [Indexed: 03/02/2023]
Abstract
The cancer syndrome polymerase proofreading-associated polyposis results from germline mutations in the POLE and POLD1 genes. Mutations in the exonuclease domain of these genes are associated with hyper- and ultra-mutated tumors with a predominance of base substitutions resulting from faulty proofreading during DNA replication. When a new variant is identified by gene testing of POLE and POLD1, it is important to verify whether the variant is associated with PPAP or not, to guide genetic counseling of mutation carriers. In 2015, we reported the likely pathogenic (class 4) germline POLE c.1373A > T p.(Tyr458Phe) variant and we have now characterized this variant to verify that it is a class 5 pathogenic variant. For this purpose, we investigated (1) mutator phenotype in tumors from two carriers, (2) mutation frequency in cell-based mutagenesis assays, and (3) structural consequences based on protein modeling. Whole-exome sequencing of two tumors identified an ultra-mutator phenotype with a predominance of base substitutions, the majority of which are C > T. A SupF mutagenesis assay revealed increased mutation frequency in cells overexpressing the variant of interest as well as in isogenic cells encoding the variant. Moreover, exonuclease repair yeast-based assay supported defect in proofreading activity. Lastly, we present a homology model of human POLE to demonstrate structural consequences leading to pathogenic impact of the p.(Tyr458Phe) mutation. The three lines of evidence, taken together with updated co-segregation and previously published data, allow the germline variant POLE c.1373A > T p.(Tyr458Phe) to be reclassified as a class 5 variant. That means the variant is associated with PPAP.
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Affiliation(s)
- Mariève J Rocque
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Vilde Leipart
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, NMBU, 1432, Ås, Norway
| | - Ashish Kumar Singh
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Pilar Mur
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Maren F Olsen
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Lars F Engebretsen
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway
| | - Edgar Martin-Ramos
- Department of Biomedical Sciences, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Rosa Aligué
- Department of Biomedical Sciences, School of Medicine, University of Barcelona, IDIBAPS, Barcelona, Spain
| | - Pål Sætrom
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
- Department of Computer and Information Science, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
- Bioinformatics Core Facility-BioCore, NTNU-Norwegian University of Science and Technology, 7491, Trondheim, Norway
- K.G. Jebsen Center for Genetic Epidemiology, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
| | - Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Oncobell Program, Bellvitge Biomedical Research Institute (IDIBELL), Hospitalet de Llobregat, Barcelona, Spain
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Finn Drabløs
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
| | - Marit Otterlei
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway
| | - Wenche Sjursen
- Department of Clinical and Molecular Medicine, NTNU-Norwegian University of Science and Technology, 7030, Trondheim, Norway.
- Department of Medical Genetics, St. Olavs Hospital, 7030, Trondheim, Norway.
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KANNO DT, de MATTOS RLM, CAMPOS FG, SIQUEIRA RM, de CARVALHO RB, REAL MARTINEZ CA. MULTIPLE NEUROENDOCRINE NEOPLASIA IN A PATIENT WITH TYPE I NEUROFIBROMATOSIS (NF1): REPORT OF A NEW MUTATION (NF1, EXONS 2-30 DELETION) AND LITERATURE REVIEW. ARQUIVOS BRASILEIROS DE CIRURGIA DIGESTIVA : ABCD = BRAZILIAN ARCHIVES OF DIGESTIVE SURGERY 2023; 35:e1702. [PMID: 36629684 PMCID: PMC9831629 DOI: 10.1590/0102-672020220002e1702] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/23/2022] [Accepted: 10/01/2022] [Indexed: 01/11/2023]
Abstract
BACKGROUND Plexiform neurofibromas represent a common neoplasia of type 1 neurofibromatosis in which neurofibromas arise from multiple nerves involving connective tissue and skin and rarely affect the colon and rectum. Co-occurrence of plexiform neurofibromas, neuroendocrine tumors with primary involvement of the rectum, and medullary thyroid carcinoma in patients with neurofibromatosis type 1 is a previously undescribed condition. The aim of this manuscript was to present a case of primary plexiform neurofibroma and neuroendocrine tumors of the upper rectum in a patient with neurofibromatosis type 1 whose genetic sequencing found a novel mutation in the neurofibromatosis type 1 gene and to review the literature. CASE REPORT A 49-year-old woman with a familial history of neurofibromatosis type 1 complained of abdominal cramps for 6 months. She had previously been submitted for a total thyroidectomy due to medullary thyroid carcinoma. She was submitted to a colonoscopy, which identified a submucosa lesion located in the upper rectum. The patient was referred for a laparoscopic rectosigmoidectomy, and the histopathological study of the surgical specimen identified two different tumors. An immunohistochemical panel was done for histopathological confirmation of the etiology of both lesions. The results of the panel showed intense immunoexpression of S100 protein in the largest and superficial lesion, as well as positivity for chromogranin and synaptophysin in the minor and deep lesion confirming the diagnosis of rectal plexiform neurofibromas concomitant with neuroendocrine tumors. The proliferative activity rate using Ki-67 antibodies showed that both tumors had a low rate of mitotic activity (<1%). Genetic sequence panel identified an undescribed mutation in the neurofibromatosis type 1 gene (deletion, exons 2-30). The patient's postoperative evolution was uneventful, and she remains well, without recurrence, 3 years after surgery. CONCLUSION The co-occurrence of medullary thyroid carcinoma, plexiform neurofibromas, and neuroendocrine tumors of the rectum in patients with neurofibromatosis type 1 is an exceptional and undescribed possibility, whose diagnosis can be confirmed by the immunohistochemical staining and genetic panel.
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Affiliation(s)
- Danilo Toshio KANNO
- Universidade São Francisco, Graduate Program in Health Sciences – Bragança Paulista (SP), Brazil
| | | | - Fábio Guilherme CAMPOS
- Universidade São Francisco, Graduate Program in Health Sciences – Bragança Paulista (SP), Brazil
| | - Rayama Moreira SIQUEIRA
- Universidade São Francisco, Graduate Program in Health Sciences – Bragança Paulista (SP), Brazil
| | | | - Carlos Augusto REAL MARTINEZ
- Universidade São Francisco, Graduate Program in Health Sciences – Bragança Paulista (SP), Brazil;,Universidade Estadual de Campinas, Department of Surgery, Gastrocenter – Campinas (SP), Brazil
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9
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Abstract
The traditional approach of one-size-fits-all for colorectal cancer has been replaced by personalized interventions to an individual's unique genetic, molecular, and environmental profile, seeking to identify high-risk individuals who would benefit from individualized screening and surveillance. This change in approach is due, in part, to emerging technologies, such as next-generation DNA sequencing.
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10
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Ma X, Dong L, Liu X, Ou K, Yang L. POLE/POLD1 mutation and tumor immunotherapy. JOURNAL OF EXPERIMENTAL & CLINICAL CANCER RESEARCH : CR 2022; 41:216. [PMID: 35780178 PMCID: PMC9250176 DOI: 10.1186/s13046-022-02422-1] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/06/2022] [Accepted: 06/17/2022] [Indexed: 12/30/2022]
Abstract
POLE and POLD1 encode the catalytic and proofreading subunits of DNA polymerase ε and polymerase δ, and play important roles in DNA replication and proofreading. POLE/POLD1 exonuclease domain mutations lead to loss of proofreading function, which causes the accumulation of mutant genes in cells. POLE/POLD1 mutations are not only closely related to tumor formation, but are also a potential molecular marker for predicting the efficacy of immunotherapy in pan-carcinomatous species. The association of POLE/POLD1 mutation, ultra-high mutation load, and good prognosis have recently become the focus of clinical research. This article reviews the function of POLE/POLD1, its relationship with deficient mismatch repair/high microsatellite instability, and the role of POLE/POLD1 mutation in the occurrence and development of various tumors.
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Affiliation(s)
- Xiaoting Ma
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin Dong
- Department of Pathology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Xiu Liu
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Kai Ou
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China
| | - Lin Yang
- Department of Medical Oncology, National Cancer Center/National Clinical Research Center for Cancer/Cancer Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, 100021, China.
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11
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Hampel H, Kalady MF, Pearlman R, Stanich PP. Hereditary Colorectal Cancer. Hematol Oncol Clin North Am 2022; 36:429-447. [DOI: 10.1016/j.hoc.2022.02.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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12
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Palles C, Martin L, Domingo E, Chegwidden L, McGuire J, Cuthill V, Heitzer E, Kerr R, Kerr D, Kearsey S, Clark SK, Tomlinson I, Latchford A. The clinical features of polymerase proof-reading associated polyposis (PPAP) and recommendations for patient management. Fam Cancer 2022; 21:197-209. [PMID: 33948826 PMCID: PMC8964588 DOI: 10.1007/s10689-021-00256-y] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Accepted: 04/07/2021] [Indexed: 10/28/2022]
Abstract
Pathogenic germline exonuclease domain (ED) variants of POLE and POLD1 cause the Mendelian dominant condition polymerase proof-reading associated polyposis (PPAP). We aimed to describe the clinical features of all PPAP patients with probably pathogenic variants. We identified patients with a variants mapping to the EDs of POLE or POLD1 from cancer genetics clinics, a colorectal cancer (CRC) clinical trial, and systematic review of the literature. We used multiple evidence sources to separate ED variants into those with strong evidence of pathogenicity and those of uncertain importance. We performed quantitative analysis of the risk of CRC, colorectal adenomas, endometrial cancer or any cancer in the former group. 132 individuals carried a probably pathogenic ED variant (105 POLE, 27 POLD1). The earliest malignancy was colorectal cancer at 14. The most common tumour types were colorectal, followed by endometrial in POLD1 heterozygotes and duodenal in POLE heterozygotes. POLD1-mutant cases were at a significantly higher risk of endometrial cancer than POLE heterozygotes. Five individuals with a POLE pathogenic variant, but none with a POLD1 pathogenic variant, developed ovarian cancer. Nine patients with POLE pathogenic variants and one with a POLD1 pathogenic variant developed brain tumours. Our data provide important evidence for PPAP management. Colonoscopic surveillance is recommended from age 14 and upper-gastrointestinal surveillance from age 25. The management of other tumour risks remains uncertain, but surveillance should be considered. In the absence of strong genotype-phenotype associations, these recommendations should apply to all PPAP patients.
