101
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Bosse KR, Majzner RG, Mackall CL, Maris JM. Immune-Based Approaches for the Treatment of Pediatric Malignancies. ANNUAL REVIEW OF CANCER BIOLOGY-SERIES 2020; 4:353-370. [PMID: 34113750 PMCID: PMC8189419 DOI: 10.1146/annurev-cancerbio-030419-033436] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Immune-based therapies have now been credentialed for pediatric cancers with the robust efficacy of chimeric antigen receptor (CAR) T cells for pediatric B cell acute lymphocytic leukemia (ALL), offering a chance of a cure for children with previously lethal disease and a potentially more targeted therapy to limit treatment-related morbidities. The developmental origins of most pediatric cancers make them ideal targets for immune-based therapies that capitalize on the differential expression of lineage-specific cell surface molecules such as antibodies, antibody-drug conjugates, or CAR T cells, while the efficacy of other therapies that depend on tumor immunogenicity such as immune checkpoint inhibitors has been limited to date. Here we review the current status of immune-based therapies for childhood cancers, discuss challenges to developing immunotherapeutics for these diseases, and outline future directions of pediatric immunotherapy discovery and development.
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Affiliation(s)
- Kristopher R Bosse
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Robbie G Majzner
- Department of Pediatrics and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305, USA
| | - Crystal L Mackall
- Department of Pediatrics and Stanford Cancer Institute, Stanford University School of Medicine, Stanford, California 94305, USA
| | - John M Maris
- Division of Oncology and Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Philadelphia, Pennsylvania 19104, USA.,Department of Pediatrics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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102
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López S, Lim EL, Horswell S, Haase K, Huebner A, Dietzen M, Mourikis TP, Watkins TBK, Rowan A, Dewhurst SM, Birkbak NJ, Wilson GA, Van Loo P, Jamal-Hanjani M, Swanton C, McGranahan N. Interplay between whole-genome doubling and the accumulation of deleterious alterations in cancer evolution. Nat Genet 2020; 52:283-293. [PMID: 32139907 PMCID: PMC7116784 DOI: 10.1038/s41588-020-0584-7] [Citation(s) in RCA: 137] [Impact Index Per Article: 34.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Accepted: 01/28/2020] [Indexed: 01/24/2023]
Abstract
Whole-genome doubling (WGD) is a prevalent event in cancer, involving a doubling of the entire chromosome complement. However, despite its prevalence and prognostic relevance, the evolutionary selection pressures for WGD in cancer have not been investigated. Here, we combine evolutionary simulations with an analysis of cancer sequencing data to explore WGD during cancer evolution. Simulations suggest that WGD can be selected to mitigate the irreversible, ratchet-like, accumulation of deleterious somatic alterations, provided that they occur at a sufficiently high rate. Consistent with this, we observe an enrichment for WGD in tumor types with extensive loss of heterozygosity, including lung squamous cell carcinoma and triple-negative breast cancers, and we find evidence for negative selection against homozygous loss of essential genes before, but not after, WGD. Finally, we demonstrate that loss of heterozygosity and temporal dissection of mutations can be exploited to identify novel tumor suppressor genes and to obtain a deeper characterization of known cancer genes.
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Affiliation(s)
- Saioa López
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Emilia L Lim
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Stuart Horswell
- Bioinformatics and Biostatistics Group, Francis Crick Institute, London, UK
| | - Kerstin Haase
- Cancer Genomics Laboratory, Francis Crick Institute, London, UK
| | - Ariana Huebner
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Michelle Dietzen
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Thanos P Mourikis
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
| | - Thomas B K Watkins
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Andrew Rowan
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Sally M Dewhurst
- Laboratory for Cell Biology and Genetics, The Rockefeller University, New York, NY, USA
| | - Nicolai J Birkbak
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
- Department of Molecular Medicine, Aarhus University, Aarhus, Denmark
| | - Gareth A Wilson
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK
| | - Peter Van Loo
- Cancer Genomics Laboratory, Francis Crick Institute, London, UK
- Department of Human Genetics, University of Leuven, Leuven, Belgium
| | - Mariam Jamal-Hanjani
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK
- Department of Medical Oncology, University College London Hospitals NHS Foundation Trust, London, UK
| | - Charles Swanton
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
- Cancer Evolution and Genome Instability Laboratory, Francis Crick Institute and University College London Cancer Institute, London, UK.
| | - Nicholas McGranahan
- Cancer Genome Evolution Research Group, University College London Cancer Institute, London, UK.
- Cancer Research UK Lung Cancer Centre of Excellence, University College London Cancer Institute, London, UK.
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103
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Heidemann S, Bursic B, Zandi S, Li H, Abelson S, Klaassen RJ, Abish S, Rayar M, Breakey VR, Moshiri H, Dhanraj S, de Borja R, Shlien A, Dick JE, Dror Y. Cellular and molecular architecture of hematopoietic stem cells and progenitors in genetic models of bone marrow failure. JCI Insight 2020; 5:131018. [PMID: 31990679 DOI: 10.1172/jci.insight.131018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 01/15/2020] [Indexed: 12/26/2022] Open
Abstract
Inherited bone marrow failure syndromes, such as Fanconi anemia (FA) and Shwachman-Diamond syndrome (SDS), feature progressive cytopenia and a risk of acute myeloid leukemia (AML). Using deep phenotypic analysis of early progenitors in FA/SDS bone marrow samples, we revealed selective survival of progenitors that phenotypically resembled granulocyte-monocyte progenitors (GMP). Whole-exome and targeted sequencing of GMP-like cells in leukemia-free patients revealed a higher mutation load than in healthy controls and molecular changes that are characteristic of AML: increased G>A/C>T variants, decreased A>G/T>C variants, increased trinucleotide mutations at Xp(C>T)pT, and decreased mutation rates at Xp(C>T)pG sites compared with other Xp(C>T)pX sites and enrichment for Cancer Signature 1 (X indicates any nucleotide). Potential preleukemic targets in the GMP-like cells from patients with FA/SDS included SYNE1, DST, HUWE1, LRP2, NOTCH2, and TP53. Serial analysis of GMPs from an SDS patient who progressed to leukemia revealed a gradual increase in mutational burden, enrichment of G>A/C>T signature, and emergence of new clones. Interestingly, the molecular signature of marrow cells from 2 FA/SDS patients with leukemia was similar to that of FA/SDS patients without transformation. The predicted founding clones in SDS-derived AML harbored mutations in several genes, including TP53, while in FA-derived AML the mutated genes included ARID1B and SFPQ. We describe an architectural change in the hematopoietic hierarchy of FA/SDS with remarkable preservation of GMP-like populations harboring unique mutation signatures. GMP-like cells might represent a cellular reservoir for clonal evolution.
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Affiliation(s)
- Stephanie Heidemann
- Genetics & Genome Biology Program and.,Marrow Failure and Myelodysplasia (Pre-leukemia) Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Sasan Zandi
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Sagi Abelson
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | - Robert J Klaassen
- Department of Pediatrics, Children's Hospital of Eastern Ontario, Ottawa, Ontario, Canada
| | - Sharon Abish
- Hematology-Oncology, Montreal Children's Hospital, Montreal, Quebec, Canada
| | - Meera Rayar
- Division of Hematology, Oncology & Bone Marrow Transplant, University of British Columbia and British Columbia Children's Hospital, Vancouver, British Columbia, Canada
| | - Vicky R Breakey
- Department of Pediatrics, McMaster University, Hamilton, Ontario, Canada
| | | | - Santhosh Dhanraj
- Genetics & Genome Biology Program and.,Institute of Medical Science and
| | | | | | - John E Dick
- Princess Margaret Cancer Centre, Toronto, Ontario, Canada.,Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Yigal Dror
- Genetics & Genome Biology Program and.,Marrow Failure and Myelodysplasia (Pre-leukemia) Program, Division of Hematology/Oncology, Department of Pediatrics, The Hospital for Sick Children, Toronto, Ontario, Canada.,Institute of Medical Science and
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104
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Nakamori M, Panigrahi GB, Lanni S, Gall-Duncan T, Hayakawa H, Tanaka H, Luo J, Otabe T, Li J, Sakata A, Caron MC, Joshi N, Prasolava T, Chiang K, Masson JY, Wold MS, Wang X, Lee MYWT, Huddleston J, Munson KM, Davidson S, Layeghifard M, Edward LM, Gallon R, Santibanez-Koref M, Murata A, Takahashi MP, Eichler EE, Shlien A, Nakatani K, Mochizuki H, Pearson CE. A slipped-CAG DNA-binding small molecule induces trinucleotide-repeat contractions in vivo. Nat Genet 2020; 52:146-159. [PMID: 32060489 PMCID: PMC7043212 DOI: 10.1038/s41588-019-0575-8] [Citation(s) in RCA: 90] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2018] [Accepted: 12/19/2019] [Indexed: 01/07/2023]
Abstract
In many repeat diseases, such as Huntington's disease (HD), ongoing repeat expansions in affected tissues contribute to disease onset, progression and severity. Inducing contractions of expanded repeats by exogenous agents is not yet possible. Traditional approaches would target proteins driving repeat mutations. Here we report a compound, naphthyridine-azaquinolone (NA), that specifically binds slipped-CAG DNA intermediates of expansion mutations, a previously unsuspected target. NA efficiently induces repeat contractions in HD patient cells as well as en masse contractions in medium spiny neurons of HD mouse striatum. Contractions are specific for the expanded allele, independently of DNA replication, require transcription across the coding CTG strand and arise by blocking repair of CAG slip-outs. NA-induced contractions depend on active expansions driven by MutSβ. NA injections in HD mouse striatum reduce mutant HTT protein aggregates, a biomarker of HD pathogenesis and severity. Repeat-structure-specific DNA ligands are a novel avenue to contract expanded repeats.
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Affiliation(s)
- Masayuki Nakamori
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Gagan B Panigrahi
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Stella Lanni
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Terence Gall-Duncan
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Hideki Hayakawa
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Hana Tanaka
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Jennifer Luo
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Takahiro Otabe
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Jinxing Li
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Akihiro Sakata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Marie-Christine Caron
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Quebec, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec, Quebec, Canada
| | - Niraj Joshi
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Quebec, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec, Quebec, Canada
| | - Tanya Prasolava
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Karen Chiang
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
- Program of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec Research Center, HDQ Pavilion, Oncology Division, Quebec, Quebec, Canada
- Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec, Quebec, Canada
| | - Marc S Wold
- Department of Biochemistry, Carver College of Medicine, University of Iowa, Iowa City, IA, USA
| | - Xiaoxiao Wang
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, USA
| | - Marietta Y W T Lee
- Department of Biochemistry and Molecular Biology, New York Medical College, Valhalla, NY, USA
| | - John Huddleston
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Katherine M Munson
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
| | - Scott Davidson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Mehdi Layeghifard
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Lisa-Monique Edward
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Richard Gallon
- Institute of Genetic Medicine, Newcastle University, Newcastle upon Tyne, UK
| | | | - Asako Murata
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Masanori P Takahashi
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Evan E Eichler
- Department of Genome Sciences, University of Washington, Seattle, WA, USA
- Howard Hughes Medical Institute, University of Washington, Seattle, WA, USA
| | - Adam Shlien
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada
| | - Kazuhiko Nakatani
- Department of Regulatory Bioorganic Chemistry, The Institute of Scientific and Industrial Research, Osaka University, Osaka, Japan
| | - Hideki Mochizuki
- Department of Neurology, Osaka University Graduate School of Medicine, Osaka, Japan
| | - Christopher E Pearson
- Program of Genetics & Genome Biology, The Hospital for Sick Children, The Peter Gilgan Centre for Research and Learning, Toronto, Ontario, Canada.
- Program of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada.
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105
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106
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Sharma R, Lewis S, Wlodarski MW. DNA Repair Syndromes and Cancer: Insights Into Genetics and Phenotype Patterns. Front Pediatr 2020; 8:570084. [PMID: 33194896 PMCID: PMC7644847 DOI: 10.3389/fped.2020.570084] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/06/2020] [Accepted: 09/18/2020] [Indexed: 12/15/2022] Open
Abstract
DNA damage response is essential to human physiology. A broad spectrum of pathologies are displayed by individuals carrying monoallelic or biallelic loss-of-function mutations in DNA damage repair genes. DNA repair syndromes with biallelic disturbance of essential DNA damage response pathways manifest early in life with multi-systemic involvement and a high propensity for hematologic and solid cancers, as well as bone marrow failure. In this review, we describe classic biallelic DNA repair cancer syndromes arising from faulty single- and double-strand DNA break repair, as well as dysfunctional DNA helicases. These clinical entities include xeroderma pigmentosum, constitutional mismatch repair deficiency, ataxia telangiectasia, Nijmegen breakage syndrome, deficiencies of DNA ligase IV, NHEJ/Cernunnos, and ERCC6L2, as well as Bloom, Werner, and Rothmund-Thompson syndromes. To give an in-depth understanding of these disorders, we provide historical overview and discuss the interplay between complex biology and heterogeneous clinical manifestations.
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Affiliation(s)
- Richa Sharma
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, United States.,Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Sara Lewis
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, United States
| | - Marcin W Wlodarski
- Department of Hematology, St. Jude Children's Research Hospital, Memphis, TN, United States.,Division of Pediatric Hematology and Oncology, Department of Pediatrics and Adolescent Medicine, Medical Center, Faculty of Medicine, University of Freiburg, Freiburg, Germany
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107
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Wedekind MF, Cripe TP. Oncolytic Viruses and Their Potential as a Therapeutic Opportunity in Osteosarcoma. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2020; 1258:77-89. [PMID: 32767235 DOI: 10.1007/978-3-030-43085-6_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Osteosarcoma remains an unmet medical need. Oncolytic viruses are gaining traction as novel cancer therapeutics. These viruses are either naturally nonpathogenic or engineered to be safe by specific genetic deletions yet retain the ability to infect and kill human cancer cells and elicit anticancer immunity. Some versions are being specifically designed and tested in patients with osteosarcoma, though due to their generalized mechanism of action most are being tested in patients across a broad range of cancer types. The activity of these viruses is impacted not only by the susceptibility of tumor cells to infection but also by the tumor microenvironment (TME) and by tumor immunogenicity. Here we review the field of oncolytic viruses with a particular emphasis on highlighting any available data in preclinical osteosarcoma models or in patients with osteosarcoma. While in general the viruses have been shown safe to administer to patients by a variety of routes, their therapeutic efficacy to date has been limited. Given the low rate of adverse events and the likely absence of long-term side effects, the utility of oncolytic viruses will most likely be realized when used in combination with other agents.