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Affiliation(s)
- Claire Palles
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK.
| | - Lynn Martin
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Enric Domingo
- Department of Oncology, Old Road Campus Research Building, University of Oxford, Roosevelt Drive, Oxford, UK
| | - Laura Chegwidden
- Gastrointestinal Cancer Genetics Laboratory, Institute of Cancer and Genomic Sciences, College of Medical and Dental Sciences, University of Birmingham, Birmingham, B15 2TT, UK
| | - Josh McGuire
- Wellcome Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Vicky Cuthill
- Polyposis Registry, St Mark's Hospital, Harrow, London, HA1 3UJ, UK
| | - Ellen Heitzer
- Diagnostic and Research Institute of Human Genetics, University of Gratz, Graz, Austria
| | - Rachel Kerr
- Department of Oncology, Old Road Campus Research Building, University of Oxford, Roosevelt Drive, Oxford, UK
| | - David Kerr
- Nuffield Department of Clinical Laboratory Sciences, University of Oxford, John Radcliffe Hospital, Oxford, OX3 9DU, UK
| | - Stephen Kearsey
- ZRAB, University of Oxford, 11a Mansfield Road, Oxford, OX1 3SZ, UK
| | - Susan K Clark
- Polyposis Registry, St Mark's Hospital, Harrow, London, HA1 3UJ, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
| | - Ian Tomlinson
- Edinburgh Cancer Research Centre, Institute of Genetics and Cancer, University of Edinburgh, Crewe Road South, Edinburgh, EH4 2XU, UK
| | - Andrew Latchford
- Polyposis Registry, St Mark's Hospital, Harrow, London, HA1 3UJ, UK
- Department of Surgery and Cancer, Imperial College London, London, UK
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13
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Toss A, Quarello P, Mascarin M, Banna GL, Zecca M, Cinieri S, Peccatori FA, Ferrari A. Cancer Predisposition Genes in Adolescents and Young Adults (AYAs): a Review Paper from the Italian AYA Working Group. Curr Oncol Rep 2022; 24:843-860. [PMID: 35320498 PMCID: PMC9170630 DOI: 10.1007/s11912-022-01213-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/18/2021] [Indexed: 12/17/2022]
Abstract
PURPOSE OF REVIEW The present narrative systematic review summarizes current knowledge on germline gene mutations predisposing to solid tumors in adolescents and young adults (AYAs). RECENT FINDINGS AYAs with cancer represent a particular group of patients with specific challenging characteristics and yet unmet needs. A significant percentage of AYA patients carry pathogenic or likely pathogenic variants (PV/LPVs) in cancer predisposition genes. Nevertheless, knowledge on spectrum, frequency, and clinical implications of germline variants in AYAs with solid tumors is limited. The identification of PV/LPV in AYA is especially critical given the need for appropriate communicative strategies, risk of second primary cancers, need for personalized long-term surveillance, potential reproductive implications, and cascade testing of at-risk family members. Moreover, these gene alterations may potentially provide novel biomarkers and therapeutic targets that are lacking in AYA patients. Among young adults with early-onset phenotypes of malignancies typically presenting at later ages, the increased prevalence of germline PV/LPVs supports a role for genetic counseling and testing irrespective of tumor type.
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Affiliation(s)
- Angela Toss
- Department of Oncology and Hematology, Azienda Ospedaliero-Universitaria di Modena, Modena, Italy
- Department of Medical and Surgical Sciences for Children and Adults, University of Modena and Reggio Emilia, Modena, Italy
| | - Paola Quarello
- Paediatric Onco-Haematology, Stem Cell Transplantation and Cellular Therapy Division, Regina Margherita Children's Hospital, Turin, Italy
- Department of Public Health and Paediatric Sciences, University of Torino, Turin, Italy
| | - Maurizio Mascarin
- AYA Oncology and Pediatric Radiotherapy Unit, Centro di Riferimento Oncologico IRCCS, Aviano, Italy
| | - Giuseppe Luigi Banna
- Candiolo Cancer Institute, FPO-IRCCS, SP142, km 3.95, 10060, Candiolo, Turin, Italy.
| | - Marco Zecca
- Department of Pediatric Hematology/Oncology, Fondazione IRCCS Policlinico San Matteo, Pavia, Italy
| | - Saverio Cinieri
- Medical Oncology Unit and Breast Unit Ospedale Perrino ASL, Brindisi, Italy
| | - Fedro Alessandro Peccatori
- Fertility and Procreation Unit, Gynecologic Oncology Program, European Institute of Oncology IRCCS, Milan, Italy
| | - Andrea Ferrari
- Pediatric Oncology Unit, Fondazione IRCCS Istituto Nazionale dei Tumori, Via Venezian 1, 20133, Milan, Italy
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14
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Durando ML, Menghani SV, Baumann JL, Robles DG, Day TA, Vaziri C, Scott AJ. Four-Year Disease-Free Remission in a Patient With POLE Mutation-Associated Colorectal Cancer Treated Using Anti-PD-1 Therapy. J Natl Compr Canc Netw 2022; 20:218-223. [PMID: 35276675 DOI: 10.6004/jnccn.2021.7115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2021] [Accepted: 11/18/2021] [Indexed: 11/17/2022]
Abstract
The stability of the human genome depends upon a delicate balance between replication by high- and low-fidelity DNA polymerases. Aberrant replication by error-prone polymerases or loss of function of high-fidelity polymerases predisposes to genetic instability and, in turn, cancer. DNA polymerase epsilon (Pol ε) is a high-fidelity, processive polymerase that is responsible for the majority of leading strand synthesis, and mutations in Pol ε have been increasingly associated with various human malignancies. The clinical significance of Pol ε mutations, including how and whether they should influence management decisions, remains poorly understood. In this report, we describe a 24-year-old man with an aggressive stage IV high-grade, poorly differentiated colon carcinoma who experienced a dramatic response to single-agent checkpoint inhibitor immunotherapy after rapidly progressing on standard chemotherapy. His response was complete and durable and has been maintained for more than 48 months. Genetic testing revealed a P286R mutation in the endonuclease domain of POLE and an elevated tumor mutational burden of 126 mutations per megabase, both of which have been previously associated with response to immunotherapy. Interestingly, tumor staining for PD-L1 was negative. This case study highlights the importance of genetic profiling of both early and late-stage cancers, the clinical significance of POLE mutations, and how the interplay between genetic instability and immune-checkpoint blockade can impact clinical decision-making.
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Affiliation(s)
- Michael L Durando
- 1Banner-University Medical Center Tucson, Tucson, Arizona.,2Division of Hematology and Oncology, Department of Medicine.,3University of Arizona Cancer Center
| | | | - Jessica L Baumann
- 5Department of Pathology, University of Arizona College of Medicine-Tucson, Tucson, Arizona.,6Now with Roche Tissue Diagnostics, Tucson, Arizona
| | - Danny G Robles
- 1Banner-University Medical Center Tucson, Tucson, Arizona.,7Department of Surgery, University of Arizona College of Medicine-Tucson, Tucson, Arizona
| | - Tovah A Day
- 8Department of Biology, Northeastern University, Boston, Massachusetts; and
| | - Cyrus Vaziri
- 9Department of Pathology and Laboratory Medicine, University of North Carolina, Chapel Hill, North Carolina
| | - Aaron J Scott
- 1Banner-University Medical Center Tucson, Tucson, Arizona.,2Division of Hematology and Oncology, Department of Medicine.,3University of Arizona Cancer Center
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15
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Dahl JM, Thomas N, Tracy MA, Hearn BL, Perera L, Kennedy SR, Herr AJ, Kunkel TA. Probing the mechanisms of two exonuclease domain mutators of DNA polymerase ϵ. Nucleic Acids Res 2022; 50:962-974. [PMID: 35037018 DOI: 10.1093/nar/gkab1255] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 11/21/2021] [Accepted: 12/08/2021] [Indexed: 11/15/2022] Open
Abstract
We report the properties of two mutations in the exonuclease domain of the Saccharomyces cerevisiae DNA polymerase ϵ. One, pol2-Y473F, increases the mutation rate by about 20-fold, similar to the catalytically dead pol2-D290A/E290A mutant. The other, pol2-N378K, is a stronger mutator. Both retain the ability to excise a nucleotide from double-stranded DNA, but with impaired activity. pol2-Y473F degrades DNA poorly, while pol2-N378K degrades single-stranded DNA at an elevated rate relative to double-stranded DNA. These data suggest that pol2-Y473F reduces the capacity of the enzyme to perform catalysis in the exonuclease active site, while pol2-N378K impairs partitioning to the exonuclease active site. Relative to wild-type Pol ϵ, both variants decrease the dNTP concentration required to elicit a switch between proofreading and polymerization by more than an order of magnitude. While neither mutation appears to alter the sequence specificity of polymerization, the N378K mutation stimulates polymerase activity, increasing the probability of incorporation and extension of a mismatch. Considered together, these data indicate that impairing the primer strand transfer pathway required for proofreading increases the probability of common mutations by Pol ϵ, elucidating the association of homologous mutations in human DNA polymerase ϵ with cancer.
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Affiliation(s)
- Joseph M Dahl
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
| | - Natalie Thomas
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
| | - Maxwell A Tracy
- Department of Laboratory Medicine and Pathology, UW Medicine, Seattle, WA 98195, USA
| | - Brady L Hearn
- Department of Laboratory Medicine and Pathology, UW Medicine, Seattle, WA 98195, USA
| | - Lalith Perera
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
| | - Scott R Kennedy
- Department of Laboratory Medicine and Pathology, UW Medicine, Seattle, WA 98195, USA
| | - Alan J Herr
- Department of Laboratory Medicine and Pathology, UW Medicine, Seattle, WA 98195, USA
| | - Thomas A Kunkel
- Genome Integrity Structural Biology Laboratory, National Institute of Environmental Health Sciences, National Institutes of Health, DHHS, Research Triangle Park, NC 27709, USA
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16
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Ying J, Yang L, Yin JC, Xia G, Xing M, Chen X, Pang J, Wu Y, Bao H, Wu X, Shao Y, Zhu L, Cheng X. Additive effects of variants of unknown significance in replication repair-associated DNA polymerase genes on mutational burden and prognosis across diverse cancers. J Immunother Cancer 2021; 9:jitc-2021-002336. [PMID: 34479923 PMCID: PMC8420654 DOI: 10.1136/jitc-2021-002336] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/26/2021] [Indexed: 12/15/2022] Open
Abstract
BACKGROUND Defects in replication repair-associated DNA polymerases often manifest an ultra-high tumor mutational burden (TMB), which is associated with higher probabilities of response to immunotherapies. The functional and clinical implications of different polymerase variants remain unclear. METHODS Targeted next-generation sequencing using a 425-cancer gene panel, which covers all exonic regions of three polymerase genes (POLE, POLD1, and POLH), was conducted in a cohort of 12,266 patients across 16 different tumor types from January 2017 to January 2019. Prognostication of POL variant-positive patients was performed using a cohort of 4679 patients from the The Cancer Genome Atlas (TCGA) datasets. RESULTS The overall prevalence of somatic and germline polymerase variants was 4.2% (95% CI 3.8% to 4.5%) and 0.7% (95% CI 0.5% to 0.8%), respectively, with highest frequencies in endometrial, urinary, prostate, and colorectal cancers (CRCs). While most germline polymerase variants showed no clear functional consequences, we identified a candidate p.T466A affecting the exonuclease domain of POLE, which might be underlying the early onset in a case with childhood CRC. Low frequencies of known hot-spot somatic mutations in POLE were detected and were associated with younger age, the male sex, and microsatellite stability. In both the panel and TCGA cohorts, POLE drivers exhibited high frequencies of alterations in genes in the DNA damage and repair (DDR) pathways, including BRCA2, ATM, MSH6, and ATR. Variants of unknown significance (VUS) of different polymerase domains showed variable penetrance with those in the exonuclease domain of POLE and POLD1 displaying high TMB. VUS in POL genes exhibited an additive effect as carriers of multiple VUS had exponentially increased TMB and prolonged overall survival. Similar to cases with driver mutations, the TMB-high POL VUS samples showed DDR pathway involvement and polymerase hypermutation signatures. Combinatorial analysis of POL and DDR pathway status further supported the potential additive effects of POL VUS and DDR pathway genes and revealed distinct prognostic subclasses that were independent of cancer type and TMB. CONCLUSIONS Our results demonstrate the pathogenicity and additive prognostic value of POL VUS and DDR pathway gene alterations and suggest that genetic testing may be warranted in patients with diverse solid tumors.
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Affiliation(s)
- Jieer Ying
- Department of Abdominal Medical Oncology, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China.,Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China
| | - Lin Yang
- Department of Medical Oncology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiani C Yin
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Guojie Xia
- Department of Medical Oncology, Traditional Chinese Medical Hospital of Huzhou, Huzhou, China
| | - Minyan Xing
- Department of Medical Oncology, The First Affiliated Hospital of Zhejiang University, Haining, Zhejiang, China
| | - Xiaoxi Chen
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Jiaohui Pang
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Yong Wu
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Hua Bao
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Xue Wu
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China
| | - Yang Shao
- Nanjing Geneseeq Technology Inc, Nanjing, Jiangsu, China.,School of Public Health, Nanjing Medical University, Nanjing, Jiangsu, China
| | - Lingjun Zhu
- Department of Oncology, Sir Run Run Hospital Nanjing Medical University, Nanjing, Jiangsu, China.,Department of Oncology, The First Affiliated Hospital of Nanjing Medical University, Nanjing, Jiangsu, China
| | - Xiangdong Cheng
- Institute of Cancer and Basic Medicine (IBMC), Chinese Academy of Sciences, Hangzhou, Zhejiang, China .,Department of Gastric Surgery, Cancer Hospital of the University of Chinese Academy of Sciences (Zhejiang Cancer Hospital), Hangzhou, Zhejiang, China
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17
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Unravelling roles of error-prone DNA polymerases in shaping cancer genomes. Oncogene 2021; 40:6549-6565. [PMID: 34663880 PMCID: PMC8639439 DOI: 10.1038/s41388-021-02032-9] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2021] [Revised: 09/01/2021] [Accepted: 09/20/2021] [Indexed: 12/12/2022]
Abstract
Mutagenesis is a key hallmark and enabling characteristic of cancer cells, yet the diverse underlying mutagenic mechanisms that shape cancer genomes are not understood. This review will consider the emerging challenge of determining how DNA damage response pathways-both tolerance and repair-act upon specific forms of DNA damage to generate mutations characteristic of tumors. DNA polymerases are typically the ultimate mutagenic effectors of DNA repair pathways. Therefore, understanding the contributions of DNA polymerases is critical to develop a more comprehensive picture of mutagenic mechanisms in tumors. Selection of an appropriate DNA polymerase-whether error-free or error-prone-for a particular DNA template is critical to the maintenance of genome stability. We review different modes of DNA polymerase dysregulation including mutation, polymorphism, and over-expression of the polymerases themselves or their associated activators. Based upon recent findings connecting DNA polymerases with specific mechanisms of mutagenesis, we propose that compensation for DNA repair defects by error-prone polymerases may be a general paradigm molding the mutational landscape of cancer cells. Notably, we demonstrate that correlation of error-prone polymerase expression with mutation burden in a subset of patient tumors from The Cancer Genome Atlas can identify mechanistic hypotheses for further testing. We contrast experimental approaches from broad, genome-wide strategies to approaches with a narrower focus on a few hundred base pairs of DNA. In addition, we consider recent developments in computational annotation of patient tumor data to identify patterns of mutagenesis. Finally, we discuss the innovations and future experiments that will develop a more comprehensive portrait of mutagenic mechanisms in human tumors.
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18
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Hodan R, Kingham K, Cotter K, Folkins AK, Kurian AW, Ford JM, Longacre T. Prevalence of Lynch syndrome in women with mismatch repair-deficient ovarian cancer. Cancer Med 2020; 10:1012-1017. [PMID: 33369189 PMCID: PMC7897945 DOI: 10.1002/cam4.3688] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Revised: 11/13/2020] [Accepted: 12/06/2020] [Indexed: 01/03/2023] Open
Abstract
BACKGROUND There are limited data on the prevalence of Lynch syndrome (LS) in women with primary ovarian cancer with mismatch repair deficiency (MMR-D) by immunohistochemistry (IHC). MATERIALS AND METHODS Three hundred and eight cases of primary ovarian, fallopian, and peritoneal cancer between January 2012 and December 2019 were evaluated for MMR-D by IHC. The incidence of LS in this cohort was evaluated. RESULTS MMR-D by IHC was identified in 16 of 308 (5.2%) (95% CI: 3.2%-8.3%) primary ovarian-related cancers. Most cases with MMR-D were endometrioid (n = 11, 68.7%); (95% CI: 44.2%-86.1%). MSH2/MSH6 protein loss was detected in eight cases (50.0%); (95% CI: 28.0%-72.0%) and MLH1/PMS2 protein loss was detected in four cases (25.0%); (95% CI: 9.7%-50.0%). MSH6 protein loss was detected in two cases (12.5%); (95% CI: 2.2%-37.3%) and PMS2 protein loss was detected in two cases (12.5%); (95% CI: 2.2%-37.3%). All four cases with MLH1/PMS2 protein loss had MLH1 promotor hypermethylation. All 12 women with ovarian cancer suggestive of LS underwent germline testing and 8 (66.6%); (95% CI: 38.8%-86.5%) were confirmed to have LS. CONCLUSIONS Most ovarian cancers with somatic MMR-D were confirmed to have LS in this cohort. Germline testing for LS in addition to BRCA1/2 for all women with an epithelial ovarian cancer would be efficient and would approach 100% sensitivity for identifying Lynch syndrome. Utilization of a multigene panel should also be considered, given the additional non-Lynch germline mutation identified in this cohort.
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Affiliation(s)
- Rachel Hodan
- Cancer Genetics and Genomics, Stanford Health Care, Stanford, CA, USA.,Department of Pediatrics (Genetics), Stanford University School of Medicine, Stanford, CA, USA
| | - Kerry Kingham
- Cancer Genetics and Genomics, Stanford Health Care, Stanford, CA, USA.,Department of Pediatrics (Genetics), Stanford University School of Medicine, Stanford, CA, USA
| | - Kristina Cotter
- Department of Pediatrics (Genetics), Stanford University School of Medicine, Stanford, CA, USA
| | - Ann K Folkins
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
| | - Allison W Kurian
- Cancer Genetics and Genomics, Stanford Health Care, Stanford, CA, USA.,Department of Oncology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Epidemiology and Population Health, Stanford University School of Medicine, Stanford, CA, USA
| | - James M Ford
- Cancer Genetics and Genomics, Stanford Health Care, Stanford, CA, USA.,Department of Oncology, Stanford University School of Medicine, Stanford, CA, USA.,Department of Genetics, Stanford University School of Medicine, Stanford, CA, USA
| | - Teri Longacre
- Department of Pathology, Stanford University School of Medicine, Stanford, CA, USA
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19
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te Paske IBAW, Ligtenberg MJL, Hoogerbrugge N, de Voer RM. Candidate Gene Discovery in Hereditary Colorectal Cancer and Polyposis Syndromes-Considerations for Future Studies. Int J Mol Sci 2020; 21:E8757. [PMID: 33228212 PMCID: PMC7699508 DOI: 10.3390/ijms21228757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Revised: 11/17/2020] [Accepted: 11/18/2020] [Indexed: 12/15/2022] Open
Abstract
To discover novel high-penetrant risk loci for hereditary colorectal cancer (hCRC) and polyposis syndromes many whole-exome and whole-genome sequencing (WES/WGS) studies have been performed. Remarkably, these studies resulted in only a few novel high-penetrant risk genes. Given this observation, the possibility and strategy to identify high-penetrant risk genes for hCRC and polyposis needs reconsideration. Therefore, we reviewed the study design of WES/WGS-based hCRC and polyposis gene discovery studies (n = 37) and provide recommendations to optimize discovery and validation strategies. The group of genetically unresolved patients is phenotypically heterogeneous, and likely composed of distinct molecular subtypes. This knowledge advocates for the screening of a homogeneous, stringently preselected discovery cohort and obtaining multi-level evidence for variant pathogenicity. This evidence can be collected by characterizing the molecular landscape of tumors from individuals with the same affected gene or by functional validation in cell-based models. Together, the combined approach of a phenotype-driven, tumor-based candidate gene search might elucidate the potential contribution of novel genetic predispositions in genetically unresolved hCRC and polyposis.
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Affiliation(s)
- Iris B. A. W. te Paske
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
| | - Marjolijn J. L. Ligtenberg
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
- Department of Pathology, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands
| | - Nicoline Hoogerbrugge
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
| | - Richarda M. de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, 6525 GA Nijmegen, The Netherlands; (I.B.A.W.t.P.); (M.J.L.L.); (N.H.)
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20
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Djursby M, Madsen MB, Frederiksen JH, Berchtold LA, Therkildsen C, Willemoe GL, Hasselby JP, Wikman F, Okkels H, Skytte AB, Nilbert M, Wadt K, Gerdes AM, van Overeem Hansen T. New Pathogenic Germline Variants in Very Early Onset and Familial Colorectal Cancer Patients. Front Genet 2020; 11:566266. [PMID: 33193653 PMCID: PMC7541943 DOI: 10.3389/fgene.2020.566266] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 08/24/2020] [Indexed: 12/30/2022] Open
Abstract
A genetic diagnosis facilitates personalized cancer treatment and clinical care of relatives at risk, however, although 25% of colorectal cancer cases are familial, around 95% of the families are genetically unresolved. In this study, we performed gene panel analysis on germline DNA of 32 established or candidate colorectal cancer predisposing genes in 149 individuals from either families with an accumulation of colorectal cancers or families with only one sporadic case of very early onset colorectal cancer (≤40 years at diagnosis). We identified pathogenic or likely pathogenic genetic variants in 10.1% of the participants in genes such as APC, POLE, MSH2 or PMS2. The MSH2 variant, c.2168C>T, p.(Ser723Phe) was previously described as a variant of unknown significance, but we have now reclassified it to be likely pathogenic. The POLE variant, c.1089C>A, p.(Asn363Lys) was identified in a patient with three metachronous colorectal cancers from age 28 and turned out to be de novo. One pathogenic PMS2 variant was novel. We also identified a number of highly interesting variants of unknown significance in APC, BUB1, TP53 and RPS20. The RPS20 variant is novel and was found in a large Amsterdam I positive family with a multi tumor phenotype including 12 cases of CRC from as early as age 24. This variant was found to segregate with cancer in the family and multiple in silico tools predict it to be pathogenic. Our data further support the shift from phenotypic-based cancer panels to large panels including all established genes involved in hereditary cancer syndromes or (targeted) whole genome sequencing. Additionally, identification of a likely disease-predisposing variant in RPS20 expands the phenotypic spectrum of RPS20-related cancers and emphasize that this gene is relevant to include in colorectal cancer gene panels.
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Affiliation(s)
- Malene Djursby
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Majbritt B Madsen
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jane H Frederiksen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Lukas A Berchtold
- Center for Genomic Medicine, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Christina Therkildsen
- The Danish HNPCC Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark
| | - Gro L Willemoe
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Jane P Hasselby
- Department of Pathology, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Friedrik Wikman
- Department of Molecular Medicine, Aarhus University Hospital, Aarhus, Denmark
| | - Henrik Okkels
- Section of Molecular Diagnostics, Department of Clinical Chemistry, Aalborg University Hospital, Aalborg, Denmark
| | - Anne-Bine Skytte
- Department of Clinical Genetics, Aarhus University Hospital, Aarhus, Denmark
| | - Mef Nilbert
- The Danish HNPCC Register, Clinical Research Centre, Copenhagen University Hospital, Hvidovre, Denmark
| | - Karin Wadt
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
| | - Thomas van Overeem Hansen
- Department of Clinical Genetics, Rigshospitalet, Copenhagen University Hospital, Copenhagen, Denmark
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21
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Dörk T, Hillemanns P, Tempfer C, Breu J, Fleisch MC. Genetic Susceptibility to Endometrial Cancer: Risk Factors and Clinical Management. Cancers (Basel) 2020; 12:cancers12092407. [PMID: 32854222 PMCID: PMC7565375 DOI: 10.3390/cancers12092407] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Revised: 08/18/2020] [Accepted: 08/20/2020] [Indexed: 02/06/2023] Open
Abstract
Endometrial cancer (EC) is the most common cancer affecting the female reproductive organs in higher-income states. Apart from reproductive factors and excess weight, genetic predisposition is increasingly recognized as a major factor in endometrial cancer risk. Endometrial cancer is genetically heterogeneous: while a subgroup of patients belongs to cancer predisposition syndromes (most notably the Lynch Syndrome) with high to intermediate lifetime risks, there are also several common genomic polymorphisms contributing to the spectrum of germline predispositions. Germline variants and somatic events may act in concert to modulate the molecular evolution of the tumor, where mismatch-repair deficiency is common in endometrioid endometrial tumors whereas homologous recombinational repair deficiency has been described for non-endometrioid endometrial tumors. In this review, we will survey the currently known genomic predispositions for endometrial cancer and discuss their relevance for clinical management in terms of counseling, screening and novel treatments.