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Affiliation(s)
| | - Timothy P Cripe
- Nationwide Children's Hospital, The Ohio State University, Columbus, OH, USA.
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108
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Guerrini-Rousseau L, Varlet P, Colas C, Andreiuolo F, Bourdeaut F, Dahan K, Devalck C, Faure-Conter C, Genuardi M, Goldberg Y, Kuhlen M, Moalla S, Opocher E, Perez-Alonso V, Sehested A, Slavc I, Unger S, Wimmer K, Grill J, Brugières L. Constitutional mismatch repair deficiency-associated brain tumors: report from the European C4CMMRD consortium. Neurooncol Adv 2019; 1:vdz033. [PMID: 32642664 PMCID: PMC7212899 DOI: 10.1093/noajnl/vdz033] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Background Malignant brain tumors (BT) are among the cancers most frequently associated with constitutional mismatch repair deficiency (CMMRD), a rare childhood cancer predisposition syndrome resulting from biallelic germline mutations in mismatch repair genes. This study analyzed data from the European “Care for CMMRD” (C4CMMRD) database to describe their clinical characteristics, treatments, and outcome with the aim of improving its diagnosis/treatment. Methods Retrospective analysis of data on patients with CMMRD and malignant BT from the C4CMMRD database up to July 2017. Results Among the 87 registered patients, 49 developed 56 malignant BTs: 50 high-grade gliomas (HGG) (with giant multinucleated cells in 16/21 histologically reviewed tumors) and 6 embryonal tumors. The median age at first BT was 9.2 years [1.1–40.6], with nine patients older than 18. Twenty-seven patients developed multiple malignancies (including16 before the BT). Most patients received standard treatment, and eight patients immunotherapy for relapsed HGG. The 3- and 5-year overall survival (OS) rates were 30% (95% CI: 19–45) and 22% (95% CI: 12–37) after the first BT, with worse prognosis for HGG (3-year OS = 20.5%). Six patients were alive (median follow-up 2.5 years) and 43 dead (38 deaths, 88%, were BT-related). Other CMMRD-specific features were café-au-lait macules (40/41), multiple BTs (5/15), developmental brain anomalies (11/15), and consanguinity (20/38 families). Conclusions Several characteristics could help suspecting CMMRD in pediatric malignant BTs: giant cells on histology, previous malignancies, parental consanguinity, café-au-lait macules, multiple BTs, and developmental brain anomalies. The prognosis of CMMRD-associated BT treated with standard therapies is poor requiring new therapeutic up-front approaches.
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Affiliation(s)
- Léa Guerrini-Rousseau
- Department of Pediatric and Adolescents Oncology, Gustave Roussy Cancer Center, Paris-Saclay University, Villejuif, France.,Gustave Roussy Cancer Center, Unite Mixte de Recherche 8203, Centre National de la Recherche Scientifique, Paris-Saclay University, Villejuif, France
| | - Pascale Varlet
- Department of Neuropathology, Sainte Anne Hospital, Rene Descartes University, Paris, France
| | | | - Felipe Andreiuolo
- Department of Neuropathology, Sainte Anne Hospital, Rene Descartes University, Paris, France
| | - Franck Bourdeaut
- Curie Institute, SIREDO Cancer Center (Care, innovation and research in pediatric, adolescents and young adults oncology), Paris, France
| | - Karin Dahan
- Hôpital Universitaire Reine Fabiola (HUDERF), Genetic department, Université Libre de Belgique (ULB), Brussels, Belgium
| | - Christine Devalck
- Department of Hemato-Oncology, Hôpital Universitaire Reine Fabiola (HUDERF), Université Libre de Belgique (ULB). Brussels - Belgium
| | - Cécile Faure-Conter
- Centre Leon Berard, Pediatric hemato-oncology institute (IHOPe), Lyon, France
| | - Maurizio Genuardi
- Fondazione Policlinico Universitario A. Gemelli IRCCS, UOC Genetica Medica, Rome, Italy.,Istituto di Medicina Genomica, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Yael Goldberg
- Raphael Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petach Tikva, Israel
| | - Michaela Kuhlen
- Department of Pediatric Oncology, University Children´s Hospital, Hematology and Clinical Immunology Duesseldorf, Germany
| | - Salma Moalla
- Department of Radiology, Gustave Roussy Cancer Center, Université Paris-Saclay, Villejuif, France
| | - Enrico Opocher
- Azienda Ospedaliera di Padova, Pediatric Oncology & Hematology, Padova, Italy
| | - Vanessa Perez-Alonso
- Hospital Universitario Doce de Octubre, Unidad de Oncología Pediátrica, Madrid, Spain
| | - Astrid Sehested
- Copenhagen University Hospital, Department of pediatrics and adolescent medicin, Copenhagen, Denmark
| | - Irene Slavc
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Sheila Unger
- Centre Hospitalier Universitaire Vaudois, Division of Genetic Medicine, University of Lausanne, Lausanne Switzerland
| | - Katharina Wimmer
- Institute of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Jacques Grill
- Department of Pediatric and Adolescents Oncology, Gustave Roussy Cancer Center, Paris-Saclay University, Villejuif, France.,Gustave Roussy Cancer Center, Unite Mixte de Recherche 8203, Centre National de la Recherche Scientifique, Paris-Saclay University, Villejuif, France
| | - Laurence Brugières
- Department of Pediatric and Adolescents Oncology, Gustave Roussy Cancer Center, Paris-Saclay University, Villejuif, France
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109
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Mardis ER. Neoantigens and genome instability: impact on immunogenomic phenotypes and immunotherapy response. Genome Med 2019; 11:71. [PMID: 31747945 PMCID: PMC6865009 DOI: 10.1186/s13073-019-0684-0] [Citation(s) in RCA: 65] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2019] [Accepted: 11/05/2019] [Indexed: 12/13/2022] Open
Abstract
The resurgence of immune therapies in cancer medicine has elicited a corresponding interest in understanding the basis of patient response or resistance to these treatments. One aspect of patient response clearly lies in the genomic alterations that are associated with cancer onset and progression, including those that contribute to genomic instability and the resulting creation of novel peptide sequences that may present as neoantigens. The immune reaction to these unique ‘non-self’ peptides is frequently suppressed by the tumor itself, but the use of checkpoint blockade therapies, personalized vaccines, or a combination of these treatments may elicit a tumor-specific immune response that results in cell death. Massively parallel sequencing, coupled with different computational analyses, provides unbiased identification of the germline and somatic alterations that drive cancer development, and of those alterations that lead to neoantigens. These range from simple point mutations that change single amino acids to complex alterations, such as frameshift insertion or deletion mutations, splice-site alterations that lead to exon skipping, structural alterations that lead to the formation of fusion proteins, and other forms of collateral damage caused by genome instability that result in new protein sequences unique to the cancer. The various genome instability phenotypes can be identified as alterations that impact DNA replication or mismatch repair pathways or by their genomic signatures. This review provides an overview of current knowledge regarding the fundamentals of genome replication and of both germline and somatic alterations that disrupt normal replication, leading to various forms of genomic instability in cancers, to the resulting generation of neoantigens and, ultimately, to immune-responsive and resistant phenotypes.
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Affiliation(s)
- Elaine R Mardis
- Institute for Genomic Medicine at Nationwide Children's Hospital, The Ohio State University College of Medicine, Children's Drive, Colombus, OH, 43205, USA.
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110
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Caval V, Jiao W, Berry N, Khalfi P, Pitré E, Thiers V, Vartanian JP, Wain-Hobson S, Suspène R. Mouse APOBEC1 cytidine deaminase can induce somatic mutations in chromosomal DNA. BMC Genomics 2019; 20:858. [PMID: 31726973 PMCID: PMC6854741 DOI: 10.1186/s12864-019-6216-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 10/22/2019] [Indexed: 02/06/2023] Open
Abstract
Background APOBEC1 (A1) enzymes are cytidine deaminases involved in RNA editing. In addition to this activity, a few A1 enzymes have been shown to be active on single stranded DNA. As two human ssDNA cytidine deaminases APOBEC3A (A3A), APOBEC3B (A3B) and related enzymes across the spectrum of placental mammals have been shown to introduce somatic mutations into nuclear DNA of cancer genomes, we explored the mutagenic threat of A1 cytidine deaminases to chromosomal DNA. Results Molecular cloning and expression of various A1 enzymes reveal that the cow, pig, dog, rabbit and mouse A1 have an intracellular ssDNA substrate specificity. However, among all the enzymes studied, mouse A1 appears to be singular, being able to introduce somatic mutations into nuclear DNA with a clear 5’TpC editing context, and to deaminate 5-methylcytidine substituted DNA which are characteristic features of the cancer related mammalian A3A and A3B enzymes. However, mouse A1 activity fails to elicit formation of double stranded DNA breaks, suggesting that mouse A1 possess an attenuated nuclear DNA mutator phenotype reminiscent of human A3B. Conclusions At an experimental level mouse APOBEC1 is remarkable among 12 mammalian A1 enzymes in that it represents a source of somatic mutations in mouse genome, potentially fueling oncogenesis. While the order Rodentia is bereft of A3A and A3B like enzymes it seems that APOBEC1 may well substitute for it, albeit remaining much less active. This modifies the paradigm that APOBEC3 and AID enzymes are the sole endogenous mutator enzymes giving rise to off-target editing of mammalian genomes.
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Affiliation(s)
- Vincent Caval
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.
| | - Wenjuan Jiao
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Université Paris Diderot, Sorbonne Paris Cité, Paris, France
| | - Noémie Berry
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Pierre Khalfi
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Emmanuelle Pitré
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France.,Sorbonne Université, Complexité du Vivant, ED515, 75005, Paris, France
| | - Valérie Thiers
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Jean-Pierre Vartanian
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Simon Wain-Hobson
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
| | - Rodolphe Suspène
- Molecular Retrovirology Unit, Institut Pasteur, CNRS UMR 3569, 28 rue du Dr. Roux, 75724, Paris cedex 15, France
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111
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Shi Z, Li KK, Kwan JSH, Yang RR, Aibaidula A, Tang Q, Bao Y, Mao Y, Chen H, Ng H. Whole-exome sequencing revealed mutational profiles of giant cell glioblastomas. Brain Pathol 2019; 29:782-792. [PMID: 30861589 PMCID: PMC8028679 DOI: 10.1111/bpa.12720] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 03/04/2019] [Indexed: 01/03/2023] Open
Abstract
Giant cell glioblastoma (gcGBM) is a rare histological variant of GBM, accounting for about 1% of all GBM. The prognosis is poor generally though gcGBM does slightly better than the other IDH-wild-type GBM. Because of the rarity of the cases, there has been no comprehensive molecular analysis of gcGBM. Previously, single-gene study identified genetic changes in TP53, PTEN and TERT promoter mutation in gcGBM. In this report, we performed whole-exome sequencing (WES) to identify somatically acquired mutations and copy number variations (CNVs) in 10 gcGBM genomes. We also examined TERT promoter mutation and MGMT methylation in our cohort. On top of the reported mutations, WES revealed ATRX, PIK3R1, RB1 and SETD2 as the recurrent mutations in gcGBM. Notably, one tumor harbored a mutation in MutS homolog 6 (MSH6) that is a key mismatch repair (MMR) gene. This tumor demonstrated hypermutation phenotype and showed an increased number of somatic mutations. TERT promoter mutation and MGMT methylation were observed in 20% and 40% of our samples, respectively. In conclusion, we described relevant mutation profiling for developing future targeted therapies in gcGBM.
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Affiliation(s)
- Zhi‐feng Shi
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityWulumuqi Zhong Road 12Shanghai200040China
| | - Kay Ka‐Wai Li
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong Kong, Prince of Wales Hospital30‐32 Ngan Shing Street, ShatinHong KongChina
- Shenzhen Research InstituteThe Chinese University of Hong KongNo.10, 2nd Yuexing Road, Nanshan DistrictShenzhen518057China
| | - Johnny Sheung Him Kwan
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong Kong, Prince of Wales Hospital30‐32 Ngan Shing Street, ShatinHong KongChina
| | - Rui Ryan Yang
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong Kong, Prince of Wales Hospital30‐32 Ngan Shing Street, ShatinHong KongChina
| | - Abudumijiti Aibaidula
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityWulumuqi Zhong Road 12Shanghai200040China
| | - Qisheng Tang
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityWulumuqi Zhong Road 12Shanghai200040China
| | - Yifeng Bao
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityWulumuqi Zhong Road 12Shanghai200040China
| | - Ying Mao
- Department of NeurosurgeryHuashan Hospital, Fudan UniversityWulumuqi Zhong Road 12Shanghai200040China
| | - Hong Chen
- Department of PathologyHuashan Hospital, Fudan UniversityWulumuqi Zhong Road 12Shanghai200040China
| | - Ho‐Keung Ng
- Department of Anatomical and Cellular PathologyThe Chinese University of Hong Kong, Prince of Wales Hospital30‐32 Ngan Shing Street, ShatinHong KongChina
- Shenzhen Research InstituteThe Chinese University of Hong KongNo.10, 2nd Yuexing Road, Nanshan DistrictShenzhen518057China
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112
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Yang C, Austin F, Richard H, Idowu M, Williamson V, Sabato F, Ferreira-Gonzalez A, Turner SA. Lynch syndrome-associated ultra-hypermutated pediatric glioblastoma mimicking a constitutional mismatch repair deficiency syndrome. Cold Spring Harb Mol Case Stud 2019; 5:mcs.a003863. [PMID: 31604779 PMCID: PMC6824252 DOI: 10.1101/mcs.a003863] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2018] [Accepted: 08/19/2019] [Indexed: 01/25/2023] Open
Abstract
Pediatric glioblastoma multiforme (GBM) has a poor prognosis as a result of recurrence after treatment of surgery and radiochemotherapy. A small subset of pediatric GBMs presenting with an ultra-high tumor mutational burden (TMB) may be sensitive to immune checkpoint inhibition. Here we report a 16-yr-old male with an ultra-hypermutated GBM. After incomplete surgical resection, molecular analysis of the tumor identified unusually high numbers of mutations and intratumor heterogeneity by a hotspot next-generation sequencing (NGS) panel. Further comprehensive molecular profiling identified a TMB of 343 mutations/Mb. An ultra-hypermutation genotype in pediatric GBMs is suggestive of a constitutive mismatch repair deficiency syndrome (CMMRD), which often acquires additional somatic driver mutations in replicating DNA polymerase genes. Tumor sequencing identified two MSH6 nonsense variants, a hotspot POLE mutation and a mutational signature supportive of a germline MMR deficiency with a somatic POLE mutation. However, constitutional testing identified only one nonsense MSH6 variant consistent with a Lynch syndrome diagnosis. This case represents the first confirmed Lynch syndrome case mimicking CMMRD by manifesting as an ultra-hypermutated pediatric GBM, following somatic mutations in MSH6 and POLE These findings permitted the patient's enrollment in an anti-PD-1 clinical trial for children with ultra-hypermutated GBM. Immunotherapy response has resulted in the patient's stable condition for over more than 1 year postdiagnosis.