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Affiliation(s)
- Thilo Dörk
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center, Hannover Medical School, 30625 Hannover, Germany;
- Correspondence:
| | - Peter Hillemanns
- Department of Gynecology and Obstetrics, Comprehensive Cancer Center, Hannover Medical School, 30625 Hannover, Germany;
| | - Clemens Tempfer
- Department of Gynaecology, Marien-Hospital, Ruhr University of Bochum, 44625 Herne, Germany;
| | - Julius Breu
- Department of Gynecology and Obstetrics, University of Witten/Herdecke, 42283 Wuppertal, Germany; (J.B.); (M.C.F.)
| | - Markus C. Fleisch
- Department of Gynecology and Obstetrics, University of Witten/Herdecke, 42283 Wuppertal, Germany; (J.B.); (M.C.F.)
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22
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Role of POLE and POLD1 in familial cancer. Genet Med 2020; 22:2089-2100. [PMID: 32792570 PMCID: PMC7708298 DOI: 10.1038/s41436-020-0922-2] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2020] [Revised: 07/20/2020] [Accepted: 07/21/2020] [Indexed: 02/06/2023] Open
Abstract
Purpose Germline pathogenic variants in the exonuclease domain (ED) of polymerases POLE and POLD1 predispose to adenomatous polyps, colorectal cancer (CRC), endometrial tumors, and other malignancies, and exhibit increased mutation rate and highly specific associated mutational signatures. The tumor spectrum and prevalence of POLE and POLD1 variants in hereditary cancer are evaluated in this study. Methods POLE and POLD1 were sequenced in 2813 unrelated probands referred for genetic counseling (2309 hereditary cancer patients subjected to a multigene panel, and 504 patients selected based on phenotypic characteristics). Cosegregation and case–control studies, yeast-based functional assays, and tumor mutational analyses were performed for variant interpretation. Results Twelve ED missense variants, 6 loss-of-function, and 23 outside-ED predicted-deleterious missense variants, all with population allele frequencies <1%, were identified. One ED variant (POLE p.Met294Arg) was classified as likely pathogenic, four as likely benign, and seven as variants of unknown significance. The most commonly associated tumor types were colorectal, endometrial and ovarian cancers. Loss-of-function and outside-ED variants are likely not pathogenic for this syndrome. Conclusions Polymerase proofreading–associated syndrome constitutes 0.1–0.4% of familial cancer cases, reaching 0.3–0.7% when only CRC and polyposis are considered. ED variant interpretation is challenging and should include multiple pieces of evidence.
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Abstract
Medullary pancreatic carcinoma (MPC) is a rare histological variant of pancreatic ductal adenocarcinoma (PDAC). Because of its rarity, data on the molecular background of MPC are limited. Previous studies have shown that a subset of MPCs is microsatellite instable due to mismatch repair deficiency. Here, we present a unique case of a female patient in her 60s who is a long-term survivor after surgery for pancreatic cancer. The patient had a microsatellite stable MPC with a somatic mutation of the polymerase epsilon gene (POLE). Both microsatellite instable and POLE-mutated cancers are usually associated with high tumor mutational burden and antigen load, resulting in a prominent antitumor immune response and overall better survival. The current case illustrates that, in addition to mismatch repair deficiency, MPC can develop because of a somatic POLE mutation, resulting in a tumor with a high tumor mutational burden and leading to a better prognosis compared with conventional PDAC. This new finding may have important implications in the management of patients with MPC and calls for further studies on the role of POLE in PDAC.
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24
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Schubert SA, Morreau H, de Miranda NFCC, van Wezel T. The missing heritability of familial colorectal cancer. Mutagenesis 2020; 35:221-231. [PMID: 31605533 PMCID: PMC7352099 DOI: 10.1093/mutage/gez027] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Accepted: 09/05/2019] [Indexed: 02/06/2023] Open
Abstract
Pinpointing heritability factors is fundamental for the prevention and early detection of cancer. Up to one-quarter of colorectal cancers (CRCs) occur in the context of familial aggregation of this disease, suggesting a strong genetic component. Currently, only less than half of the heritability of CRC can be attributed to hereditary syndromes or common risk loci. Part of the missing heritability of this disease may be explained by the inheritance of elusive high-risk variants, polygenic inheritance, somatic mosaicism, as well as shared environmental factors, among others. A great deal of the missing heritability in CRC is expected to be addressed in the coming years with the increased application of cutting-edge next-generation sequencing technologies, routine multigene panel testing and tumour-focussed germline predisposition screening approaches. On the other hand, it will be important to define the contribution of environmental factors to familial aggregation of CRC incidence. This review provides an overview of the known genetic causes of familial CRC and aims at providing clues that explain the missing heritability of this disease.
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Affiliation(s)
- Stephanie A Schubert
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Noel F C C de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden University, Leiden, The Netherlands
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25
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Rotunno M, Barajas R, Clyne M, Hoover E, Simonds NI, Lam TK, Mechanic LE, Goldstein AM, Gillanders EM. A Systematic Literature Review of Whole Exome and Genome Sequencing Population Studies of Genetic Susceptibility to Cancer. Cancer Epidemiol Biomarkers Prev 2020; 29:1519-1534. [PMID: 32467344 DOI: 10.1158/1055-9965.epi-19-1551] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2019] [Revised: 03/17/2020] [Accepted: 05/13/2020] [Indexed: 01/03/2023] Open
Abstract
The application of next-generation sequencing (NGS) technologies in cancer research has accelerated the discovery of somatic mutations; however, progress in the identification of germline variation associated with cancer risk is less clear. We conducted a systematic literature review of cancer genetic susceptibility studies that used NGS technologies at an exome/genome-wide scale to obtain a fuller understanding of the research landscape to date and to inform future studies. The variability across studies on methodologies and reporting was considerable. Most studies sequenced few high-risk (mainly European) families, used a candidate analysis approach, and identified potential cancer-related germline variants or genes in a small fraction of the sequenced cancer cases. This review highlights the importance of establishing consensus on standards for the application and reporting of variants filtering strategies. It also describes the progress in the identification of cancer-related germline variation to date. These findings point to the untapped potential in conducting studies with appropriately sized and racially diverse families and populations, combining results across studies and expanding beyond a candidate analysis approach to advance the discovery of genetic variation that accounts for the unexplained cancer heritability.
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Affiliation(s)
- Melissa Rotunno
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland.
| | - Rolando Barajas
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Mindy Clyne
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elise Hoover
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | | | - Tram Kim Lam
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Leah E Mechanic
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Alisa M Goldstein
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
| | - Elizabeth M Gillanders
- National Cancer Institute, National Institutes of Health, U.S. Department of Health and Human Services, Bethesda, Maryland
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26
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Kastrinos F, Samadder NJ, Burt RW. Use of Family History and Genetic Testing to Determine Risk of Colorectal Cancer. Gastroenterology 2020; 158:389-403. [PMID: 31759928 DOI: 10.1053/j.gastro.2019.11.029] [Citation(s) in RCA: 44] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Revised: 11/11/2019] [Accepted: 11/18/2019] [Indexed: 12/20/2022]
Abstract
Approximately 35% of patients with colorectal cancer (CRC) have a family history of the disease attributed to genetic factors, common exposures, or both. Some families with a history of CRC carry genetic variants that cause CRC with high or moderate penetrance, but these account for only 5% to 10% of CRC cases. Most families with a history of CRC and/or adenomas do not carry genetic variants associated with cancer syndromes; this is called common familial CRC. Our understanding of familial predisposition to CRC and cancer syndromes has increased rapidly due to advances in next-generation sequencing technologies. As a result, there has been a shift from genetic testing for specific inherited cancer syndromes based on clinical criteria alone, to simultaneous testing of multiple genes for cancer-associated variants. We summarize current knowledge of common familial CRC, provide an update on syndromes associated with CRC (including the nonpolyposis and polyposis types), and review current recommendations for CRC screening and surveillance. We also provide an approach to genetic evaluation and testing in clinical practice. Determination of CRC risk based on family cancer history and results of genetic testing can provide a personalized approach to cancer screening and prevention, with optimal use of colonoscopy to effectively decrease CRC incidence and mortality.
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Affiliation(s)
- Fay Kastrinos
- Herbert Irving Comprehensive Cancer Center, Columbia University Irving Medical Center, New York, New York; Division of Digestive and Liver Diseases, Columbia University Irving Medical Center and the Vagelos College of Physicians and Surgeons, New York, New York.
| | - N Jewel Samadder
- Division of Gastroenterology and Hepatology, Mayo Clinic, Scottsdale, Arizona
| | - Randall W Burt
- Department of Gastroenterology, University of Utah, Salt Lake City, Utah; Emeritus Professor of Medicine, University of Utah, Salt Lake City, Utah
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27
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Germline POLE mutation in a child with hypermutated medulloblastoma and features of constitutional mismatch repair deficiency. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a004499. [PMID: 31624068 PMCID: PMC6824253 DOI: 10.1101/mcs.a004499] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2019] [Accepted: 08/15/2019] [Indexed: 01/02/2023] Open
Abstract
Ultra-hypermutation (>100 mutations/Mb) is rare in childhood cancer genomes and has been primarily reported in patients with constitutional mismatch repair deficiency (CMMRD) caused by biallelic germline mismatch repair (MMR) gene mutations. We report a 5-yr-old child with classic clinical features of CMMRD and an ultra-hypermutated medulloblastoma with retained MMR protein expression and absence of germline MMR mutations. Mutational signature analysis of tumor panel sequencing data revealed a canonical DNA polymerase-deficiency-associated signature, prompting further genetic testing that uncovered a germline POLE p.A456P missense variant, which has previously been reported as a recurrent somatic driver mutation in cancers. This represents the earliest known onset of malignancy in a patient with a germline mutation in the POLE proofreading polymerase. The clinical features in this child, virtually indistinguishable from those of CMMRD, suggest that polymerase-proofreading deficiency should be considered in the differential diagnosis of CMMRD patients with retained MMR function.
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28
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DeLeonardis K, Hogan L, Cannistra SA, Rangachari D, Tung N. When Should Tumor Genomic Profiling Prompt Consideration of Germline Testing? J Oncol Pract 2019; 15:465-473. [DOI: 10.1200/jop.19.00201] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Somatic genomic testing is rapidly becoming an integral part of care for patients with metastatic cancer. Extrapolation of these results beyond personalized cancer therapy is a skill being demanded of practicing oncologists without prior specialty in genetics. Up to 12% of tumor genomic profiling reports will reveal a germline pathogenic variant. Recognition of these germline variants is essential not only for optimal care of the patient with cancer but also to initiate cascade genetic testing in at-risk family members who also may carry the familial mutation. This article provides a concise and methodical, evidence-based strategy to guide oncology providers about how to identify genes associated with an inherited predisposition for cancer, determine the pathogenicity of variants reported within those genes, and understand the likelihood that these variants are of germline origin in a particular patient with cancer. Case examples are provided to illustrate clinical scenarios and facilitate application of the proposed approach.
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Affiliation(s)
| | - Lauren Hogan
- Beth Israel Deaconess Medical Center, Boston, MA
| | | | | | - Nadine Tung
- Beth Israel Deaconess Medical Center, Boston, MA
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29
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Germline mutation p.N363K in POLE is associated with an increased risk of colorectal cancer and giant cell glioblastoma. Fam Cancer 2019; 18:173-178. [PMID: 30368636 DOI: 10.1007/s10689-018-0102-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
Germline mutations of the POLE gene are responsible for polymerase proofreading-associated polyposis syndrome (PPAP). These mutations were hypothesised to predispose to extra-gastrointestinal tumours (ovary, endometrium, brain), but this association has not been confirmed so far. We report a family with an autosomal dominant inheritance of PPAP due to a c.1089C>A; p.Asn363Lys mutation in the proofreading exonuclease domain of POLE. Ten patients presenting a history of colorectal tumours and three patients with polyposis are indexed in this family. Three carriers (including siblings and a distant cousin at 30, 45 and 52 respectively) and another member (at 37 not tested) presented glioblastoma. This is the second family reported to carry this mutation. Among the four glioblastomas in the family that we report, both show similar pathology: giant cell glioblastoma. These cases suggest that the c.1089C>A germline POLE mutation may confer an increased risk of brain cancer [incidence 17.4% (4/23) in mutation carriers combining the two families]. More observations are needed to support this hypothesis. It seems that not all mutations of POLE are equally associated with extra-gastrointestinal tumours. Although carriers of a mutation responsible for PPAP should benefit from screening for colorectal and uterine cancer, due to the rapid evolution of glioblastoma the value of neurological follow-up and brain imaging screening remains questionable. Nevertheless, considering the limitations of standard therapy for glioblastoma, mutation status could be useful for targeting therapy. The biological mechanism linking POLE mutation to glioblastoma remains to be determined.
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30
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Zhu Q, Zhang J, Chen Y, Hu Q, Shen H, Huang RY, Liu Q, Kaur J, Long M, Battaglia S, Eng KH, Lele SB, Zsiros E, Villella J, Lugade A, Yao S, Liu S, Moysich K, Odunsi KO. Whole-exome sequencing of ovarian cancer families uncovers putative predisposition genes. Int J Cancer 2019; 146:2147-2155. [PMID: 31265121 PMCID: PMC7065147 DOI: 10.1002/ijc.32545] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2019] [Revised: 06/10/2019] [Accepted: 06/21/2019] [Indexed: 01/05/2023]
Abstract
Despite the identification of several ovarian cancer (OC) predisposition genes, a large proportion of familial OC risk remains unexplained. We adopted a two-stage design to identify new OC predisposition genes. We first carried out a large germline whole-exome sequencing study on 158 patients from 140 families with significant OC history, but without evidence of genetic predisposition due to BRCA1/2. We then evaluated the potential candidate genes in a large case-control association study involving 381 OC cases in the Cancer Genome Atlas project and 27,173 population controls from the Exome Aggregation Consortium. Two new putative OC risk genes were identified, namely, ANKRD11, a putative tumor suppressor, and POLE, an enzyme involved in DNA repair and replication. These two genes likely confer moderate OC risk. We performed in vitro experiments and showed an ANKRD11 mutation identified in our patients markedly lowered the protein expression by compromising protein stability. Upon future validation and functional characterization, these genes may shed light on cancer etiology along with improving ascertainment power and preventive care of individuals at high risk of OC.
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Affiliation(s)
- Qianqian Zhu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Jianmin Zhang
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Yanmin Chen
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Qiang Hu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - He Shen
- Department of Cancer Genetics and Genomics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Ruea-Yea Huang
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Qian Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Jasmine Kaur
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Mark Long
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | | | - Kevin H Eng
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Shashikant B Lele
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Emese Zsiros
- Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Jeannine Villella
- Division of Gynecologic Oncology, Lenox Hill Hospital/ Northwell Health Cancer Institute, Donald and Barbara Zucker School of Medicine at Hofstra/Northwell, New York, NY
| | - Amit Lugade
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Song Yao
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Song Liu
- Department of Biostatistics & Bioinformatics, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Kirsten Moysich
- Department of Cancer Prevention and Control, Roswell Park Comprehensive Cancer Center, Buffalo, NY
| | - Kunle O Odunsi
- Center for Immunotherapy, Roswell Park Comprehensive Cancer Center, Buffalo, NY.,Department of Gynecologic Oncology, Roswell Park Comprehensive Cancer Center, Buffalo, NY
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31
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Valle L, de Voer RM, Goldberg Y, Sjursen W, Försti A, Ruiz-Ponte C, Caldés T, Garré P, Olsen MF, Nordling M, Castellvi-Bel S, Hemminki K. Update on genetic predisposition to colorectal cancer and polyposis. Mol Aspects Med 2019; 69:10-26. [PMID: 30862463 DOI: 10.1016/j.mam.2019.03.001] [Citation(s) in RCA: 99] [Impact Index Per Article: 19.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2019] [Revised: 02/26/2019] [Accepted: 03/05/2019] [Indexed: 02/06/2023]
Abstract
The present article summarizes recent developments in the characterization of genetic predisposition to colorectal cancer (CRC). The main themes covered include new hereditary CRC and polyposis syndromes, non-CRC hereditary cancer genes found mutated in CRC patients, strategies used to identify novel causal genes, and review of candidate genes that have been proposed to predispose to CRC and/or colonic polyposis. We provide an overview of newly described genes and syndromes associated with predisposition to CRC and polyposis, including: polymerase proofreading-associated polyposis, NTHL1-associated polyposis, mismatch repair gene biallelic inactivation-related adenomatous polyposis (including MSH3- and MLH3-associated polyposes), GREM1-associated mixed polyposis, RNF43-associated serrated polyposis, and RPS20 mutations as a rare cause of hereditary nonpolyposis CRC. The implementation of next generation sequencing approaches for genetic testing has exposed the presence of pathogenic germline variants in genes associated with hereditary cancer syndromes not traditionally linked to CRC, which may have an impact on genetic testing, counseling and surveillance. The identification of new hereditary CRC and polyposis genes has not deemed an easy endeavor, even though known CRC-related genes explain a small proportion of the estimated familial risk. Whole-genome sequencing may offer a technology for increasing this proportion, particularly if applied on pedigree data allowing linkage type of analysis. The final section critically surveys the large number of candidate genes that have been recently proposed for CRC predisposition.
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Affiliation(s)
- Laura Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Hospitalet de Llobregat, Spain; Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Spain; Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain.
| | - Richarda M de Voer
- Department of Human Genetics, Radboud Institute for Molecular Life Sciences, Radboud University Medical Center, Nijmegen, the Netherlands
| | - Yael Goldberg
- Raphael Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Wenche Sjursen
- Department of Clinical and Molecular Medicine, Norwegian University of Science and Technology, Trondheim, Norway; Department of Medical Genetics, St Olavs University Hospital, Trondheim, Norway
| | - Asta Försti
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany
| | - Clara Ruiz-Ponte
- Fundación Pública Galega de Medicina Xenómica, Grupo de Medicina Xenómica, Santiago de Compostela, Spain; Instituto de Investigación Sanitaria de Santiago (IDIS), Santiago de Compostela, Spain; Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Spain
| | - Trinidad Caldés
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain; Oncology Molecular Laboratory, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Pilar Garré
- Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Spain; Oncology Molecular Laboratory, Instituto de Investigación Sanitaria San Carlos (IdISSC), Hospital Clínico San Carlos, Madrid, Spain
| | - Maren F Olsen
- Department of Medical Genetics, St Olavs University Hospital, Trondheim, Norway
| | - Margareta Nordling
- Department of Pathology and Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden; Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Sergi Castellvi-Bel
- Genetic Predisposition to Gastrointestinal Cancer Group, Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Hospital Clínic de Barcelona, Universitat de Barcelona, Barcelona, Spain; Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Barcelona, Spain.
| | - Kari Hemminki
- Division of Molecular Genetic Epidemiology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 580, D-69120, Heidelberg, Germany.
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Gahlon HL, Walker AR, Cisneros GA, Lamers MH, Rueda DS. Reduced structural flexibility for an exonuclease deficient DNA polymerase III mutant. Phys Chem Chem Phys 2018; 20:26892-26902. [PMID: 30345999 PMCID: PMC6278910 DOI: 10.1039/c8cp04112a] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
DNA synthesis, carried out by DNA polymerases, requires balancing speed and accuracy for faithful replication of the genome. High fidelity DNA polymerases contain a 3'-5' exonuclease domain that can remove misincorporated nucleotides on the 3' end of the primer strand, a process called proofreading. The E. coli replicative polymerase, DNA polymerase III, has spatially separated (∼55 Å apart) polymerase and exonuclease subunits. Here, we report on the dynamics of E. coli DNA polymerase III proofreading in the presence of its processivity factor, the β2-sliding clamp, at varying base pair termini using single-molecule FRET. We find that the binding kinetics do not depend on the base identity at the termini, indicating a tolerance for DNA mismatches. Further, our single-molecule data and MD simulations show two previously unobserved features: (1) DNA Polymerase III is a highly dynamic protein that adopts multiple conformational states while bound to DNA with matched or mismatched ends, and (2) an exonuclease-deficient DNA polymerase III has reduced conformational flexibility. Overall, our single-molecule experiments provide high time-resolution insight into a mechanism that ensures high fidelity DNA replication to maintain genome integrity.
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Affiliation(s)
- Hailey L Gahlon
- Department of Medicine, Molecular Virology, Imperial College London, Du Cane Road, London W12 0NN, UK.
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Mirza-Aghazadeh-Attari M, Darband SG, Kaviani M, Mihanfar A, Aghazadeh Attari J, Yousefi B, Majidinia M. DNA damage response and repair in colorectal cancer: Defects, regulation and therapeutic implications. DNA Repair (Amst) 2018; 69:34-52. [PMID: 30055507 DOI: 10.1016/j.dnarep.2018.07.005] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2018] [Revised: 07/15/2018] [Accepted: 07/15/2018] [Indexed: 12/11/2022]
Abstract
DNA damage response, a key factor involved in maintaining genome integrity and stability, consists of several kinase-dependent signaling pathways, which sense and transduce DNA damage signal. The severity of damage appears to determine DNA damage responses, which can include cell cycle arrest, damage repair and apoptosis. A number of recent studies have demonstrated that defection in signaling through this network is thought to be an underlying mechanism behind the development and progression of various types of human malignancies, including colorectal cancer. In this review, colorectal cancer and its molecular pathology as well as DNA damage response is briefly introduced. Finally, the involvement of key components of this network in the initiation/progression, prognosis, response to treatment and development of drug resistance is comprehensively discussed.
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Affiliation(s)
- Mohammad Mirza-Aghazadeh-Attari
- Aging Research Institute, Tabriz University of Medical Sciences, Tabriz, Iran; Student Research Committee, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Saber Ghazizadeh Darband
- Danesh Pey Hadi Co., Health Technology Development Center, Urmia University of Medical Sciences, Urmia, Iran
| | - Mojtaba Kaviani
- School of Nutrition and Dietetics, Acadia University, Wolfville, Nova Scotia, Canada
| | - Ainaz Mihanfar
- Stem Cell and Regenerative Medicine Institute, Tabriz University of Medical Sciences, Tabriz, Iran
| | | | - Bahman Yousefi
- Molecular Medicine Research Center, Tabriz University of Medical Sciences, Tabriz, Iran; Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran.
| | - Maryam Majidinia
- Solid Tumor Research Center, Urmia University of Medical Sciences, Urmia, Iran.