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Affiliation(s)
- Chen Yang
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Frances Austin
- Department of Pediatrics, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Hope Richard
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Michael Idowu
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Vernell Williamson
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Fernanda Sabato
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | | | - Scott A Turner
- Department of Pathology, Virginia Commonwealth University, Richmond, Virginia 23284, USA
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113
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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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114
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Gladbach YS, Wiegele L, Hamed M, Merkenschläger AM, Fuellen G, Junghanss C, Maletzki C. Unraveling the Heterogeneous Mutational Signature of Spontaneously Developing Tumors in MLH1 -/- Mice. Cancers (Basel) 2019; 11:cancers11101485. [PMID: 31581674 PMCID: PMC6827043 DOI: 10.3390/cancers11101485] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2019] [Revised: 09/18/2019] [Accepted: 09/26/2019] [Indexed: 02/07/2023] Open
Abstract
Mismatch repair deficient (MMR-D) tumors exemplify the prototypic hypermutator phenotype. Owing to the high mutation rates, plenty of neo-antigens are present on the tumor cells' surface, ideally shared among different cancer types. The MLH1 knock out mouse represents a preclinical model that resembles features of the human MMR-D counterpart. While these mice develop neoplasias in a sequential twin-peaked manner (lymphomas > gastrointestinal tumors (GIT)) we aimed at identification of underlying molecular mechanisms. Using whole-genome sequencing, we focused on (I) shared and (II) mutually exclusive mutations and describe the process of ongoing mutational events in tumor-derived cell cultures. The landscape of MLH1-/- tumors is heterogeneous with only a few shared mutations being detectable among different tumor entities (ARID1A and IDH2). With respect to coding microsatellite analysis of MMR-D-related target genes, partial overlap was detectable, yet recognizing shared antigens. The present study is the first reporting results of a comparison between spontaneously developing tumors in MMR-D driven tumorigenesis. Additionally to identifying ARID1A as potential causative mutation hotspot, this comprehensive characterization of the mutational landscape may be a good starting point to refine therapeutic concepts.
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Affiliation(s)
- Yvonne Saara Gladbach
- Institute for Biostatistics and Informatics in Medicine and Ageing Research (IBIMA), Rostock University Medical Center, University of Rostock, 18057 Rostock, Germany.
- Faculty of Biosciences, Heidelberg University, 69120 Heidelberg, Germany.
- Division of Applied Bioinformatics, German Cancer Research Center (DKFZ) and National Center for Tumor Diseases (NCT) Heidelberg, 69120 Heidelberg, Germany.
| | - Leonie Wiegele
- Department of Internal Medicine, Medical Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, University of Rostock, 18057 Rostock, Germany.
| | - Mohamed Hamed
- Institute for Biostatistics and Informatics in Medicine and Ageing Research (IBIMA), Rostock University Medical Center, University of Rostock, 18057 Rostock, Germany.
| | - Anna-Marie Merkenschläger
- Institute for Biostatistics and Informatics in Medicine and Ageing Research (IBIMA), Rostock University Medical Center, University of Rostock, 18057 Rostock, Germany.
| | - Georg Fuellen
- Institute for Biostatistics and Informatics in Medicine and Ageing Research (IBIMA), Rostock University Medical Center, University of Rostock, 18057 Rostock, Germany.
| | - Christian Junghanss
- Department of Internal Medicine, Medical Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, University of Rostock, 18057 Rostock, Germany.
| | - Claudia Maletzki
- Department of Internal Medicine, Medical Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, University of Rostock, 18057 Rostock, Germany.
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115
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Houghton PJ, Kurmasheva RT. Challenges and Opportunities for Childhood Cancer Drug Development. Pharmacol Rev 2019; 71:671-697. [PMID: 31558580 PMCID: PMC6768308 DOI: 10.1124/pr.118.016972] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Cancer in children is rare with approximately 15,700 new cases diagnosed in the United States annually. Through use of multimodality therapy (surgery, radiation therapy, and aggressive chemotherapy), 70% of patients will be "cured" of their disease, and 5-year event-free survival exceeds 80%. However, for patients surviving their malignancy, therapy-related long-term adverse effects are severe, with an estimated 50% having chronic life-threatening toxicities related to therapy in their fourth or fifth decade of life. While overall intensive therapy with cytotoxic agents continues to reduce cancer-related mortality, new understanding of the molecular etiology of many childhood cancers offers an opportunity to redirect efforts to develop effective, less genotoxic therapeutic options, including agents that target oncogenic drivers directly, and the potential for use of agents that target the tumor microenvironment and immune-directed therapies. However, for many high-risk cancers, significant challenges remain.
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Affiliation(s)
- Peter J Houghton
- Greehey Children's Cancer Research Institute, University of Texas Health, San Antonio, Texas
| | - Raushan T Kurmasheva
- Greehey Children's Cancer Research Institute, University of Texas Health, San Antonio, Texas
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116
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Choi S, Yu Y, Grimmer MR, Wahl M, Chang SM, Costello JF. Temozolomide-associated hypermutation in gliomas. Neuro Oncol 2019; 20:1300-1309. [PMID: 29452419 DOI: 10.1093/neuonc/noy016] [Citation(s) in RCA: 120] [Impact Index Per Article: 24.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Low-grade gliomas cause considerable morbidity and most will recur after initial therapy. At recurrence, low-grade gliomas can undergo transformation to high-grade gliomas (grade III or grade IV), which are associated with worse prognosis. Temozolomide (TMZ) provides survival benefit in patients with glioblastomas, but its value in patients with low-grade gliomas is less clear. A subset of TMZ-treated, isocitrate dehydrogenase‒mutant, low-grade astrocytomas recur as more malignant tumors with thousands of de novo, coding mutations bearing a signature of TMZ-induced hypermutation. Preliminary studies raise the hypothesis that TMZ-induced hypermutation may contribute to malignant transformation, although with highly variable latency. On the other hand, hypermutated gliomas have radically altered genomes that present new opportunities for therapeutic intervention. In light of these findings and the immunotherapy clinical trials they inspired, how do patients and providers approach the risks and benefits of TMZ therapy? This review discusses what is known about the mechanisms and consequences of TMZ-induced hypermutation and outstanding questions regarding its clinical significance.
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Affiliation(s)
- Serah Choi
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Yao Yu
- Department of Radiation Oncology, University of California San Francisco, San Francisco, California
| | - Matthew R Grimmer
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
| | - Michael Wahl
- Samaritan Pastega Regional Cancer Center, Corvallis, Oregon
| | - Susan M Chang
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
| | - Joseph F Costello
- Department of Neurological Surgery, University of California San Francisco, San Francisco, California
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117
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Toledano H, Orenstein N, Sofrin E, Ruhrman-Shahar N, Amarilyo G, Basel-Salmon L, Shuldiner AR, Smirin-Yosef P, Aronson M, Al-Tarrah H, Bazak L, Gonzaga-Jauregui C, Tabori U, Wimmer K, Goldberg Y. Paediatric systemic lupus erythematosus as a manifestation of constitutional mismatch repair deficiency. J Med Genet 2019; 57:505-508. [PMID: 31501241 DOI: 10.1136/jmedgenet-2019-106303] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2019] [Revised: 08/01/2019] [Accepted: 08/26/2019] [Indexed: 12/14/2022]
Abstract
Biallelic mutations in any of the four mismatch repair genes MSH2, MSH6, MLH1 and PMS2 result in one of the most aggressive childhood cancer predisposition syndromes, termed constitutional mismatch repair deficiency (CMMRD) syndrome. In addition to a very high tumour risk, the CMMRD phenotype is often characterised by the presence of signs reminiscent of neurofibromatosis type 1. Although paediatric systemic lupus erythematosus (pSLE) has been reported so far in three patients with CMMRD, it has not been considered a diagnostic feature of the syndrome. We report here two additional female patients with pSLE and CMMRD due to biallelic pathogenic variants in MSH6 Hence, there are a total of five out of approximately 200 (2.5%) currently reported patients with CMMRD that also have pSLE, suggesting pSLE should raise the suspicion of a diagnosis of CMMRD, especially if supported by additional indicative features.
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Affiliation(s)
- Helen Toledano
- Department of Pediatric Hematology Oncology, Schneider Children's Medical Center of Israel, Petah Tikva, Israel.,Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel
| | - Naama Orenstein
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Pediatric Genetic Clinic, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | - Efrat Sofrin
- Pediatric Genetic Clinic, Schneider Children's Medical Center of Israel, Petah Tikva, Israel
| | | | - Gil Amarilyo
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Felsenstein Medical Research Center, Rabin Medical Center, Petah Tikva, Israel
| | - Lina Basel-Salmon
- Sackler Faculty of Medicine, Tel Aviv University, Tel Aviv, Israel.,Recanati Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | | | - Pola Smirin-Yosef
- Department of Molecular Biology, Genomic Bioinformatics Laboratory, Ariel University, Ariel, Israel
| | - Melyssa Aronson
- Zane Cohen Centre, Mount Sinai Hospital, Toronto, Ontario, Canada.,Department of Haematology-Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Hibs Al-Tarrah
- Zane Cohen Centre, Mount Sinai Hospital, Toronto, Ontario, Canada
| | - Lili Bazak
- Recanati Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
| | | | - Uri Tabori
- Zane Cohen Centre, Mount Sinai Hospital, Toronto, Ontario, Canada.,The Arthur and Sonia Labbatt Brain Tumour Research Centre, The Hospital for Sick Children, Institute of Medical Sciences, The University of Toronto, Toronto, Ontario, Canada
| | - Katharina Wimmer
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Yael Goldberg
- Recanati Genetics Institute, Rabin Medical Center, Petah Tikva, Israel
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118
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González-Acosta M, Marín F, Puliafito B, Bonifaci N, Fernández A, Navarro M, Salvador H, Balaguer F, Iglesias S, Velasco A, Grau Garces E, Moreno V, Gonzalez-Granado LI, Guerra-García P, Ayala R, Florkin B, Kratz C, Ripperger T, Rosenbaum T, Januszkiewicz-Lewandowska D, Azizi AA, Ragab I, Nathrath M, Pander HJ, Lobitz S, Suerink M, Dahan K, Imschweiler T, Demirsoy U, Brunet J, Lázaro C, Rueda D, Wimmer K, Capellá G, Pineda M. High-sensitivity microsatellite instability assessment for the detection of mismatch repair defects in normal tissue of biallelic germline mismatch repair mutation carriers. J Med Genet 2019; 57:269-273. [PMID: 31494577 PMCID: PMC7146943 DOI: 10.1136/jmedgenet-2019-106272] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2019] [Revised: 07/16/2019] [Accepted: 07/16/2019] [Indexed: 01/08/2023]
Abstract
INTRODUCTION Lynch syndrome (LS) and constitutional mismatch repair deficiency (CMMRD) are hereditary cancer syndromes associated with mismatch repair (MMR) deficiency. Tumours show microsatellite instability (MSI), also reported at low levels in non-neoplastic tissues. Our aim was to evaluate the performance of high-sensitivity MSI (hs-MSI) assessment for the identification of LS and CMMRD in non-neoplastic tissues. MATERIALS AND METHODS Blood DNA samples from 131 individuals were grouped into three cohorts: baseline (22 controls), training (11 CMMRD, 48 LS and 15 controls) and validation (18 CMMRD and 18 controls). Custom next generation sequencing panel and bioinformatics pipeline were used to detect insertions and deletions in microsatellite markers. An hs-MSI score was calculated representing the percentage of unstable markers. RESULTS The hs-MSI score was significantly higher in CMMRD blood samples when compared with controls in the training cohort (p<0.001). This finding was confirmed in the validation set, reaching 100% specificity and sensitivity. Higher hs-MSI scores were detected in biallelic MSH2 carriers (n=5) compared with MSH6 carriers (n=15). The hs-MSI analysis did not detect a difference between LS and control blood samples (p=0.564). CONCLUSIONS The hs-MSI approach is a valuable tool for CMMRD diagnosis, especially in suspected patients harbouring MMR variants of unknown significance or non-detected biallelic germline mutations.
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Affiliation(s)
- Maribel González-Acosta
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Fátima Marín
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Benjamin Puliafito
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Nuria Bonifaci
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Matilde Navarro
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Hector Salvador
- Pediatric Oncology Unit, Hospital Sant Joan de Déu, Esplugues, Barcelona, Spain
| | - Francesc Balaguer
- Department of Gastroenterology, Hospital Clínic, Centro de Investigación Biomédica en Red en Enfermedades Hepáticas y Digestivas (CIBERehd), Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Silvia Iglesias
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Angela Velasco
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Institut d'Investigació Biomèdica de Girona - IDIBGI, Girona, Spain
| | - Elia Grau Garces
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Victor Moreno
- Cancer Prevention and Control Program, Catalan Institute of Oncology - ICO, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, CIBERESP, L'Hospitalet de Llobregat, Barcelona, Spain.,Department of Clinical Sciences, Faculty of Medicine, University of Barcelona, Barcelona, Spain
| | - Luis Ignacio Gonzalez-Granado
- Immunodeficiencies Unit, Department of Pediatrics, Doce de Octubre University Hospital, i+12 Research Institute; Complutense University of Madrid, Madrid, Spain
| | - Pilar Guerra-García
- Hematology and Oncology Unit, Department of Pediatrics, Doce de Octubre University Hospital, Madrid, Spain
| | - Rosa Ayala
- Department of Hematology, Doce de Octubre University Hospital, i+12 Research Institute, Madrid, Spain
| | - Benoît Florkin
- University Department of Pediatrics, CHR Citadelle, Liege, Belgium
| | - Christian Kratz
- Department of Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | | | | | - Amedeo A Azizi
- Department of Pediatrics and Adolescent Medicine, Medical University of Vienna, Vienna, Austria
| | - Iman Ragab
- Pediatrics Department, Hematology-Oncology Unit, Faculty of Medicine, Ain Shams University, Cairo, Egypt
| | - Michaela Nathrath
- Pediatric Hematology and Oncology, Klinikum Kassel, Kassel, Germany.,Pediatric Oncology Center, Department of Pediatrics, Technische Universität München, Munchen, Germany
| | | | - Stephan Lobitz
- Department of Pediatric Oncology/Pediatric Hematology, Kliniken der Stadt Köln gGmbH, Children's Hospital Amsterdamer Strasse, Koln, Germany
| | - Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Karin Dahan
- Centre de Génétique Humaine, Institut de Pathologie et de Génétique (IPG), Gosselies, Belgium
| | | | - Ugur Demirsoy
- Department of Pediatric Oncology, Kocaeli Universitesi, Kocaeli, Turkey
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Institut d'Investigació Biomèdica de Girona - IDIBGI, Girona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Daniel Rueda
- Hereditary Cancer Laboratory, Doce de Octubre University Hospital, i+12 Research Institute, Madrid, Spain
| | - Katharina Wimmer
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology - ICO, Hereditary Cancer Group, Molecular Mechanisms and Experimental Therapy in Oncology Program, Institut d'Investigació Biomèdica de Bellvitge - IDIBELL, Ciber Oncología (CIBERONC) - Instituto de Salud Carlos III, L'Hospitalet de Llobregat, Barcelona, Spain
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119
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MacFarland SP, Zelley K, Katona BW, Wilkins BJ, Brodeur GM, Mamula P. Gastrointestinal Polyposis in Pediatric Patients. J Pediatr Gastroenterol Nutr 2019; 69:273-280. [PMID: 31211762 PMCID: PMC7336255 DOI: 10.1097/mpg.0000000000002421] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Gastrointestinal polyps are mucosal overgrowths that, if unchecked, can undergo malignant transformation. Although relatively uncommon in the pediatric age group, they can be the harbingers of multiorgan cancer risk and require close management and follow-up. Additionally, as many polyposis syndromes are inherited, appropriate genetic testing and management of relatives is vital for the health of the entire family. In this review, we discuss both common and uncommon childhood gastrointestinal polyposis syndromes in terms of clinical presentation, management, and surveillance. We also detail any additional malignancy risk and surveillance required in the pediatric age group (<21 years old). Through this review, we provide a framework for gastroenterologists to manage the multifaceted nature of pediatric polyposis syndromes.
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Affiliation(s)
- Suzanne P. MacFarland
- Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Kristin Zelley
- Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Bryson W. Katona
- Division of Gastroenterology, Department of Medicine, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Benjamin J. Wilkins
- Department of Pathology and Laboratory Medicine, The Children’s Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Garrett M. Brodeur
- Division of Oncology, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
| | - Petar Mamula
- Division of Gastroenterology, Hepatology, and Nutrition, Department of Pediatrics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA
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120
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Moreno-Vicente J, Beers SA, Gray JC. PD-1/PD-L1 blockade in paediatric cancers: What does the future hold? Cancer Lett 2019; 457:74-85. [PMID: 31055109 DOI: 10.1016/j.canlet.2019.04.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2019] [Revised: 04/23/2019] [Accepted: 04/25/2019] [Indexed: 12/28/2022]
Abstract
Checkpoint blockade (CPB) immunotherapy has shown unprecedented success in a wide range of adult malignancies, and is increasingly being employed in the treatment of advanced cancers. However, the experience in the paediatric population remains limited and the small number of single agent studies reported have shown disappointing response rates. Paediatric cancers offer unique challenges that can hinder the translation of CPB into the paediatric clinic, and combinational therapies are likely to be needed to achieve therapeutic success. As the number of paediatric trials using CPB rapidly increases, understanding the challenges that these agents may encounter in this population is of special significance to allow the design of optimal combinatorial strategies for each tumour type. Here, we offer an overview of the unique biological and immunological features of paediatric cancers as compared to adult malignancies, and how these might impact the overall success of CPB in the paediatric population. We review the growing body of pre-clinical and clinical experiences to date, and discuss future strategies involving the combination of CPB with traditionally used therapies (chemotherapy and radiotherapy) or with other newly developed immunotherapies.
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Affiliation(s)
- Julia Moreno-Vicente
- Antibody and Vaccine Group, Centre for Cancer Immunology, University of Southampton Faculty of Medicine, Department of Paediatric Oncology, Southampton, Hants, SO16 6YD, UK
| | - Stephen A Beers
- Antibody and Vaccine Group, Centre for Cancer Immunology, University of Southampton Faculty of Medicine, Department of Paediatric Oncology, Southampton, Hants, SO16 6YD, UK
| | - Juliet C Gray
- Antibody and Vaccine Group, Centre for Cancer Immunology, University of Southampton Faculty of Medicine, Department of Paediatric Oncology, Southampton, Hants, SO16 6YD, UK.
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121
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Natali F, Rancati G. The Mutator Phenotype: Adapting Microbial Evolution to Cancer Biology. Front Genet 2019; 10:713. [PMID: 31447882 PMCID: PMC6691094 DOI: 10.3389/fgene.2019.00713] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2018] [Accepted: 07/05/2019] [Indexed: 01/07/2023] Open
Abstract
The mutator phenotype hypothesis was postulated almost 40 years ago to reconcile the observation that while cancer cells display widespread mutational burden, acquisition of mutations in non-transformed cells is a rare event. Moreover, it also suggested that cancer evolution could be fostered by increased genome instability. Given the evolutionary conservation throughout the tree of life and the genetic tractability of model organisms, yeast and bacterial species pioneered studies to dissect the functions of genes required for genome maintenance (caretaker genes) or for cell growth control (gatekeeper genes). In this review, we first provide an overview of what we learned from model organisms about the roles of these genes and the genome instability that arises as a consequence of their dysregulation. We then discuss our current understanding of how mutator phenotypes shape the evolution of bacteria and yeast species. We end by bringing clinical evidence that lessons learned from single-cell organisms can be applied to tumor evolution.
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Affiliation(s)
- Federica Natali
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore.,School of Biological Sciences, Nanyang Technological University, Singapore, Singapore
| | - Giulia Rancati
- Institute of Medical Biology (IMB), Agency for Science, Technology and Research (ASTAR), Singapore, Singapore
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122
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Ihara K. Immune checkpoint inhibitor therapy for pediatric cancers: A mini review of endocrine adverse events. Clin Pediatr Endocrinol 2019; 28:59-68. [PMID: 31384097 PMCID: PMC6646237 DOI: 10.1297/cpe.28.59] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/14/2019] [Accepted: 03/15/2019] [Indexed: 12/27/2022] Open
Abstract
In recent years, immune checkpoint inhibitor therapy has attracted a great deal of attention in the field of cancer treatment. In the clinical setting, antibodies targeting programmed cell death-1 (PD-1) and cytotoxic T-lymphocyte-associated protein 4 (CTLA-4) have been successfully used to treat adult patients with various types of intractable cancer. However, in a substantial number of patients, ICI therapy is associated with autoimmune toxicities known as immune-related adverse events (IRAEs). Endocrinopathies, such as hypophysitis or autoimmune thyroid disease, may occur and can present unique clinical features that have not been documented with traditional chemotherapies. A Japanese clinical trial evaluating the anti-PD-1 antibody nivolumab for the treatment of pediatric patients with refractory malignant solid tumors and Hodgkin lymphoma has been ongoing since 2017. Moreover, tumors associated with Lynch syndrome, a hereditary form of mismatch repair deficiency, are being focused and represent the next target for ICI therapy in Japan. For the safe management of pediatric cancer patients treated with ICIs, pediatric endocrinologists must be aware of the risk of autoimmune endocrinopathies and perform relevant screening tests at appropriate stages of growth and development.
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Affiliation(s)
- Kenji Ihara
- Department of Pediatrics, Oita University Faculty of Medicine, Yufu, Japan
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123
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Rogozin IB, Pavlov YI, Goncearenco A, De S, Lada AG, Poliakov E, Panchenko AR, Cooper DN. Mutational signatures and mutable motifs in cancer genomes. Brief Bioinform 2019; 19:1085-1101. [PMID: 28498882 DOI: 10.1093/bib/bbx049] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Indexed: 12/22/2022] Open
Abstract
Cancer is a genetic disorder, meaning that a plethora of different mutations, whether somatic or germ line, underlie the etiology of the 'Emperor of Maladies'. Point mutations, chromosomal rearrangements and copy number changes, whether they have occurred spontaneously in predisposed individuals or have been induced by intrinsic or extrinsic (environmental) mutagens, lead to the activation of oncogenes and inactivation of tumor suppressor genes, thereby promoting malignancy. This scenario has now been recognized and experimentally confirmed in a wide range of different contexts. Over the past decade, a surge in available sequencing technologies has allowed the sequencing of whole genomes from liquid malignancies and solid tumors belonging to different types and stages of cancer, giving birth to the new field of cancer genomics. One of the most striking discoveries has been that cancer genomes are highly enriched with mutations of specific kinds. It has been suggested that these mutations can be classified into 'families' based on their mutational signatures. A mutational signature may be regarded as a type of base substitution (e.g. C:G to T:A) within a particular context of neighboring nucleotide sequence (the bases upstream and/or downstream of the mutation). These mutational signatures, supplemented by mutable motifs (a wider mutational context), promise to help us to understand the nature of the mutational processes that operate during tumor evolution because they represent the footprints of interactions between DNA, mutagens and the enzymes of the repair/replication/modification pathways.
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Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, USA
| | - Youri I Pavlov
- Eppley Institute for Cancer Research, University of Nebraska Medical Center, USA
| | | | | | - Artem G Lada
- Department Microbiology and Molecular Genetics, University of California, Davis, USA
| | - Eugenia Poliakov
- Laboratory of Retinal Cell and Molecular Biology, National Eye Institute, National Institutes of Health, USA
| | - Anna R Panchenko
- National Center for Biotechnology Information, National Institutes of Health, USA
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124
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Evolving neoantigen profiles in colorectal cancers with DNA repair defects. Genome Med 2019; 11:42. [PMID: 31253177 PMCID: PMC6599263 DOI: 10.1186/s13073-019-0654-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 06/13/2019] [Indexed: 12/21/2022] Open
Abstract
Background Neoantigens that arise as a consequence of tumor-specific mutations can be recognized by T lymphocytes leading to effective immune surveillance. In colorectal cancer (CRC) and other tumor types, a high number of neoantigens is associated with patient response to immune therapies. The molecular processes governing the generation of neoantigens and their turnover in cancer cells are poorly understood. We exploited CRC as a model system to understand how alterations in DNA repair pathways modulate neoantigen profiles over time. Methods We performed whole exome sequencing (WES) and RNA sequencing (RNAseq) in CRC cell lines, in vitro and in vivo, and in CRC patient-derived xenografts (PDXs) to track longitudinally genomic profiles, clonal evolution, mutational signatures, and predicted neoantigens. Results The majority of CRC models showed remarkably stable mutational and neoantigen profiles; however, those carrying defects in DNA repair genes continuously diversified. Rapidly evolving and evolutionary stable CRCs displayed characteristic genomic signatures and transcriptional profiles. Downregulation of molecules implicated in antigen presentation occurred selectively in highly mutated and rapidly evolving CRC. Conclusions These results indicate that CRCs carrying alterations in DNA repair pathways display dynamic neoantigen patterns that fluctuate over time. We define CRC subsets characterized by slow and fast evolvability and link this phenotype to downregulation of antigen-presenting cellular mechanisms. Longitudinal monitoring of the neoantigen landscape could be relevant in the context of precision medicine. Electronic supplementary material The online version of this article (10.1186/s13073-019-0654-6) contains supplementary material, which is available to authorized users.
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125
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Ongoing issues with the management of children with Constitutional Mismatch Repair Deficiency syndrome. Eur J Med Genet 2019; 62:103706. [PMID: 31233827 DOI: 10.1016/j.ejmg.2019.103706] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2019] [Revised: 05/28/2019] [Accepted: 06/19/2019] [Indexed: 11/22/2022]
Abstract
Constitutional Mismatch Repair Deficiency (CMMRD) is a rare cancer predisposition syndrome, presenting in childhood, in which affected patients develop various malignancies such as hematological, gastrointestinal and central nervous system tumors. Although guidelines are being increasingly developed for surveillance and early detection of cancers in affected families, there are no clear recommendations regarding choice of therapy and very scarce information about tolerance to chemotherapy and radiation in these patients. We report the pedigree of a consanguineous family with four affected children. Although clinical and molecular tests confirm CMMRD, genetic testing revealed heterogeneous mutations. The index case developed severe toxicity from therapy for glioblastoma and T-cell leukemia and died from an infection while in complete remission. His sister developed a malignant brain tumor while undergoing surveillance for a low grade brain lesion and is still undergoing follow-up. This family illustrates the difficulties and opportunities with challenging diagnosis, surveillance and choice of therapy for children with CMMRD and the need for increased awareness and more information about this rare but important syndrome.
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126
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Hereditary myeloid malignancies. Best Pract Res Clin Haematol 2019; 32:163-176. [DOI: 10.1016/j.beha.2019.05.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2019] [Accepted: 05/01/2019] [Indexed: 12/18/2022]
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127
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Yamamoto H, Imai K. An updated review of microsatellite instability in the era of next-generation sequencing and precision medicine. Semin Oncol 2019; 46:261-270. [DOI: 10.1053/j.seminoncol.2019.08.003] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Revised: 03/27/2019] [Accepted: 08/14/2019] [Indexed: 12/23/2022]
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128
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Ma K, Jin Q, Wang M, Li X, Zhang Y. Research progress and clinical application of predictive biomarker for immune checkpoint inhibitors. Expert Rev Mol Diagn 2019; 19:517-529. [PMID: 31079502 DOI: 10.1080/14737159.2019.1617702] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
INTRODUCTION Immune checkpoint inhibitors (ICIs) have emerged as epochal milestones in the field of anti-cancer immunotherapy. With promising clinical effectiveness, ICIs can significantly prolong the overall survival of patients with advanced cancer of different types. Although their remarkable effectiveness has been demonstrated in clinical application, ICIs display limitations in terms of unique response patterns. Only a subset of patients exhibits objective responses, while others show rapid disease progression. Considering that there is a fair representation of both subsets of patients (responders and non-responders), clinicians ought to effectively stratify patients who will potentially benefit from ICI therapy, and optimize a strategy for patient selection. Areas covered: In this review, the authors have summarized several key factors involved in the biomarker development of ICI therapy, such as neoantigen production and presentation, the tumor microenvironment, and alternation in specific gene signaling pathways. Expert opinion: Considering the extreme complexity of the immune system, a single biomarker may fail to appropriately stratify patients for ICI therapy. Therefore, future biomarker research should focus on designing an integrated biomarker system that will successfully guide combination therapies to overcome resistance to immunotherapy.