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Esteban-Jurado C, Giménez-Zaragoza D, Muñoz J, Franch-Expósito S, Álvarez-Barona M, Ocaña T, Cuatrecasas M, Carballal S, López-Cerón M, Marti-Solano M, Díaz-Gay M, van Wezel T, Castells A, Bujanda L, Balmaña J, Gonzalo V, Llort G, Ruiz-Ponte C, Cubiella J, Balaguer F, Aligué R, Castellví-Bel S. POLE and POLD1 screening in 155 patients with multiple polyps and early-onset colorectal cancer. Oncotarget 2018; 8:26732-26743. [PMID: 28423643 PMCID: PMC5432293 DOI: 10.18632/oncotarget.15810] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2017] [Accepted: 02/18/2017] [Indexed: 12/31/2022] Open
Abstract
Germline mutations in POLE and POLD1 have been shown to cause predisposition to colorectal multiple polyposis and a wide range of neoplasms, early-onset colorectal cancer being the most prevalent. In order to find additional mutations affecting the proofreading activity of these polymerases, we sequenced its exonuclease domain in 155 patients with multiple polyps or an early-onset colorectal cancer phenotype without alterations in the known hereditary colorectal cancer genes. Interestingly, none of the previously reported mutations in POLE and POLD1 were found. On the other hand, among the genetic variants detected, only two of them stood out as putative pathogenic in the POLE gene, c.1359 + 46del71 and c.1420G > A (p.Val474Ile). The first variant, detected in two families, was not proven to alter correct RNA splicing. Contrarily, c.1420G > A (p.Val474Ile) was detected in one early-onset colorectal cancer patient and located right next to the exonuclease domain. The pathogenicity of this change was suggested by its rarity and bioinformatics predictions, and it was further indicated by functional assays in Schizosaccharomyces pombe. This is the first study to functionally analyze a POLE genetic variant outside the exonuclease domain and widens the spectrum of genetic changes in this DNA polymerase that could lead to colorectal cancer predisposition.
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Affiliation(s)
- Clara Esteban-Jurado
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia, Spain
| | - David Giménez-Zaragoza
- Biomedical Sciences Department, School of Medicine, University de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - Jenifer Muñoz
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia, Spain
| | - Sebastià Franch-Expósito
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia, Spain
| | - Miriam Álvarez-Barona
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Teresa Ocaña
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia, Spain
| | - Miriam Cuatrecasas
- Department of Pathology, Hospital Clinic, Biobanc Clinic-IDIBAPS, Barcelona, Catalonia, Spain
| | - Sabela Carballal
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia, Spain
| | - María López-Cerón
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia, Spain
| | - Maria Marti-Solano
- Department of Pharmaceutical Chemistry, Philipps-University Marburg, Marburg, Germany
| | - Marcos Díaz-Gay
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia, Spain
| | - Tom van Wezel
- Leiden University Medical Center (LUMC), Leiden, Netherlands
| | - Antoni Castells
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia, Spain
| | - Luis Bujanda
- Gastroenterology Department, Hospital Donostia-Instituto Biodonostia, Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), Basque Country University (UPV/EHU), San Sebastián, Spain
| | - Judith Balmaña
- High Risk and Cancer Prevention Unit, Medical Oncology Department, University Hospital Vall d'Hebron and Vall d'Hebron Institute of Oncology, Barcelona, Spain
| | - Victoria Gonzalo
- Gastroenterology Department, Hospital Universitari Mútua de Terrassa, Terrassa, Barcelona, Spain
| | - Gemma Llort
- Clinical Oncology Department, Corporacio Parc Tauli, Sabadell, Barcelona, Spain
| | - Clara Ruiz-Ponte
- Galician Public Foundation of Genomic Medicine (FPGMX), Centro de Investigación Biomédica en Red de Enfermedades Raras (CIBERER), Genomics Medicine Group, Hospital Clínico, Santiago de Compostela, University of Santiago de Compostela, Galicia, Spain
| | - Joaquín Cubiella
- Gastroenterology Department, Complexo Hospitalario Universitario de Ourense, Instituto de Investigación Biomédica Ourense, Pontevedra y Vigo, Ourense, Spain
| | - Francesc Balaguer
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia, Spain
| | - Rosa Aligué
- Biomedical Sciences Department, School of Medicine, University de Barcelona, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Catalonia, Spain
| | - Sergi Castellví-Bel
- Gastroenterology Department, Hospital Clínic, Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Centro de Investigación Biomédica en Red de Enfermedades Hepáticas y Digestivas (CIBEREHD), University of Barcelona, Barcelona, Catalonia, Spain
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Barbari SR, Kane DP, Moore EA, Shcherbakova PV. Functional Analysis of Cancer-Associated DNA Polymerase ε Variants in Saccharomyces cerevisiae. G3 (BETHESDA, MD.) 2018; 8:1019-1029. [PMID: 29352080 PMCID: PMC5844290 DOI: 10.1534/g3.118.200042] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/25/2017] [Accepted: 01/17/2018] [Indexed: 01/17/2023]
Abstract
DNA replication fidelity relies on base selectivity of the replicative DNA polymerases, exonucleolytic proofreading, and postreplicative DNA mismatch repair (MMR). Ultramutated human cancers without MMR defects carry alterations in the exonuclease domain of DNA polymerase ε (Polε). They have been hypothesized to result from defective proofreading. However, modeling of the most common variant, Polε-P286R, in yeast produced an unexpectedly strong mutator effect that exceeded the effect of proofreading deficiency by two orders of magnitude and indicated the involvement of other infidelity factors. The in vivo consequences of many additional Polε mutations reported in cancers remain poorly understood. Here, we genetically characterized 13 cancer-associated Polε variants in the yeast system. Only variants directly altering the DNA binding cleft in the exonuclease domain elevated the mutation rate. Among these, frequently recurring variants were stronger mutators than rare variants, in agreement with the idea that mutator phenotype has a causative role in tumorigenesis. In nearly all cases, the mutator effects exceeded those of an exonuclease-null allele, suggesting that mechanisms distinct from loss of proofreading may drive the genome instability in most ultramutated tumors. All mutator alleles were semidominant, supporting the view that heterozygosity for the polymerase mutations is sufficient for tumor development. In contrast to the DNA binding cleft alterations, peripherally located variants, including a highly recurrent V411L, did not significantly elevate mutagenesis. Finally, the analysis of Polε variants found in MMR-deficient tumors suggested that the majority cause no mutator phenotype alone but some can synergize with MMR deficiency to increase the mutation rate.
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Affiliation(s)
- Stephanie R Barbari
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Daniel P Kane
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Elizabeth A Moore
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
| | - Polina V Shcherbakova
- Eppley Institute for Research in Cancer and Allied Diseases, Fred & Pamela Buffett Cancer Center, University of Nebraska Medical Center, Omaha, Nebraska 68198
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36
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Lorans M, Dow E, Macrae FA, Winship IM, Buchanan DD. Update on Hereditary Colorectal Cancer: Improving the Clinical Utility of Multigene Panel Testing. Clin Colorectal Cancer 2018; 17:e293-e305. [PMID: 29454559 DOI: 10.1016/j.clcc.2018.01.001] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2017] [Revised: 12/17/2017] [Accepted: 01/09/2018] [Indexed: 12/30/2022]
Abstract
Colorectal cancer (CRC), one of the most common cancers, is a major public health issue globally, especially in Westernized countries. Up to 35% of CRCs are thought to be due to heritable factors, but currently only 5% to 10% of CRCs are attributable to high-risk mutations in known CRC susceptibility genes, predominantly the mismatch repair genes (Lynch syndrome) and adenomatous polyposis coli gene (APC; familial adenomatous polyposis). In this era of precision medicine, high-risk mutation carriers, when identified, can be offered various risk management options that prevent cancers and improve survival, including risk-reducing medication, screening for early detection, and surgery. The practice of clinical genetics is currently transitioning from phenotype-directed single gene testing to multigene panels, now offered by numerous providers. For CRC, the genes included across these panels vary, ranging from well established, clinically actionable susceptibility genes with quantified magnitude of risk, to genes that lack extensive validation or have less evidence of association with CRC and, therefore, have minimal clinical utility. The current lack of consensus regarding inclusion of genes in CRC panels presents challenges in patient counseling and management, particularly when a variant in a less validated gene is identified. Furthermore, there remain considerable challenges regarding variant interpretation even for the well established CRC susceptibility genes. Ironically though, only through more widespread testing and the accumulation of large international data sets will sufficient information be generated to (i) enable well powered studies to determine if a gene is associated with CRC susceptibility, (ii) to develop better models for variant interpretation and (iii) to facilitate clinical translation.
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Affiliation(s)
- Marie Lorans
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia
| | - Eryn Dow
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Finlay A Macrae
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia; Colorectal Medicine and Genetics, Royal Melbourne Hospital, Parkville, Victoria, Australia
| | - Ingrid M Winship
- Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Department of Medicine, The University of Melbourne, Parkville, Victoria, Australia
| | - Daniel D Buchanan
- Colorectal Oncogenomics Group, Department of Clinical Pathology, The University of Melbourne, Parkville, Victoria, Australia; Genetic Medicine and Family Cancer Clinic, Royal Melbourne Hospital, Parkville, Victoria, Australia; Centre for Epidemiology and Biostatistics, Melbourne School of Population and Global Health, The University of Melbourne, Carlton, Victoria, Australia; University of Melbourne Centre for Cancer Research, Victorian Comprehensive Cancer Centre, Parkville, Victoria, Australia.
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Application of single nucleotide extension and MALDI-TOF mass spectrometry in proofreading and DNA repair assay. DNA Repair (Amst) 2017; 61:63-75. [PMID: 29223016 DOI: 10.1016/j.dnarep.2017.11.011] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Revised: 10/07/2017] [Accepted: 11/30/2017] [Indexed: 01/20/2023]
Abstract
Proofreading and DNA repair are important factors in maintaining the high fidelity of genetic information during DNA replication. Herein, we designed a non-labeled and non-radio-isotopic simple method to measure proofreading. An oligonucleotide primer is annealed to a template DNA forming a mismatched site and is proofread by Klenow fragment of Escherichia coli DNA polymerase I (pol I) in the presence of all four dideoxyribonucleotide triphosphates. The proofreading excision products and re-synthesis products of single nucleotide extension are subjected to MALDI-TOF mass spectrometry (MS). The proofreading at the mismatched site is identified by the mass change of the primer. We examined proofreading of Klenow fragment with DNAs containing various base mismatches. Single mismatches at the primer terminus can be proofread efficiently. Internal single mismatches can also be proofread at different efficiencies, with the best correction for mismatches located 2-4-nucleotides from the primer terminus. For mismatches located 5-nucleotides from the primer terminus there was partial correction and extension. No significant proofreading was observed for mismatches located 6-9-nucleotides from the primer terminus. We also subjected primers containing 3' penultimate deoxyinosine (dI) lesions, which mimic endonuclease V nicked repair intermediates, to pol I repair assay. The results showed that T-I was a better substrate than G-I and A-I, however C-I was refractory to repair. The high resolution of MS results clearly demonstrated that all the penultimate T-I, G-I and A-I substrates had been excised last 2 dI-containing nucleotides by pol I before adding a correct ddNMP, however, pol I proofreading exonuclease tolerated the penultimate C-I mismatch allowing the primer to be extended by polymerase activity.
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38
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Rohlin A, Rambech E, Kvist A, Törngren T, Eiengård F, Lundstam U, Zagoras T, Gebre-Medhin S, Borg Å, Björk J, Nilbert M, Nordling M. Expanding the genotype-phenotype spectrum in hereditary colorectal cancer by gene panel testing. Fam Cancer 2017; 16:195-203. [PMID: 27696107 PMCID: PMC5357488 DOI: 10.1007/s10689-016-9934-0] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Hereditary syndromes causing colorectal cancer include both polyposis and non-polyposis syndromes. Overlapping phenotypes between the syndromes have been recognized and this make targeted molecular testing for single genes less favorable, instead there is a gaining interest for multi-gene panel-based approaches detecting both SNVs, indels and CNVs in the same assay. We applied a panel including 19 CRC susceptibility genes to 91 individuals of six phenotypic subgroups. Targeted NGS-based sequencing of the whole gene regions including introns of the 19 genes was used. The individuals had a family history of CRC or had a phenotype consistent with a known CRC syndrome. The purpose of the study was to demonstrate the diagnostic difficulties linked to genotype-phenotype diversity and the benefits of using a gene panel. Pathogenicity classification was carried out on 46 detected variants. In total we detected sixteen pathogenic or likely pathogenic variants and 30 variants of unknown clinical significance. Four of the pathogenic or likely pathogenic variants were found in BMPR1A in patients with unexplained familial adenomatous polyposis or atypical adenomatous polyposis, which extends the genotype-phenotype spectrum for this gene. Nine patients had more than one variant remaining after the filtration, including three with truncating mutations in BMPR1A, PMS2 and AXIN2. CNVs were found in three patients, in upstream regions of SMAD4, MSH3 and CTNNB1, and one additional individual harbored a 24.2 kb duplication in CDH1 intron1.
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Affiliation(s)
- Anna Rohlin
- Department of Molecular and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.
| | - Eva Rambech
- Division of Oncology and Pathology Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
| | - Anders Kvist
- Division of Oncology and Pathology Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
| | - Therese Törngren
- Division of Oncology and Pathology Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
| | - Frida Eiengård
- Department of Molecular and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Ulf Lundstam
- Department of Surgery, Sahlgrenska Academy at University of Gothenburg, Sahlgrenska University Hospital/Östra, 416 85, Gothenburg, Sweden
| | - Theofanis Zagoras
- Department of Molecular and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Samuel Gebre-Medhin
- Division of Clinical Genetics, Department of Laboratory Medicine, Lund University, Lund, Sweden
- Department of Clinical Genetics, Office for Medical Services, Division of Laboratory Medicine, Lund, Sweden
| | - Åke Borg
- Division of Oncology and Pathology Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
| | - Jan Björk
- The Swedish Polyposis Registry, Department of Medicine, Karolinska Institute, Stockholm, Sweden
| | - Mef Nilbert
- Division of Oncology and Pathology Department of Clinical Sciences Lund, Lund University, Medicon Village, 22381, Lund, Sweden
- The HNPCC-register, Hvidovre University Hospital, Copenhagen University, Hvidovre, Denmark
| | - Margareta Nordling
- Department of Molecular and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
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Endometrial cancer gene panels: clinical diagnostic vs research germline DNA testing. Mod Pathol 2017; 30:1048-1068. [PMID: 28452373 DOI: 10.1038/modpathol.2017.20] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2016] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 12/12/2022]
Abstract
Endometrial cancer is the most common gynecological cancer, but is nevertheless uncommon enough to have value as a signature cancer for some hereditary cancer syndromes. Commercial multigene testing panels include up to 13 different genes annotated for germline DNA testing of patients with endometrial cancer. Many other genes have been reported as relevant to familial endometrial cancer from directed genome-wide sequencing studies or multigene panel testing, or research. This review assesses the evidence supporting association with endometrial cancer risk for 32 genes implicated in hereditary endometrial cancer, and presents a summary of rare germline variants in these 32 genes detected by analysis of quasi-population-based endometrial cancer patients from The Cancer Genome Atlas project. This comprehensive investigation has led to the conclusion that convincing evidence currently exists to support clinical testing of only six of these genes for diagnosis of hereditary endometrial cancer. Testing of endometrial cancer patients for the remaining genes should be considered in the context of research studies, as a means to better establish the level of endometrial cancer risk, if any, associated with genetic variants that are deleterious to gene or protein function. It is acknowledged that clinical testing of endometrial cancer patients for several genes included on commercial panels may provide actionable findings in relation to risk of other cancers, but these should be considered secondary or incidental findings and not conclusive evidence for diagnosis of inherited endometrial cancer. In summary, this review and analysis provides a comprehensive report of current evidence to guide the selection of genes for clinical and research gene testing of germline DNA from endometrial cancer patients.
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Replicative DNA polymerase defects in human cancers: Consequences, mechanisms, and implications for therapy. DNA Repair (Amst) 2017; 56:16-25. [PMID: 28687338 DOI: 10.1016/j.dnarep.2017.06.003] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
The fidelity of DNA replication relies on three error avoidance mechanisms acting in series: nucleotide selectivity of replicative DNA polymerases, exonucleolytic proofreading, and post-replicative DNA mismatch repair (MMR). MMR defects are well known to be associated with increased cancer incidence. Due to advances in DNA sequencing technologies, the past several years have witnessed a long-predicted discovery of replicative DNA polymerase defects in sporadic and hereditary human cancers. The polymerase mutations preferentially affect conserved amino acid residues in the exonuclease domain and occur in tumors with an extremely high mutation load. Thus, a concept has formed that defective proofreading of replication errors triggers the development of these tumors. Recent studies of the most common DNA polymerase variants, however, suggested that their pathogenicity may be determined by functional alterations other than loss of proofreading. In this review, we summarize our current understanding of the consequences of DNA polymerase mutations in cancers and the mechanisms of their mutator effects. We also discuss likely explanations for a high recurrence of some but not other polymerase variants and new ideas for therapeutic interventions emerging from the mechanistic studies.
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41
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Recent Discoveries in the Genetics of Familial Colorectal Cancer and Polyposis. Clin Gastroenterol Hepatol 2017; 15:809-819. [PMID: 27712984 DOI: 10.1016/j.cgh.2016.09.148] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/30/2016] [Revised: 09/26/2016] [Accepted: 09/27/2016] [Indexed: 02/07/2023]
Abstract
The development of genome-wide massively parallel sequencing, ie, whole-genome and whole-exome sequencing, and copy number approaches has raised high expectations for the identification of novel hereditary colorectal cancer genes. Although relatively successful for genes causing adenomatous polyposis syndromes, both autosomal dominant and recessive, the identification of genes associated with hereditary non-polyposis colorectal cancer has proven extremely challenging, mainly because of the absence of major high-penetrance genes and the difficulty in demonstrating the functional impact of the identified variants and their causal association with tumor development. Indeed, most, if not all, novel candidate non-polyposis colorectal cancer genes identified so far lack corroborative data in independent studies. Here we review the novel hereditary colorectal cancer genes and syndromes identified and the candidate genes proposed in recent years as well as discuss the challenges we face.
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Hansen MF, Johansen J, Sylvander AE, Bjørnevoll I, Talseth-Palmer BA, Lavik LAS, Xavier A, Engebretsen LF, Scott RJ, Drabløs F, Sjursen W. Use of multigene-panel identifies pathogenic variants in several CRC-predisposing genes in patients previously tested for Lynch Syndrome. Clin Genet 2017; 92:405-414. [PMID: 28195393 DOI: 10.1111/cge.12994] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2016] [Revised: 02/06/2017] [Accepted: 02/08/2017] [Indexed: 12/28/2022]
Abstract
BACKGROUND Many families with a high burden of colorectal cancer fulfil the clinical criteria for Lynch Syndrome. However, in about half of these families, no germline mutation in the mismatch repair genes known to be associated with this disease can be identified. The aim of this study was to find the genetic cause for the increased colorectal cancer risk in these unsolved cases. MATERIALS AND METHODS To reach the aim, we designed a gene panel targeting 112 previously known or candidate colorectal cancer susceptibility genes to screen 274 patient samples for mutations. Mutations were validated by Sanger sequencing and, where possible, segregation analysis was performed. RESULTS We identified 73 interesting variants, of whom 17 were pathogenic and 19 were variants of unknown clinical significance in well-established cancer susceptibility genes. In addition, 37 potentially pathogenic variants in candidate colorectal cancer susceptibility genes were detected. CONCLUSION In conclusion, we found a promising DNA variant in more than 25 % of the patients, which shows that gene panel testing is a more effective method to identify germline variants in CRC patients compared to a single gene approach.
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Affiliation(s)
- Maren F Hansen
- Department of Laboratory Medicine, Children's and Women's Health, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway
| | - Jostein Johansen
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Anna E Sylvander
- Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway
| | - Inga Bjørnevoll
- Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway
| | - Bente A Talseth-Palmer
- Department of Laboratory Medicine, Children's and Women's Health, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,School of Biomedical Science and Pharmacy, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.,Clinic for Medicine, Møre and Romsdal Hospital Trust, Molde, Norway
| | - Liss A S Lavik
- Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway
| | - Alexandre Xavier
- School of Biomedical Science and Pharmacy, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia
| | - Lars F Engebretsen
- Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway
| | - Rodney J Scott
- School of Biomedical Science and Pharmacy, University of Newcastle and Hunter Medical Research Institute, Newcastle, Australia.,Division of Molecular Medicine Pathology North, NSW Pathology, Newcastle, Australia
| | - Finn Drabløs
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology (NTNU), Trondheim, Norway
| | - Wenche Sjursen
- Department of Laboratory Medicine, Children's and Women's Health, Norwegian University of Science and Technology (NTNU), Trondheim, Norway.,Department of Pathology and Medical Genetics, St. Olavs University Hospital, Trondheim, Norway
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Talseth-Palmer BA. The genetic basis of colonic adenomatous polyposis syndromes. Hered Cancer Clin Pract 2017; 15:5. [PMID: 28331556 PMCID: PMC5353802 DOI: 10.1186/s13053-017-0065-x] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 03/07/2017] [Indexed: 02/08/2023] Open
Abstract
Colorectal cancer (CRC) is one of the most common forms of cancer worldwide and familial adenomatous polyposis (FAP) accounts for approximately 1% of all CRCs. Adenomatous polyposis syndromes can be divided into; familial adenomatous polyposis (FAP) – classic FAP and attenuated familial adenomatous polyposis (AFAP), MUTYH-associated polyposis (MAP), NTHL1-associated polyposis (NAP) and polymerase proofreading-associated polyposis (PPAP). The polyposis syndromes genetics and clinical manifestation of disease varies and cases with clinical diagnosis of FAP might molecularly show a different diagnosis. This review examines different aspects of the adenomatous polyposis syndromes genetics and clinical manifestation of disease; in addition the genotype-phenotype and modifier alleles of FAP will be discussed. New technology has made it possible to diagnose some of the APC mutation negative patients into their respective syndromes. There still remain many molecularly undiagnosed adenomatous polyposis patients indicating that there remain causative genes to be discovered and with today’s technology these are expected to be identified in the near future. The knowledge about the role of modifier alleles in FAP will contribute to improved pre-symptomatic diagnosis and treatment. New novel mutations will continually be discovered in genes already associated with disease and new genes will be discovered that are associated with adenomatous polyposis. The search for modifier alleles in FAP should be made a priority.
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Affiliation(s)
- Bente A Talseth-Palmer
- Department of Laboratory Medicine, Children's and Women's Health, Faculty of Medicine and Health Sciences, Norwegian University of Science and Technology, Trondheim, 7491 Norway.,Clinic for Medicine, Møre og Romsdal Hospital Trust, Molde, Norway.,School of Biomedical Sciences and Pharmacy, Faculty of Health and Medicine, University of Newcastle, Newcastle, NSW Australia.,Hunter Medical Research Institute, Newcastle, NSW Australia.,Clinic for Medicine, Library, Molde Hospital, Parkvegen 84, Molde, 6407 Norway
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44
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Risks at the DNA Replication Fork: Effects upon Carcinogenesis and Tumor Heterogeneity. Genes (Basel) 2017; 8:genes8010046. [PMID: 28117753 PMCID: PMC5295039 DOI: 10.3390/genes8010046] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2016] [Revised: 01/09/2017] [Accepted: 01/17/2017] [Indexed: 12/27/2022] Open
Abstract
The ability of all organisms to copy their genetic information via DNA replication is a prerequisite for cell division and a biological imperative of life. In multicellular organisms, however, mutations arising from DNA replication errors in the germline and somatic cells are the basis of genetic diseases and cancer, respectively. Within human tumors, replication errors additionally contribute to mutator phenotypes and tumor heterogeneity, which are major confounding factors for cancer therapeutics. Successful DNA replication involves the coordination of many large-scale, complex cellular processes. In this review, we focus on the roles that defects in enzymes that normally act at the replication fork and dysregulation of enzymes that inappropriately damage single-stranded DNA at the fork play in causing mutations that contribute to carcinogenesis. We focus on tumor data and experimental evidence that error-prone variants of replicative polymerases promote carcinogenesis and on research indicating that the primary target mutated by APOBEC (apolipoprotein B mRNA-editing enzyme catalytic polypeptide-like) cytidine deaminases is ssDNA present at the replication fork. Furthermore, we discuss evidence from model systems that indicate replication stress and other cancer-associated metabolic changes may modulate mutagenic enzymatic activities at the replication fork.