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Affiliation(s)
- Ke Ma
- a Department of Pharmacology , School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University , Shenyang , China
| | - Qingqing Jin
- a Department of Pharmacology , School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University , Shenyang , China
| | - Miao Wang
- a Department of Pharmacology , School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University , Shenyang , China
| | - Xin Li
- a Department of Pharmacology , School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University , Shenyang , China
| | - Yuyang Zhang
- a Department of Pharmacology , School of Life Science and Biopharmaceutics, Shenyang Pharmaceutical University , Shenyang , China
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129
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Response to Yang et al. Genet Med 2019; 21:2652-2653. [PMID: 31043712 DOI: 10.1038/s41436-019-0530-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Accepted: 04/19/2019] [Indexed: 11/09/2022] Open
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130
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Delineating a new feature of constitutional mismatch repair deficiency (CMMRD) syndrome: breast cancer. Fam Cancer 2019; 18:105-108. [PMID: 29785566 DOI: 10.1007/s10689-018-0088-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Constitutional mismatch repair deficiency (CMMRD) syndrome is a rare autosomal recessive hereditary cancer condition, characterized by an exceptionally high risk of cancer, a propensity for childhood malignancies, and cutaneous features reminiscent of neurofibromatosis type 1 (NF1). We report on two sisters originally suspected of having CMMRD syndrome due to their history of colonic polyps and NF1 associated skin findings, both were subsequently found to have biallelic MSH6 mutations. After years of CMMRD syndrome follow-up, the proband was diagnosed with breast cancer at age 29, while her sister was diagnosed with a glioblastoma at age 27. Immunohistochemistry analysis on the breast tumor tissue revealed weak MSH6 protein staining. Exome sequencing revealed a hypermutated breast tumor and an ultra-hypermutated brain tumor. Multi-gene panel testing was also performed and revealed no additional mutations which might explain the proband's early onset breast cancer. This is the first documented case of breast cancer in an individual with CMMRD syndrome. We summarize the evidence supporting the possible association between breast cancer and biallelic MMR mutations. Healthcare providers should be aware of this possible association and follow-up appropriately for suspicious breast findings. In addition, this case highlights the need for frequent central nervous system screenings due to rapid progression of brain tumors.
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131
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Frank MO, Koyama T, Rhrissorrakrai K, Robine N, Utro F, Emde AK, Chen BJ, Arora K, Shah M, Geiger H, Felice V, Dikoglu E, Rahman S, Fang A, Vacic V, Bergmann EA, Vogel JLM, Reeves C, Khaira D, Calabro A, Kim D, Lamendola-Essel MF, Esteves C, Agius P, Stolte C, Boockvar J, Demopoulos A, Placantonakis DG, Golfinos JG, Brennan C, Bruce J, Lassman AB, Canoll P, Grommes C, Daras M, Diamond E, Omuro A, Pentsova E, Orange DE, Harvey SJ, Posner JB, Michelini VV, Jobanputra V, Zody MC, Kelly J, Parida L, Wrzeszczynski KO, Royyuru AK, Darnell RB. Sequencing and curation strategies for identifying candidate glioblastoma treatments. BMC Med Genomics 2019; 12:56. [PMID: 31023376 PMCID: PMC6485090 DOI: 10.1186/s12920-019-0500-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 03/28/2019] [Indexed: 12/29/2022] Open
Abstract
Background Prompted by the revolution in high-throughput sequencing and its potential impact for treating cancer patients, we initiated a clinical research study to compare the ability of different sequencing assays and analysis methods to analyze glioblastoma tumors and generate real-time potential treatment options for physicians. Methods A consortium of seven institutions in New York City enrolled 30 patients with glioblastoma and performed tumor whole genome sequencing (WGS) and RNA sequencing (RNA-seq; collectively WGS/RNA-seq); 20 of these patients were also analyzed with independent targeted panel sequencing. We also compared results of expert manual annotations with those from an automated annotation system, Watson Genomic Analysis (WGA), to assess the reliability and time required to identify potentially relevant pharmacologic interventions. Results WGS/RNAseq identified more potentially actionable clinical results than targeted panels in 90% of cases, with an average of 16-fold more unique potentially actionable variants identified per individual; 84 clinically actionable calls were made using WGS/RNA-seq that were not identified by panels. Expert annotation and WGA had good agreement on identifying variants [mean sensitivity = 0.71, SD = 0.18 and positive predictive value (PPV) = 0.80, SD = 0.20] and drug targets when the same variants were called (mean sensitivity = 0.74, SD = 0.34 and PPV = 0.79, SD = 0.23) across patients. Clinicians used the information to modify their treatment plan 10% of the time. Conclusion These results present the first comprehensive comparison of technical and machine augmented analysis of targeted panel and WGS/RNA-seq to identify potential cancer treatments.
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Affiliation(s)
- Mayu O Frank
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.,Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Takahiko Koyama
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | | | - Nicolas Robine
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Filippo Utro
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | - Anne-Katrin Emde
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Bo-Juen Chen
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.,Present address: Google, 76 9th Avenue, New York, NY, 10011, USA
| | - Kanika Arora
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Minita Shah
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Heather Geiger
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Vanessa Felice
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Esra Dikoglu
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.,Present address: Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA
| | - Sadia Rahman
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Alice Fang
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Vladimir Vacic
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.,Present address: 23&Me, 899 W Evelyn Ave, Mountain View, CA, 94041, USA
| | - Ewa A Bergmann
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.,Present address: Max Planck Institute of Immunobiology and Epigenetics, Stübeweg 51 D-79108, Freiburg, Germany
| | - Julia L Moore Vogel
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.,Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.,Present address: The Scripps Research Institute, 10550 N. Torrey Pines Road, La Jolla, CA, 92037, USA
| | - Catherine Reeves
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Depinder Khaira
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Anthony Calabro
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.,Present address: The Tisch Cancer Institute, 1470 Madison Avenue, New York, NY, 10029, USA
| | - Duyang Kim
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Michelle F Lamendola-Essel
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.,Present address: Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Cecilia Esteves
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.,Present address: Harvard Medical School, 10 Shattuck Street, Boston, MA, 02115, USA
| | - Phaedra Agius
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - Christian Stolte
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - John Boockvar
- Northwell Health, Lenox Hill Hospital, 100 E. 77th Street, New York, NY, 10075, USA
| | - Alexis Demopoulos
- Northwell Health, The Brain Tumor Center, 450 Lakeville Road, Lake Success, Lakeville, NY, 11042, USA
| | | | - John G Golfinos
- New York University, School of Medicine, 550 First Avenue, New York, NY, 10016, USA
| | - Cameron Brennan
- Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Jeffrey Bruce
- Columbia University Medical Center, 710 West 168th Street, New York, NY, 10032, USA
| | - Andrew B Lassman
- Columbia University Medical Center, 710 West 168th Street, New York, NY, 10032, USA
| | - Peter Canoll
- Columbia University Medical Center, 710 West 168th Street, New York, NY, 10032, USA
| | - Christian Grommes
- Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Mariza Daras
- Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Eli Diamond
- Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Antonio Omuro
- Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA.,Present address: Yale School of Medicine, 333 Cedar Street, New Haven, CT, 06510, USA
| | - Elena Pentsova
- Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | - Dana E Orange
- Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.,Hospital for Special Surgery, 535 E. 70th Street, New York, NY, 10021, USA
| | - Stephen J Harvey
- IBM Watson Health, NW Broken Sound Bkwy, Boca Raton, FL, 33487, USA
| | - Jerome B Posner
- Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY, 10065, USA
| | | | - Vaidehi Jobanputra
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA.,Columbia University Medical Center, 710 West 168th Street, New York, NY, 10032, USA
| | - Michael C Zody
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA
| | - John Kelly
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | - Laxmi Parida
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | | | - Ajay K Royyuru
- IBM Thomas J. Watson Research Center, Yorktown Heights, NY, 10598, USA
| | - Robert B Darnell
- New York Genome Center, 101 Avenue of the Americas, New York, NY, 10013, USA. .,Laboratory of Molecular Neuro-Oncology, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA. .,Howard Hughes Medical Institute, The Rockefeller University, 1230 York Avenue, New York, NY, 10065, USA.
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132
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Schweizer MT, Antonarakis ES, Bismar TA, Guedes LB, Cheng HH, Tretiakova MS, Vakar-Lopez F, Klemfuss N, Konnick EQ, Mostaghel EA, Hsieh AC, Nelson PS, Yu EY, Montgomery RB, True LD, Epstein JI, Lotan TL, Pritchard CC. Genomic Characterization of Prostatic Ductal Adenocarcinoma Identifies a High Prevalence of DNA Repair Gene Mutations. JCO Precis Oncol 2019; 3. [PMID: 31123724 DOI: 10.1200/po.18.00327] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
PURPOSE Ductal prostate cancer (dPC) is a rare variant of prostatic adenocarcinoma associated with poor outcomes. Although its histopathologic features are well characterized, the underlying molecular hallmarks of this aggressive subtype are not well described. We sought to provide a comprehensive overview of the spectrum of mutations associated with dPC. METHODS Three case series across multiple institutions were assembled. All patients had a diagnosis of dPC, and histopathologic classification was confirmed by an expert genitourinary pathologist. Case series 1 included men who were prospectively enrolled in a tumor sequencing study at the University of Washington (n = 22). Case series 2 and 3 included archival samples from men treated at Johns Hopkins Hospital (n = 21) and University of Calgary (n = 8), respectively. Tumor tissue was sequenced on a targeted next-generation sequencing assay, UW-OncoPlex, according to previously published methods. The frequency of pathogenic/likely pathogenic mutations are reported. RESULTS Overall, 25 patients (49%) had at least one DNA damage repair gene alteration, including seven (14%) with a mismatch repair gene mutation and 16 (31%) with a homologous repair mutation. Germline autosomal dominant mutations were confirmed or suspected in 10 patients (20%). Activating mutations in the PI3K pathway (n = 19; 37%), WNT pathway (n = 16; 31%), and MAPK pathway (n = 8; 16%) were common. CONCLUSION This study strongly suggests that dPCs are enriched for actionable mutations, with approximately 50% of patients demonstrating DNA damage repair pathway alteration(s). Patients with dPC should be offered next-generation sequencing to guide standard-of-care treatment (eg, immune checkpoint inhibitors) or triaged toward an appropriate clinical trial (eg, poly [ADP-ribose] polymerase inhibitors).
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Affiliation(s)
- Michael T Schweizer
- University of Washington, Seattle, WA.,Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | - Heather H Cheng
- University of Washington, Seattle, WA.,Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | | | | | - Elahe A Mostaghel
- University of Washington, Seattle, WA.,Fred Hutchinson Cancer Research Center, Seattle, WA
| | | | | | - Evan Y Yu
- University of Washington, Seattle, WA.,Fred Hutchinson Cancer Research Center, Seattle, WA
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133
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Park VS, Pursell ZF. POLE proofreading defects: Contributions to mutagenesis and cancer. DNA Repair (Amst) 2019; 76:50-59. [PMID: 30818169 PMCID: PMC6467506 DOI: 10.1016/j.dnarep.2019.02.007] [Citation(s) in RCA: 41] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2018] [Revised: 02/14/2019] [Accepted: 02/15/2019] [Indexed: 12/14/2022]
Abstract
DNA polymerases are uniquely poised to contribute to the elevated mutation burdens seen in many human tumors. These mutations can arise through a number of different polymerase-dependent mechanisms, including intrinsic errors made using template DNA and precursor dNTPs free from chemical modifications, misinsertion events opposite chemically damaged template DNA or insertion events using modified nucleotides. While specific DNA repair polymerases have been known to contribute to tumorigenesis, the role of replication polymerases in mutagenesis in human disease has come into sharp focus over the last decade. This review describes how mutations in these replication DNA polymerases help to drive mutagenesis and tumor development, with particular attention to DNA polymerase epsilon. Recent studies using cancer genome sequencing, mutational signature analyses, yeast and mouse models, and the influence of mismatch repair on tumors with DNA polymerase mutations are discussed.
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Affiliation(s)
- Vivian S Park
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA
| | - Zachary F Pursell
- Department of Biochemistry and Molecular Biology, Tulane University School of Medicine, New Orleans, LA, USA; Tulane Cancer Center, Tulane University School of Medicine, 1430 Tulane Ave., New Orleans, LA, USA.
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134
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Xu Q, Uliel-Sibony S, Dunham C, Sarnat H, Flores-Sarnat L, Brunga L, Davidson S, Lo W, Shlien A, Connolly M, Boelman C, Datta A. mTOR Inhibitors as a New Therapeutic Strategy in Treatment Resistant Epilepsy in Hemimegalencephaly: A Case Report. J Child Neurol 2019; 34:132-138. [PMID: 30514132 DOI: 10.1177/0883073818813238] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Hemimegalencephaly is a hamartomatous malformation of one hemisphere. Functional hemispherectomy, the definitive treatment, is associated with significant morbidity and mortality in early infancy. Dysregulation of the mTOR pathway can result in malformations of cortical development, and mTOR inhibitors can effectively reduce seizures in tuberous sclerosis complex. We report a 6-day-old female with hemimegalencephaly and frequent seizures despite 9 antiseizure medications. At 3 months of age, while awaiting hemispherectomy, an mTOR inhibitor, rapamycin, was initiated by the neurologist. After 1 week of treatment, there was >50% reduction in seizures and total seizure burden, and after 2 weeks, development improved, resulting in deferral of surgery by 2.5 months with an increased body weight. Pathology demonstrated cortical dysplasia with upregulation of the mTOR pathway. Deep-sequencing of brain tissue demonstrated 16% mosaicism for a pathogenic de novo MTOR gene mutation. This case exemplifies how mTOR inhibitors could be considered for seizure reduction in patients with hemimegalencephaly while awaiting surgery.