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45
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An update of the classical Bokhman's dualistic model of endometrial cancer. MENOPAUSE REVIEW 2016; 15:63-8. [PMID: 27582678 PMCID: PMC4993978 DOI: 10.5114/pm.2016.61186] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/12/2016] [Accepted: 06/12/2016] [Indexed: 12/18/2022]
Abstract
According to the classical dualistic model introduced by Bokhman in 1983, endometrial cancer (EC) is divided into two basic types. The prototypical histological type for type I and type II of EC is endometrioid carcinoma and serous carcinoma, respectively. The traditional classification is based on clinical, endocrine and histopathological features, however, it sometimes does not reflect the full heterogeneity of EC. New molecular evidence, supported by clinical diversity of the cancer, indicates that the classical dualistic model is valid only to some extent. The review updates a mutational diversity of EC, introducing a new molecular classification of the tumour in regard to data presented by The Cancer Genome Atlas Research Network (TGCA).
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46
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Polymerase Epsilon Exonuclease Domain Mutations in Ovarian Endometrioid Carcinoma. Int J Gynecol Cancer 2016; 25:1187-93. [PMID: 26166557 DOI: 10.1097/igc.0000000000000492] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
OBJECTIVE Polymerase epsilon (POLE) is a DNA polymerase with a proofreading (exonuclease) domain, responsible for the recognition and excision of mispaired bases, thereby allowing high-fidelity DNA replication to occur. The Cancer Genome Atlas research network recently identified an ultramutated group of endometrial carcinomas, characterized by mutations in POLE, and exceptionally high substitution mutation rates. These POLE mutated endometrial tumors were almost exclusively of the endometrioid histotype. The prevalence and patterns of POLE mutated tumors in endometrioid carcinomas of the ovary, however, have not been studied in detail. MATERIALS AND METHODS In this study, we investigate the frequency of POLE exonuclease domain mutations in a series of 89 ovarian endometrioid carcinomas. RESULTS We found POLE mutations in 4 of 89 (4.5%) cases, occurring in 3 of 23 (13%) International Federation of Gynecology and Obstetrics (FIGO) grade 1, 1 of 43 (2%) FIGO grade 2, and 0 of 23 (0%) FIGO grade 3 tumors. All mutations were somatic missense point mutations, occurring at the commonly reported hotspots, P286R and V411L. All 3 POLE-mutated FIGO grade 1 tumors displayed prototypical histology, and the POLE-mutated FIGO grade 2 tumor displayed morphologic heterogeneity with focally high-grade features. All 4 patients with POLE-mutated tumors followed an uneventful clinical course with no disease recurrence; however, this finding was not statistically significant (P = 0.59). CONCLUSIONS The low rate of POLE mutations in ovarian endometrioid carcinoma and their predominance within the low FIGO grade tumors are in contrast to the findings in the endometrium.
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Abstract
In some families there is an increased risk for colorectal cancer, caused by heritable, but often unidentified genetic mutations predisposing to the disease. We have identified the likely genetic cause for disease predisposition in a large family with high burden of colorectal adenomas and carcinomas, in addition to extra-colonic cancers. This family had previously been tested for known cancer susceptibility genes, with negative results. Exome sequencing was used to identify a novel mutation, c.1373A>T (p.Tyr458Phe), in the gene for DNA polymerase epsilon catalytic subunit (POLE). This mutation is located in the active site of the exonuclease domain of the enzyme, and affects a residue that has previously been shown to be important for exonuclease activity. The first predisposing mutation identified in POLE (c.1270C>G, p.Leu424Val) was associated with colorectal cancer only, but another mutation with a broader tumour spectrum (c.1089C>A, p.Asn363Lys) has recently been reported. In the family described in the present study, carriers generally have multiple colorectal adenomas and cancer of colon, pancreas, ovaries and small intestine which represents an important broadening of the tumour spectrum of POLE mutation carriers. We also observe a large phenotypic variation among the POLE mutation carriers in this family, most likely explained by modifying variants in other genes. One POLE mutation carrier has a novel variant in EXO1 (c.458C>T, p.Ala153Val), which may contribute to a more severe phenotype. The findings in this study will have important implications for risk assessment and surveillance of POLE mutation carriers.
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48
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Rayner E, van Gool IC, Palles C, Kearsey SE, Bosse T, Tomlinson I, Church DN. A panoply of errors: polymerase proofreading domain mutations in cancer. Nat Rev Cancer 2016; 16:71-81. [PMID: 26822575 DOI: 10.1038/nrc.2015.12] [Citation(s) in RCA: 258] [Impact Index Per Article: 32.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Although it has long been recognized that the exonucleolytic proofreading activity intrinsic to the replicative DNA polymerases Pol δ and Pol ε is essential for faithful replication of DNA, evidence that defective DNA polymerase proofreading contributes to human malignancy has been limited. However, recent studies have shown that germline mutations in the proofreading domains of Pol δ and Pol ε predispose to cancer, and that somatic Pol ε proofreading domain mutations occur in multiple sporadic tumours, where they underlie a phenotype of 'ultramutation' and favourable prognosis. In this Review, we summarize the current understanding of the mechanisms and consequences of polymerase proofreading domain mutations in human malignancies, and highlight the potential utility of these variants as novel cancer biomarkers and therapeutic targets.
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Affiliation(s)
- Emily Rayner
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Inge C van Gool
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Claire Palles
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - Stephen E Kearsey
- Department of Zoology, University of Oxford, South Parks Road, Oxford OX1 3PS, UK
| | - Tjalling Bosse
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, Postbus 9600, 2300 RC Leiden, The Netherlands
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
| | - David N Church
- Molecular and Population Genetics Laboratory, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK
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49
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Aoude LG, Heitzer E, Johansson P, Gartside M, Wadt K, Pritchard AL, Palmer JM, Symmons J, Gerdes AM, Montgomery GW, Martin NG, Tomlinson I, Kearsey S, Hayward NK. POLE mutations in families predisposed to cutaneous melanoma. Fam Cancer 2015; 14:621-8. [PMID: 26251183 DOI: 10.1007/s10689-015-9826-8] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Germline mutations in the exonuclease domain of POLE have been shown to predispose to colorectal cancers and adenomas. POLE is an enzyme involved in DNA repair and chromosomal DNA replication. In order to assess whether such mutations might also predispose to cutaneous melanoma, we interrogated whole-genome and exome data from probands of 34 melanoma families lacking pathogenic mutations in known high penetrance melanoma susceptibility genes: CDKN2A, CDK4, BAP1, TERT, POT1, ACD and TERF2IP. We found a novel germline mutation, POLE p.(Trp347Cys), in a 7-case cutaneous melanoma family. Functional assays in S. pombe showed that this mutation led to an increased DNA mutation rate comparable to that seen with a Pol ε mutant with no exonuclease activity. We then performed targeted sequencing of POLE in 1243 cutaneous melanoma cases and found that a further ten probands had novel or rare variants in the exonuclease domain of POLE. Although this frequency is not significantly higher than that in unselected Caucasian controls, we observed multiple cancer types in the melanoma families, suggesting that some germline POLE mutations may predispose to a broad spectrum of cancers, including melanoma. In addition, we found the first mutation outside the exonuclease domain, p.(Gln520Arg), in a family with an extensive history of colorectal cancer.
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Affiliation(s)
- Lauren G Aoude
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia.
| | - Ellen Heitzer
- Institut für Humangenetik, Medizinische Universität Graz, Harrachgasse 21, 8010, Graz, Austria
| | - Peter Johansson
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Michael Gartside
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Karin Wadt
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Antonia L Pritchard
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Jane M Palmer
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Judith Symmons
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Anne-Marie Gerdes
- Department of Clinical Genetics, Rigshospitalet, Copenhagen, Denmark
| | - Grant W Montgomery
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Nicholas G Martin
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
| | - Ian Tomlinson
- Molecular and Population Genetics Laboratory and Genomic Medicine Theme Oxford NIHR Biomedical Research Centre, Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford, OX3 7BN, UK
| | - Stephen Kearsey
- Department of Zoology, University of Oxford, South Parks Road, Oxford, OX1 3PS, UK
| | - Nicholas K Hayward
- QIMR Berghofer Medical Research Institute, 300 Herston Road, Herston, Brisbane, QLD, 4006, Australia
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50
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Rohlin A, Eiengård F, Lundstam U, Zagoras T, Nilsson S, Edsjö A, Pedersen J, Svensson J, Skullman S, Karlsson BG, Björk J, Nordling M. GREM1 and POLE variants in hereditary colorectal cancer syndromes. Genes Chromosomes Cancer 2015; 55:95-106. [PMID: 26493165 PMCID: PMC5057327 DOI: 10.1002/gcc.22314] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2015] [Revised: 09/06/2015] [Accepted: 09/10/2015] [Indexed: 02/03/2023] Open
Abstract
Hereditary factors are thought to play a role in at least one third of patients with colorectal cancer (CRC) but only a limited proportion of these have mutations in known high-penetrant genes. In a relatively large part of patients with a few or multiple colorectal polyps the underlying genetic cause of the disease is still unknown. Using exome sequencing in combination with linkage analyses together with detection of copy-number variations (CNV), we have identified a duplication in the regulatory region of the GREM1 gene in a family with an attenuated/atypical polyposis syndrome. In addition, 107 patients with colorectal cancer and/or polyposis were analyzed for mutations in the candidate genes identified. We also performed screening of the exonuclease domain of the POLE gene in a subset of these patients. The duplication of 16 kb in the regulatory region of GREM1 was found to be disease-causing in the family. Functional analyses revealed a higher expression of the GREM1 gene in colorectal tissue in duplication carriers. Screening of the exonuclease domain of POLE in additional CRC patients identified a probable causative novel variant c.1274A>G, p.Lys425Arg. In conclusion a high penetrant duplication in the regulatory region of GREM1, predisposing to CRC, was identified in a family with attenuated/atypical polyposis. A POLE variant was identified in a patient with early onset CRC and a microsatellite stable (MSS) tumor. Mutations leading to increased expression of genes can constitute disease-causing mutations in hereditary CRC syndromes.
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Affiliation(s)
- Anna Rohlin
- Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Frida Eiengård
- Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Ulf Lundstam
- Department of Surgery, Sahlgrenska Academy at University of Gothenburg, Sahlgrenska University Hospital/Östra, Gothenburg, Sweden
| | - Theofanis Zagoras
- Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
| | - Staffan Nilsson
- Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
| | - Anders Edsjö
- Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden.,Department of Pathology, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden
| | - Jan Pedersen
- Department of Medical Genetics, Rikshospitalet, University Hospital, Oslo, Norway
| | | | | | - B Göran Karlsson
- The Swedish NMR-Centre at University of Gothenburg, Gothenburg, Sweden
| | - Jan Björk
- Department of Medicine, The Swedish Polyposis Registry, Karolinska Institute, Stockholm, Sweden
| | - Margareta Nordling
- Department of Medical and Clinical Genetics, Institute of Biomedicine, Sahlgrenska Academy at University of Gothenburg, Gothenburg, Sweden.,Department of Clinical Pathology and Genetics, Sahlgrenska University Hospital, Gothenburg, Sweden
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