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Affiliation(s)
- Qi Xu
- 1 Division of Neurology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Shimrit Uliel-Sibony
- 1 Division of Neurology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Christopher Dunham
- 2 Department of Pathology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Harvey Sarnat
- 3 Division of Pediatric Neurology, University of Calgary, Alberta Children's Hospital, Calgary, AB, Canada
| | - Laura Flores-Sarnat
- 3 Division of Pediatric Neurology, University of Calgary, Alberta Children's Hospital, Calgary, AB, Canada
| | - Ledia Brunga
- 4 University of Toronto, Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, ON, Canada
| | - Scott Davidson
- 4 University of Toronto, Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, ON, Canada
| | - Winnie Lo
- 4 University of Toronto, Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, ON, Canada
| | - Adam Shlien
- 4 University of Toronto, Program in Genetics and Genome Biology, the Hospital for Sick Children, Toronto, ON, Canada
| | - Mary Connolly
- 1 Division of Neurology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Cyrus Boelman
- 1 Division of Neurology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
| | - Anita Datta
- 1 Division of Neurology, University of British Columbia, BC Children's Hospital, Vancouver, BC, Canada
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135
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Lee MB, Dowsett IT, Carr DT, Wasko BM, Stanton SG, Chung MS, Ghodsian N, Bode A, Kiflezghi MG, Uppal PA, Grayden KA, Elala YC, Tang TT, Tran NHB, Tran THB, Diep AB, Hope M, Promislow DEL, Kennedy SR, Kaeberlein M, Herr AJ. Defining the impact of mutation accumulation on replicative lifespan in yeast using cancer-associated mutator phenotypes. Proc Natl Acad Sci U S A 2019; 116:3062-3071. [PMID: 30718408 PMCID: PMC6386679 DOI: 10.1073/pnas.1815966116] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Mutations accumulate within somatic cells and have been proposed to contribute to aging. It is unclear what level of mutation burden may be required to consistently reduce cellular lifespan. Human cancers driven by a mutator phenotype represent an intriguing model to test this hypothesis, since they carry the highest mutation burdens of any human cell. However, it remains technically challenging to measure the replicative lifespan of individual mammalian cells. Here, we modeled the consequences of cancer-related mutator phenotypes on lifespan using yeast defective for mismatch repair (MMR) and/or leading strand (Polε) or lagging strand (Polδ) DNA polymerase proofreading. Only haploid mutator cells with significant lifetime mutation accumulation (MA) exhibited shorter lifespans. Diploid strains, derived by mating haploids of various genotypes, carried variable numbers of fixed mutations and a range of mutator phenotypes. Some diploid strains with fewer than two mutations per megabase displayed a 25% decrease in lifespan, suggesting that moderate numbers of random heterozygous mutations can increase mortality rate. As mutation rates and burdens climbed, lifespan steadily eroded. Strong diploid mutator phenotypes produced a form of genetic anticipation with regard to aging, where the longer a lineage persisted, the shorter lived cells became. Using MA lines, we established a relationship between mutation burden and lifespan, as well as population doubling time. Our observations define a threshold of random mutation burden that consistently decreases cellular longevity in diploid yeast cells. Many human cancers carry comparable mutation burdens, suggesting that while cancers appear immortal, individual cancer cells may suffer diminished lifespan due to accrued mutation burden.
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Affiliation(s)
- Mitchell B Lee
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Ian T Dowsett
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
- Molecular Medicine and Mechanisms of Disease Program, University of Washington, Seattle, WA 98195-7705
| | - Daniel T Carr
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Brian M Wasko
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
- Department of Biology and Biotechnology, University of Houston-Clear Lake, Houston, TX 77058
| | - Sarah G Stanton
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Michael S Chung
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Niloufar Ghodsian
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Anna Bode
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Michael G Kiflezghi
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
- Molecular Medicine and Mechanisms of Disease Program, University of Washington, Seattle, WA 98195-7705
| | - Priya A Uppal
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | | | - Yordanos C Elala
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Thao T Tang
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Ngoc H B Tran
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Thu H B Tran
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Anh B Diep
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Michael Hope
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Daniel E L Promislow
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
- Department of Biology, University of Washington, Seattle, WA, 98195-1800
| | - Scott R Kennedy
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Matt Kaeberlein
- Department of Pathology, University of Washington, Seattle, WA 98195-7705
| | - Alan J Herr
- Department of Pathology, University of Washington, Seattle, WA 98195-7705;
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136
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Syndrome CMMRD (déficience constitutionnelle des gènes MMR) : bases génétiques et aspects cliniques. Bull Cancer 2019; 106:162-172. [DOI: 10.1016/j.bulcan.2018.10.008] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Revised: 10/02/2018] [Accepted: 10/07/2018] [Indexed: 11/19/2022]
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137
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Galuppini F, Opocher E, Tabori U, Mammi I, Edwards M, Campbell B, Kelly J, Viel A, Quaia M, Rivieri F, D'Avella D, Arcella A, Giangaspero F, Fassan M, Gardiman MP. Concomitant IDH wild-type glioblastoma and IDH1-mutant anaplastic astrocytoma in a patient with constitutional mismatch repair deficiency syndrome. Neuropathol Appl Neurobiol 2019; 44:233-239. [PMID: 29130549 DOI: 10.1111/nan.12450] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2017] [Accepted: 11/02/2017] [Indexed: 02/01/2023]
Affiliation(s)
- F Galuppini
- Surgical Pathology Unit, Department of Medicine (DIMED), University-Hospital of Padua, Padua, Italy
| | - E Opocher
- Pediatric Hematology-Oncology, Department of Woman and Child Health, University-Hospital of Padua, Padua, Italy
| | - U Tabori
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - I Mammi
- Center for the Study of Hereditary Colorectal Cancers, Venetian Oncology Institute, Padua, Italy
| | - M Edwards
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - B Campbell
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - J Kelly
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, ON, Canada
| | - A Viel
- Funcional Onco-Genomics and Genetics, CRO Aviano National Cancer Institute, Aviano, Italy
| | - M Quaia
- Funcional Onco-Genomics and Genetics, CRO Aviano National Cancer Institute, Aviano, Italy
| | - F Rivieri
- Medical Genetic Service, Departmen t of Laboratory, Santa Chiara Hospital, Trento, Italy
| | - D D'Avella
- Neurosurgery Unit, Department of Neurosciences (DNS), Padua University, Padua, Italy
| | | | - F Giangaspero
- IRCCS Neuromed, Pozzilli, Italy.,Department of Radiological, Oncological, and Anatomo-Pathological Science, Sapienza University of Rome, Rome, Italy
| | - M Fassan
- Surgical Pathology Unit, Department of Medicine (DIMED), University-Hospital of Padua, Padua, Italy
| | - M P Gardiman
- Surgical Pathology Unit, Department of Medicine (DIMED), University-Hospital of Padua, Padua, Italy
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138
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Maletzki C, Wiegele L, Nassar I, Stenzel J, Junghanss C. Chemo-immunotherapy improves long-term survival in a preclinical model of MMR-D-related cancer. J Immunother Cancer 2019; 7:8. [PMID: 30630527 PMCID: PMC6329128 DOI: 10.1186/s40425-018-0476-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2018] [Accepted: 12/06/2018] [Indexed: 01/12/2023] Open
Abstract
BACKGROUND Mismatch Repair Deficiency (MMR-D)-related tumors are highly immunogenic and constitute ideal vaccination targets. In a proof-of-concept study delayed tumorigenesis and prolonged survival has been shown in a clinically-relevant mouse model for MMR-D-related diseases (=MLH1 knock out mice). To refine this approach, vaccination was combined with immune modulatory low-dose chemotherapy to polarize immune regulatory subtypes. METHODS Mice (prophylactic: 8-10 weeks; therapeutic: > 36 weeks) received a single injection of cyclophosphamide (CPX, 120 mg/kg bw, i.p.) or gemcitabine (GEM, 100 mg/kg bw, i.p.) prior to vaccination (lysate of a gastrointestinal tumor allograft, 10 mg/kg bw, n = 9 mice/group). The vaccine was given repetitively (10 mg/kg bw, s.c., 4 x / once a week, followed by monthly boosts) until tumor formation or progression. Tumor growth ([18F] FDG PET/CT imaging) and immune responses were monitored (flow cytometry, IFNγ ELISpot). The microenvironment was analyzed by immunofluorescence. RESULTS Prophylactic application of GEM + lysate delayed tumorigenesis compared to lysate monotherapy and CPX-pre-treatment (median time of onset: 53 vs. 47 vs. 48 weeks). 33% of mice even remained tumor-free until the experimental endpoint (= 65 weeks). This was accompanied by long-term effect on cytokine plasma levels; splenic myeloid derived suppressor cells (MDSC) as well as regulatory T cell numbers. Assessment of tumor microenvironment from GEM + lysate treated mice revealed low numbers of MDSCs, but enhanced T cell infiltration, in some cases co-expressing PD-L1. Therapeutic chemo-immunotherapy (GEM + lysate) had minor impact on overall survival (median time: 12 (GEM + lysate) vs. 11.5 (lysate) vs. 3 weeks (control)), but induced complete remission in one case. Dendritic and T cell infiltrates increased in both treatment groups. Reactive T cells specifically recognized MLH1-/- tumor cells in IFNγ ELISpot, but lacked response towards NK cell targets YAC-1. CONCLUSIONS Combined chemo-immunotherapy impairs tumor onset and growth likely attributable to modulation of immune responses. Depleting or 're-educating' immunosuppressive cell types, such as MDSC, may help moving a step closer to combat cancer.
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Affiliation(s)
- Claudia Maletzki
- Department of Medicine, Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany.
| | - Leonie Wiegele
- Department of Medicine, Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Ingy Nassar
- Department of Medicine, Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
| | - Jan Stenzel
- Core Facility Multimodal Small Animal Imaging, Rostock University Medical Center, Schillingallee 69a, 18057, Rostock, Germany
| | - Christian Junghanss
- Department of Medicine, Clinic III - Hematology, Oncology, Palliative Medicine, Rostock University Medical Center, Ernst-Heydemann-Str. 6, 18057, Rostock, Germany
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139
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Shuen AY, Lanni S, Panigrahi GB, Edwards M, Yu L, Campbell BB, Mandel A, Zhang C, Zhukova N, Alharbi M, Bernstein M, Bowers DC, Carroll S, Cole KA, Constantini S, Crooks B, Dvir R, Farah R, Hijiya N, George B, Laetsch TW, Larouche V, Lindhorst S, Luiten RC, Magimairajan V, Mason G, Mason W, Mordechai O, Mushtaq N, Nicholas G, Oren M, Palma L, Pedroza LA, Ramdas J, Samuel D, Wolfe Schneider K, Seeley A, Semotiuk K, Shamvil A, Sumerauer D, Toledano H, Tomboc P, Wierman M, Van Damme A, Lee YY, Zapotocky M, Bouffet E, Durno C, Aronson M, Gallinger S, Foulkes WD, Malkin D, Tabori U, Pearson CE. Functional Repair Assay for the Diagnosis of Constitutional Mismatch Repair Deficiency From Non-Neoplastic Tissue. J Clin Oncol 2019; 37:461-470. [PMID: 30608896 DOI: 10.1200/jco.18.00474] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
PURPOSE Constitutional mismatch repair deficiency (CMMRD) is a highly penetrant cancer predisposition syndrome caused by biallelic mutations in mismatch repair (MMR) genes. As several cancer syndromes are clinically similar, accurate diagnosis is critical to cancer screening and treatment. As genetic diagnosis is confounded by 15 or more pseudogenes and variants of uncertain significance, a robust diagnostic assay is urgently needed. We sought to determine whether an assay that directly measures MMR activity could accurately diagnose CMMRD. PATIENTS AND METHODS In vitro MMR activity was quantified using a 3'-nicked G-T mismatched DNA substrate, which requires MSH2-MSH6 and MLH1-PMS2 for repair. We quantified MMR activity from 20 Epstein-Barr virus-transformed lymphoblastoid cell lines from patients with confirmed CMMRD. We also tested 20 lymphoblastoid cell lines from patients who were suspected for CMMRD. We also characterized MMR activity from patients with neurofibromatosis type 1, Li-Fraumeni syndrome, polymerase proofreading-associated cancer syndrome, and Lynch syndrome. RESULTS All CMMRD cell lines had low MMR activity (n = 20; mean, 4.14 ± 1.56%) relative to controls (n = 6; mean, 44.00 ± 8.65%; P < .001). Repair was restored by complementation with the missing protein, which confirmed MMR deficiency. All cases of patients with suspected CMMRD were accurately diagnosed. Individuals with Lynch syndrome (n = 28), neurofibromatosis type 1 (n = 5), Li-Fraumeni syndrome (n = 5), and polymerase proofreading-associated cancer syndrome (n = 3) had MMR activity that was comparable to controls. To accelerate testing, we measured MMR activity directly from fresh lymphocytes, which yielded results in 8 days. CONCLUSION On the basis of the current data set, the in vitro G-T repair assay was able to diagnose CMMRD with 100% specificity and sensitivity. Rapid diagnosis before surgery in non-neoplastic tissues could speed proper therapeutic management.
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Affiliation(s)
- Andrew Y Shuen
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Stella Lanni
- 2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | | | - Lisa Yu
- 2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Brittany B Campbell
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ariane Mandel
- 2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Cindy Zhang
- 2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nataliya Zhukova
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Mark Bernstein
- 4 Dalhousie University Faculty of Medicine, Halifax, Nova Scotia, Canada
| | - Daniel C Bowers
- 5 University of Texas Southwestern Medical Center, Dallas, TX.,6 Children's Health, Dallas, TX
| | | | - Kristina A Cole
- 8 Children's Hospital of Philadelphia and University of Pennsylvania, Philadelphia, PA
| | - Shlomi Constantini
- 9 Tel Aviv Sourasky Medical Center, Tel Aviv, Israel.,10 Tel Aviv University, Tel Aviv, Israel
| | - Bruce Crooks
- 4 Dalhousie University Faculty of Medicine, Halifax, Nova Scotia, Canada
| | - Rina Dvir
- 10 Tel Aviv University, Tel Aviv, Israel.,11 Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | - Roula Farah
- 12 Saint George Hospital University Medical Center, Beirut, Lebanon
| | - Nobuko Hijiya
- 13 Ann & Robert H. Lurie Children's Hospital/Northwestern University Feinberg School of Medicine, Chicago, IL
| | - Ben George
- 14 Medical College of Wisconsin, Milwaukee, WI
| | - Theodore W Laetsch
- 5 University of Texas Southwestern Medical Center, Dallas, TX.,6 Children's Health, Dallas, TX
| | | | | | | | | | - Gary Mason
- 19 Children's Hospital of Pittsburgh of University of Pittsburgh Medical Center, Pittsburgh, PA
| | - Warren Mason
- 1 University of Toronto, Toronto, Ontario, Canada.,20 Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | | | - Garth Nicholas
- 23 Ottawa Hospital Research Institute, Ottawa, Ontario, Canada
| | | | - Laura Palma
- 25 McGill University Health Centre, Montréal, Quebec, Canada
| | - Luis Alberto Pedroza
- 26 Baylor College of Medicine and Texas Children's Hospital, Houston, TX.,27 Universidad San Francisco de Quito, Quito, Ecuador
| | | | | | - Kami Wolfe Schneider
- 30 Children's Hospital Colorado, Aurora, CO.,31 University of Colorado, Anschutz Medical Campus, Aurora, CO
| | | | | | | | - David Sumerauer
- 34 University Hospital Motol, Charles University, Prague, Czech Republic
| | - Helen Toledano
- 11 Schneider Children's Medical Center of Israel, Petach Tikva, Israel
| | | | | | - An Van Damme
- 36 Université Catholique de Louvain, Brussels, Belgium
| | - Yi-Yen Lee
- 37 Taipei Veterans General Hospital, Taipei, Republic of China
| | - Michal Zapotocky
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada.,34 University Hospital Motol, Charles University, Prague, Czech Republic
| | - Eric Bouffet
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Carol Durno
- 2 The Hospital for Sick Children, Toronto, Ontario, Canada.,32 Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | - Steve Gallinger
- 32 Mount Sinai Hospital, Toronto, Ontario, Canada.,38 Toronto General Hospital, Toronto, Ontario, Canada
| | | | - David Malkin
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Uri Tabori
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Christopher E Pearson
- 1 University of Toronto, Toronto, Ontario, Canada.,2 The Hospital for Sick Children, Toronto, Ontario, Canada
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140
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Larouche V, Atkinson J, Albrecht S, Laframboise R, Jabado N, Tabori U, Bouffet E. Sustained complete response of recurrent glioblastoma to combined checkpoint inhibition in a young patient with constitutional mismatch repair deficiency. Pediatr Blood Cancer 2018; 65:e27389. [PMID: 30160041 DOI: 10.1002/pbc.27389] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/04/2018] [Revised: 07/16/2018] [Accepted: 07/18/2018] [Indexed: 02/01/2023]
Affiliation(s)
- Valerie Larouche
- Department of Paediatrics, Centre mère-enfant Soleil du CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - J Atkinson
- Department of Neurosurgery, Montreal Children's Hospital, Montréal, Quebec, Canada
| | - S Albrecht
- Department of Pathology, McGill University Health Center, McGill University, Montreal, Quebec, Canada
| | - R Laframboise
- Department of Paediatrics, Centre mère-enfant Soleil du CHU de Québec-Université Laval, Quebec City, Quebec, Canada
| | - N Jabado
- Department of Paediatrics, McGill University Health Center, McGill University, Montreal, Quebec, Canada
| | - U Tabori
- Department of Haematology-Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,The Arthur and Sonia Labbatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - E Bouffet
- Department of Haematology-Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
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141
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Abstract
PURPOSE OF REVIEW The risk of cancer is higher, and its outcome is worse in patients with primary immunodeficiency (PID) than in members of the general population. Thus, the inter-relationship of malignant diseases with PIDs requires more study. RECENT FINDINGS Large genetic screens identified a vast number of germline mutations in childhood cancer patient samples. Although TP53 was the most frequent single gene identified as mutated, many PID disorders like DNA repair defects are among the inborn causes of childhood cancer. We provide a comprehensive analysis of compiled data from seven recent studies that focused on germline genetic landscapes and preexisting conditions in pediatric oncology. As potentially causal germline variants were identified in ≈8% of malignancies in children and adolescents, we visualized this proportion as the 'tips of the icebergs'. The results of additional network analyses showed the shared patterns of germline mutations in various malignancies and yielded a spatial distribution of the 'icebergs'. SUMMARY The 'iceberg map of germline mutations in childhood cancers' was created to increase the awareness of the inborn genetic underpinnings of childhood malignancies and their relationships with immunodeficiencies. Needs and perspectives of clinical immunologists and pediatric oncologists to both improve patient care and guide research at this critical interface are discussed. VIDEO ABSTRACT.
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142
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Pathak SJ, Mueller JL, Okamoto K, Das B, Hertecant J, Greenhalgh L, Cole T, Pinsk V, Yerushalmi B, Gurkan OE, Yourshaw M, Hernandez E, Oesterreicher S, Naik S, Sanderson IR, Axelsson I, Agardh D, Boland CR, Martin MG, Putnam CD, Sivagnanam M. EPCAM mutation update: Variants associated with congenital tufting enteropathy and Lynch syndrome. Hum Mutat 2018; 40:142-161. [PMID: 30461124 PMCID: PMC6328345 DOI: 10.1002/humu.23688] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Revised: 10/24/2018] [Accepted: 11/14/2018] [Indexed: 12/30/2022]
Abstract
The epithelial cell adhesion molecule gene (EPCAM, previously known as TACSTD1 or TROP1) encodes a membrane‐bound protein that is localized to the basolateral membrane of epithelial cells and is overexpressed in some tumors. Biallelic mutations in EPCAM cause congenital tufting enteropathy (CTE), which is a rare chronic diarrheal disorder presenting in infancy. Monoallelic deletions of the 3′ end of EPCAM that silence the downstream gene, MSH2, cause a form of Lynch syndrome, which is a cancer predisposition syndrome associated with loss of DNA mismatch repair. Here, we report 13 novel EPCAM mutations from 17 CTE patients from two separate centers, review EPCAM mutations associated with CTE and Lynch syndrome, and structurally model pathogenic missense mutations. Statistical analyses indicate that the c.499dupC (previously reported as c.498insC) frameshift mutation was associated with more severe treatment regimens and greater mortality in CTE, whereas the c.556‐14A>G and c.491+1G>A splice site mutations were not correlated with treatments or outcomes significantly different than random simulation. These findings suggest that genotype–phenotype correlations may be useful in contributing to management decisions of CTE patients. Depending on the type and nature of EPCAM mutation, one of two unrelated diseases may occur, CTE or Lynch syndrome.
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Affiliation(s)
- Sagar J Pathak
- Department of Pediatrics, University of California, San Diego, La Jolla, California.,Rady Children's Hospital, San Diego, California
| | - James L Mueller
- Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Kevin Okamoto
- Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Barun Das
- Department of Pediatrics, University of California, San Diego, La Jolla, California
| | - Jozef Hertecant
- Genetics/Metabolics Service, Tawam Hospital, Al Ain, United Arab Emirates
| | | | - Trevor Cole
- West Midlands Regional Genetics Service and Birmingham Health Partners, Birmingham Women's Hospital, Birmingham, UK
| | - Vered Pinsk
- Division of Pediatrics, Pediatric Gastroenterology Unit, Soroka University Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Baruch Yerushalmi
- Division of Pediatrics, Pediatric Gastroenterology Unit, Soroka University Medical Center and Faculty of Health Sciences, Ben-Gurion University of the Negev, Beer-Sheva, Israel
| | - Odul E Gurkan
- Department of Pediatrics, Gazi University School of Medicine, Ankara, Turkey
| | - Michael Yourshaw
- Department of Human Genetics, University of California, Los Angeles, Los Angeles, California
| | - Erick Hernandez
- Pediatric Gastroenterology, Miami Children's Health System, Miami, Florida
| | | | - Sandhia Naik
- Paediatric Gastroenterology, Barts and the London School of Medicine, London, UK
| | - Ian R Sanderson
- Paediatric Gastroenterology, Barts and the London School of Medicine, London, UK
| | - Irene Axelsson
- Department of Pediatrics, Skane University Hospital, Malmo, Sweden
| | - Daniel Agardh
- Department of Clinical Sciences, Lund University, Skane University Hospital, Malmo, Sweden
| | - C Richard Boland
- Department of Medicine, University of California, San Diego, La Jolla, California
| | - Martin G Martin
- Department of Pediatrics, University of California, Los Angeles, Los Angeles, California
| | - Christopher D Putnam
- Department of Medicine, University of California, San Diego, La Jolla, California.,San Diego Branch, Ludwig Institute for Cancer Research, La Jolla, California
| | - Mamata Sivagnanam
- Department of Pediatrics, University of California, San Diego, La Jolla, California.,Rady Children's Hospital, San Diego, California
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143
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Single-cell analysis identifies CRLF2 rearrangements as both early and late events in Down syndrome and non-Down syndrome acute lymphoblastic leukaemia. Leukemia 2018; 33:893-904. [PMID: 30487598 PMCID: PMC6398588 DOI: 10.1038/s41375-018-0297-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2018] [Revised: 09/19/2018] [Accepted: 09/24/2018] [Indexed: 12/23/2022]
Abstract
Deregulated expression of the type I cytokine receptor, CRLF2, is observed in 5-15% of precursor B-cell acute lymphoblastic leukaemia (B-ALL). We have previously reported the genomic landscape of patients with CRLF2 rearrangements (CRLF2-r) using both whole genome and exome sequencing, which identified a number of potential clonal and sub-clonal genomic alterations. In this study, we aimed to assess when the CRLF2-r; IGH-CRLF2 or P2RY8-CRLF2, arose during the evolution of both Down syndrome-ALL (DS-ALL) and non-DS-ALL. Using fluorescence in situ hybridisation, we were able to track up to four structural variants in single cells from 47 CRLF2-r B-ALL patients, which in association with our multiplex single cell analysis of a further four patients, permitted simultaneous tracking of copy number alterations, structural and single nucleotide variants within individual cells. We observed CRLF2-r arising as both early and late events in DS and non-DS-ALL patients. Parallel evolution of discrete clones was observed in the development of CRLF2-r B-ALL, either involving the CRLF2-r or one of the other tracked abnormalities. In depth single cell analysis identified both linear and branching evolution with early clones harbouring a multitude of abnormalities, including the CRLF2-r in DS-ALL patients.
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144
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Castellsagué E, Li R, Aligue R, González S, Sanz J, Martin E, Velasco À, Capellá G, Stewart CJR, Vidal A, Majewski J, Rivera B, Polak P, Matias-Guiu X, Brunet J, Foulkes WD. Novel POLE pathogenic germline variant in a family with multiple primary tumors results in distinct mutational signatures. Hum Mutat 2018; 40:36-41. [PMID: 30362666 DOI: 10.1002/humu.23676] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2018] [Revised: 10/17/2018] [Accepted: 10/20/2018] [Indexed: 12/21/2022]
Abstract
We describe a family in which four siblings exhibited multiple or classic colonic polyposis with or without colorectal carcinoma (CRC). One female developed three primary tumors, including CRC and carcinomas of the ovary and breast. Whole-exome sequencing of germline DNA from affected and unaffected individuals revealed a novel missense mutation in the exonuclease domain of POLE (c.833C>A; p.Thr278Lys) associated with a highly penetrant, autosomal-dominant inheritance pattern. Functional studies in yeast and demonstration of a high mutational burden in the available tumors confirmed the pathogenicity of the novel variant. Prominent POLE-deficient somatic mutational signatures were seen in the CRCs, but in contrast, a mutational signature typical of concomitant tumoral loss of POLE and mismatch-repair function (POLE-exo* /MSI) was noted in the breast cancer. The breast cancer also showed distinctive pathological characteristics that reflect the presence of both the germline POLE variant and the secondary somatic MMR alterations.
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Affiliation(s)
- Ester Castellsagué
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Medical Genetics, The Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Translational Research Laboratory, Catalan Institute of Oncology, IDIBELL, Barcelona, Spain
| | - Rui Li
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Rosa Aligue
- Biomedical Sciences Department, School of Medicine, University de Barcelona, IDIBAPS, Barcelona, Spain
| | - Sara González
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Barcelona, Spain
| | - Judit Sanz
- Genetic Counselling Unit, Hospital Universitari de Vic, Barcelona, Spain
| | - Edgar Martin
- Biomedical Sciences Department, School of Medicine, University de Barcelona, IDIBAPS, Barcelona, Spain
| | - Àngela Velasco
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGI, Girona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Barcelona, Spain
| | - Colin J R Stewart
- Department of Histopathology, King Edward Memorial Hospital, and School for Women's and Infants' Health, University of Western Australia, Perth, Australia
| | - August Vidal
- Department of Pathology, Hospital de Bellvitge, CIBERONC, Barcelona, Spain
| | - Jacek Majewski
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Barbara Rivera
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Medical Genetics and Cancer Research Program, Research Institute McGill University Health Centre, Montreal, Quebec, Canada
| | - Paz Polak
- Icahn School of Medicine at Mount Sinai, Department of Oncological Sciences, Mount Sinai Hospital, New York City, New York
| | - Xavier Matias-Guiu
- Department of Pathology, Hospital de Bellvitge, CIBERONC, Barcelona, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, IDIBELL, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, IDIBGI, Girona, Spain.,Medical Sciences Department, School of Medicine, University of Girona, Girona, Spain
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Medical Genetics, The Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Medical Genetics and Cancer Research Program, Research Institute McGill University Health Centre, Montreal, Quebec, Canada.,Program in Cancer Genetics, Department of Oncology and Human Genetics, McGill University, Montreal, Quebec, Canada
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145
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Germano G, Amirouchene-Angelozzi N, Rospo G, Bardelli A. The Clinical Impact of the Genomic Landscape of Mismatch Repair-Deficient Cancers. Cancer Discov 2018; 8:1518-1528. [PMID: 30442708 DOI: 10.1158/2159-8290.cd-18-0150] [Citation(s) in RCA: 71] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2018] [Revised: 06/06/2018] [Accepted: 09/04/2018] [Indexed: 11/16/2022]
Abstract
The mismatch repair (MMR) system which detects and corrects base mismatches and insertions and deletions that occur during DNA synthesis is deregulated in approximately 20% of human cancers. MMR-deficient tumors have peculiar properties, including early-onset metastatic potential but generally favorable prognosis, and remarkable response to immune therapy. The functional basis of these atypical clinical features has recently started to be elucidated. Here, we discuss how the biological and clinical features of MMR-deficient tumors might be traced back to their ability to continuously produce new somatic mutations, leading to increased levels of neoantigens, which in turn stimulate immune surveillance. SIGNIFICANCE: Tumors carrying defects in DNA MMR accumulate high levels of mutations, a feature linked to rapid tumor progression and acquisition of drug resistance but also favorable prognosis and response to immune-checkpoint blockade. We discuss how the genomic landscape of MMR-deficient tumors affects their biological and clinical behaviors.
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Affiliation(s)
- Giovanni Germano
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy.,Department of Oncology, University of Torino, Candiolo, Torino, Italy
| | | | | | - Alberto Bardelli
- Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Torino, Italy. .,Department of Oncology, University of Torino, Candiolo, Torino, Italy
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146
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Suerink M, Ripperger T, Messiaen L, Menko FH, Bourdeaut F, Colas C, Jongmans M, Goldberg Y, Nielsen M, Muleris M, van Kouwen M, Slavc I, Kratz C, Vasen HF, Brugiѐres L, Legius E, Wimmer K. Constitutional mismatch repair deficiency as a differential diagnosis of neurofibromatosis type 1: consensus guidelines for testing a child without malignancy. J Med Genet 2018; 56:53-62. [PMID: 30415209 DOI: 10.1136/jmedgenet-2018-105664] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 10/05/2018] [Accepted: 10/10/2018] [Indexed: 12/15/2022]
Abstract
Constitutional mismatch repair deficiency (CMMRD) is a rare childhood cancer predisposition syndrome caused by biallelic germline mutations in one of four mismatch-repair genes. Besides very high tumour risks, CMMRD phenotypes are often characterised by the presence of signs reminiscent of neurofibromatosis type 1 (NF1). Because NF1 signs may be present prior to tumour onset, CMMRD is a legitimate differential diagnosis in an otherwise healthy child suspected to have NF1/Legius syndrome without a detectable underlying NF1/SPRED1 germline mutation. However, no guidelines indicate when to counsel and test for CMMRD in this setting. Assuming that CMMRD is rare in these patients and that expected benefits of identifying CMMRD prior to tumour onset should outweigh potential harms associated with CMMRD counselling and testing in this setting, we aimed at elaborating a strategy to preselect, among children suspected to have NF1/Legius syndrome without a causative NF1/SPRED1 mutation and no overt malignancy, those children who have a higher probability of having CMMRD. At an interdisciplinary workshop, we discussed estimations of the frequency of CMMRD as a differential diagnosis of NF1 and potential benefits and harms of CMMRD counselling and testing in a healthy child with no malignancy. Preselection criteria and strategies for counselling and testing were developed and reviewed in two rounds of critical revisions. Existing diagnostic CMMRD criteria were adapted to serve as a guideline as to when to consider CMMRD as differential diagnosis of NF1/Legius syndrome. In addition, counselling and testing strategies are suggested to minimise potential harms.
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Affiliation(s)
- Manon Suerink
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Tim Ripperger
- Department of Human Genetics, Hannover Medical School, Hannover, Germany
| | - Ludwine Messiaen
- Department of Genetics, University of Alabama, Birmingham, Alabama, USA
| | - Fred H Menko
- Family Cancer Clinic, Antoni van Leeuwenhoek Hospital and The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - Franck Bourdeaut
- Département d'Oncologie Pédiatrique et d'Adolescents Jeunes Adultes, Institut Curie, Paris, France
| | - Chrystelle Colas
- Department of Genetics, Institut Curie, Paris Sciences Lettres Research University, Paris, France.,Centre de Recherche Saint-Antoine, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Paris, France
| | - Marjolijn Jongmans
- Princess Máxima Center for Pediatric Oncology, Utrecht, The Netherlands.,Department of Genetics, University Medical Center Utrecht, Utrecht, The Netherlands
| | - Yael Goldberg
- Recanati Genetics Institute, Beilinson Hospital, Rabin Medical Center, Petah Tikva, Israel
| | - Maartje Nielsen
- Department of Clinical Genetics, Leiden University Medical Centre, Leiden, The Netherlands
| | - Martine Muleris
- Centre de Recherche Saint-Antoine, Sorbonne Universités, UPMC Univ Paris 06, INSERM, CNRS, Paris, France
| | - Mariëtte van Kouwen
- Department of Gastroenterology and Hepatology, Radboud University Medical Center, Nijmegen, The Netherlands
| | - Irene Slavc
- Department of Pediatrics, Medical University Vienna, Vienna, Austria
| | - Christian Kratz
- Pediatric Hematology and Oncology, Hannover Medical School, Hannover, Germany
| | - Hans F Vasen
- Department of Gastroenterology and Hepatology, Leiden University Medical Center, Leiden, The Netherlands
| | - Laurence Brugiѐres
- Children and Adolescent Oncology Department, Gustave Roussy Cancer Institute, Villejuif, France
| | - Eric Legius
- Department of Human Genetics, University Hospital Leuven and KU Leuven, Leuven, Belgium
| | - Katharina Wimmer
- Division of Human Genetics, Medical University Innsbruck, Innsbruck, Austria
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147
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Walsh MF, Ritter DI, Kesserwan C, Sonkin D, Chakravarty D, Chao E, Ghosh R, Kemel Y, Wu G, Lee K, Kulkarni S, Hedges D, Mandelker D, Ceyhan-Birsoy O, Luo M, Drazer M, Zhang L, Offit K, Plon SE. Integrating somatic variant data and biomarkers for germline variant classification in cancer predisposition genes. Hum Mutat 2018; 39:1542-1552. [PMID: 30311369 PMCID: PMC6310222 DOI: 10.1002/humu.23640] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2018] [Revised: 08/29/2018] [Accepted: 08/30/2018] [Indexed: 12/20/2022]
Abstract
In its landmark paper about Standards and Guidelines for the Interpretation of Sequence Variants, the American College of Medical Genetics and Genomics (ACMG), and Association for Molecular Pathology (AMP) did not address how to use tumor data when assessing the pathogenicity of germline variants. The Clinical Genome Resource (ClinGen) established a multidisciplinary working group, the Germline/Somatic Variant Subcommittee (GSVS) with this focus. The GSVS implemented a survey to determine current practices of integrating somatic data when classifying germline variants in cancer predisposition genes. The GSVS then reviewed and analyzed available resources of relevant somatic data, and performed integrative germline variant curation exercises. The committee determined that somatic hotspots could be systematically integrated into moderate evidence of pathogenicity (PM1). Tumor RNA sequencing data showing altered splicing may be considered as strong evidence in support of germline pathogenicity (PVS1) and tumor phenotypic features such as mutational signatures be considered supporting evidence of pathogenicity (PP4). However, at present, somatic data such as focal loss of heterozygosity and mutations occurring on the alternative allele are not recommended to be systematically integrated, instead, incorporation of this type of data should take place under the advisement of multidisciplinary cancer center tumor-normal sequencing boards.
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Affiliation(s)
- Michael F Walsh
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | | | | | | | | | | | | | - Yelena Kemel
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Gang Wu
- St. Jude Children's Hospital, Memphis, Tennessee, USA
| | - Kristy Lee
- University of North Carolina, Chapel Hill, North Carolina, USA
| | | | - Dale Hedges
- St. Jude Children's Hospital, Memphis, Tennessee, USA
| | - Diana Mandelker
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | | | - Minjie Luo
- Children's Hospital of Philadelphia, Philadelphia, Pennsylvania, USA
| | | | - Liying Zhang
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
| | - Kenneth Offit
- Memorial Sloan Kettering Cancer Center, New York City, New York, USA
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148
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Tomkova M, Tomek J, Kriaucionis S, Schuster-Böckler B. Mutational signature distribution varies with DNA replication timing and strand asymmetry. Genome Biol 2018; 19:129. [PMID: 30201020 PMCID: PMC6130095 DOI: 10.1186/s13059-018-1509-y] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2018] [Accepted: 08/16/2018] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND DNA replication plays an important role in mutagenesis, yet little is known about how it interacts with other mutagenic processes. Here, we use somatic mutation signatures-each representing a mutagenic process-derived from 3056 patients spanning 19 cancer types to quantify the strand asymmetry of mutational signatures around replication origins and between early and late replicating regions. RESULTS We observe that most of the detected mutational signatures are significantly correlated with the timing or direction of DNA replication. The properties of these associations are distinct for different signatures and shed new light on several mutagenic processes. For example, our results suggest that oxidative damage to the nucleotide pool substantially contributes to the mutational landscape of esophageal adenocarcinoma. CONCLUSIONS Together, our results indicate an interaction between DNA replication, the associated damage repair, and most mutagenic processes.
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Affiliation(s)
- Marketa Tomkova
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Jakub Tomek
- Department of Physiology, Anatomy and Genetics, University of Oxford, Oxford, OX1 3PT, UK
| | - Skirmantas Kriaucionis
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK
| | - Benjamin Schuster-Böckler
- Ludwig Cancer Research Oxford, University of Oxford, Old Road Campus Research Building, Oxford, OX3 7DQ, UK.
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149
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Anderson ND, de Borja R, Young MD, Fuligni F, Rosic A, Roberts ND, Hajjar S, Layeghifard M, Novokmet A, Kowalski PE, Anaka M, Davidson S, Zarrei M, Id Said B, Schreiner LC, Marchand R, Sitter J, Gokgoz N, Brunga L, Graham GT, Fullam A, Pillay N, Toretsky JA, Yoshida A, Shibata T, Metzler M, Somers GR, Scherer SW, Flanagan AM, Campbell PJ, Schiffman JD, Shago M, Alexandrov LB, Wunder JS, Andrulis IL, Malkin D, Behjati S, Shlien A. Rearrangement bursts generate canonical gene fusions in bone and soft tissue tumors. Science 2018; 361:eaam8419. [PMID: 30166462 PMCID: PMC6176908 DOI: 10.1126/science.aam8419] [Citation(s) in RCA: 98] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2017] [Revised: 03/19/2018] [Accepted: 07/13/2018] [Indexed: 12/25/2022]
Abstract
Sarcomas are cancers of the bone and soft tissue often defined by gene fusions. Ewing sarcoma involves fusions between EWSR1, a gene encoding an RNA binding protein, and E26 transformation-specific (ETS) transcription factors. We explored how and when EWSR1-ETS fusions arise by studying the whole genomes of Ewing sarcomas. In 52 of 124 (42%) of tumors, the fusion gene arises by a sudden burst of complex, loop-like rearrangements, a process called chromoplexy, rather than by simple reciprocal translocations. These loops always contained the disease-defining fusion at the center, but they disrupted multiple additional genes. The loops occurred preferentially in early replicating and transcriptionally active genomic regions. Similar loops forming canonical fusions were found in three other sarcoma types. Chromoplexy-generated fusions appear to be associated with an aggressive form of Ewing sarcoma. These loops arise early, giving rise to both primary and relapse Ewing sarcoma tumors, which can continue to evolve in parallel.
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Affiliation(s)
- Nathaniel D Anderson
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Richard de Borja
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matthew D Young
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Fabio Fuligni
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrej Rosic
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nicola D Roberts
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Simon Hajjar
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mehdi Layeghifard
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ana Novokmet
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Paul E Kowalski
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Matthew Anaka
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Scott Davidson
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Mehdi Zarrei
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Badr Id Said
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - L Christine Schreiner
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Remi Marchand
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Joseph Sitter
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Nalan Gokgoz
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
| | - Ledia Brunga
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Garrett T Graham
- Department of Oncology and Pediatrics, Georgetown University, Washington, DC, USA
| | - Anthony Fullam
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
| | - Nischalan Pillay
- University College London Cancer Institute, Huntley Street, London, UK
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, UK
| | - Jeffrey A Toretsky
- Department of Oncology and Pediatrics, Georgetown University, Washington, DC, USA
| | - Akihiko Yoshida
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Tatsuhiro Shibata
- Division of Cancer Genomics, National Cancer Center Research Institute, Tokyo, Japan
- Laboratory of Molecular Medicine, Human Genome Center, The Institute of Medical Sciences, The University of Tokyo, Minato-ku, Tokyo, Japan
| | - Markus Metzler
- Department of Pediatrics and Adolescent Medicine, University Hospital Erlangen, Erlangen, Germany
| | - Gino R Somers
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Pathology, Hospital for Sick Children, University of Toronto, Toronto, Ontario, Canada
| | - Stephen W Scherer
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
- The Centre for Applied Genomics, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
- The McLaughlin Centre, University of Toronto, Toronto, Ontario, Canada
| | - Adrienne M Flanagan
- Histopathology, Royal National Orthopaedic Hospital NHS Trust, Stanmore, Middlesex, UK
- Department of Pathology and Clinical Laboratories, National Cancer Center Hospital, Tokyo, Japan
| | - Peter J Campbell
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK
- Department of Haematology, University of Cambridge, Cambridge, UK
| | - Joshua D Schiffman
- Departments of Pediatrics and Oncological Sciences, Huntsman Cancer Institute, University of Utah, Salt Lake City, UT, USA
| | - Mary Shago
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Ludmil B Alexandrov
- Department of Cellular and Molecular Medicine and Department of Bioengineering and Moores Cancer Center, University of California, La Jolla, San Diego, CA, USA
| | - Jay S Wunder
- University Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario, Canada
- Division of Orthopaedic Surgery, Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Irene L Andrulis
- Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario, Canada
- Department of Molecular Genetics, University of Toronto, Toronto, Ontario, Canada
| | - David Malkin
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Division of Hematology-Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada
- Department of Pediatrics, University of Toronto, Ontario, Canada
| | - Sam Behjati
- Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridgeshire, UK.
- Department of Paediatrics, University of Cambridge, Cambridge, UK
| | - Adam Shlien
- Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada.
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
- Department of Paediatric Laboratory Medicine, The Hospital for Sick Children, Toronto, Ontario, Canada
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Majumder S, Shah R, Elias J, Manoharan M, Shah P, Kumari A, Chakraborty P, Kode V, Mistry Y, Coral K, Mittal B, Sm SM, Mahadevan L, Gupta R, Chaudhuri A, Khanna-Gupta A. A cancer vaccine approach for personalized treatment of Lynch Syndrome. Sci Rep 2018; 8:12122. [PMID: 30108227 PMCID: PMC6092430 DOI: 10.1038/s41598-018-30466-x] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 07/30/2018] [Indexed: 12/30/2022] Open
Abstract
Lynch syndrome (LS) is a cancer predisposition disorder wherein patients have a 70–80% lifetime risk of developing colorectal cancers (CRC). Finding germline mutations in predisposing genes allows for risk assessment of CRC development. Here we report a germline heterozygous frame-shift mutation in the mismatch repair MLH1 gene which was identified in members of two unrelated LS families. Since defects in DNA mismatch repair genes generate frame-shift mutations giving rise to highly immunogenic neoepitopes, we postulated that vaccination with these mutant peptide antigens could offer promising treatment options to LS patients. To this end we performed whole-exome and RNA seq analysis on the blood and tumour samples from an LS-CRC patient, and used our proprietary neoepitope prioritization pipeline OncoPeptVAC to select peptides, and confirm their immunogenicity in an ex vivo CD8+ T cell activation assay. Three neoepitopes derived from the tumour of this patient elicited a potent CD8+ T cell response. Furthermore, analysis of the tumour-associated immune infiltrate revealed CD8+ T cells expressing low levels of activation markers, suggesting mechanisms of immune suppression at play in this relapsed tumour. Taken together, our study paves the way towards development of a cancer vaccine to treat or delay the onset/relapse of LS-CRC.
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Affiliation(s)
| | | | - Jisha Elias
- MedGenome Labs Ltd., Bangalore, India.,KCHRC, Muni Seva Ashram, Goraj, Gujarat, India
| | | | | | | | | | | | | | | | | | | | | | | | - Amitabha Chaudhuri
- MedGenome Labs Ltd., Bangalore, India. .,MedGenome Inc, Foster City, CA, USA.
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