1
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Nakamichi K, Stacey A, Mustafi D. Targeted long-read sequencing allows for rapid identification of pathogenic disease-causing variants in retinoblastoma. Ophthalmic Genet 2022; 43:762-770. [PMID: 36325802 DOI: 10.1080/13816810.2022.2141797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Identification of disease-causing variants of the retinoblastoma gene (RB1), the predominant cause of retinoblastoma, is challenging. Targeted long-read genome sequencing offers a novel approach to resolve the diverse range of pathogenic variants in RB1 and provides haplotype information rapidly. MATERIALS AND METHODS Genomic DNA was isolated from a venipuncture blood draw of a retinoblastoma patient. Whole genome sequencing (WGS) was carried out using the short-read Ilumina platform. WGS and targeted sequencing of RB1 was accomplished using the long-read Oxford Nanopore Technologies (ONT) platform. Deep-learning frameworks allowed haplotagging, variant calling, and variant annotation of both short- and long-read data. RESULTS Targeted long-read sequencing of the RB1 gene allowed for enhanced depth of read coverage for discovery of rare variants and haplotype analysis. A duplication leading to a frameshift and early termination in RB1 was identified as the most deleterious variant by all sequencing methods, with long-read technology providing additional information of methylation signal and haplotype information. More importantly, there was greater than 98% concordance of RB1 variants identified between short-read and targeted long-read sequencing modalities. CONCLUSIONS Targeted long-read technology allows for focused sequencing effort for variant discovery. Application of this for the first time in a retinoblastoma patient allowed haplotagged variant identification and demonstrated excellent concordance with benchmark short-read sequencing. The added benefit of targeted long-read sequencing to resolve disease-causing genomic variation in RB1 rapidly from a blood draw will provide a more definitive diagnosis of heritable RB and guide management decisions for patients and their families.
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Affiliation(s)
- Kenji Nakamichi
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, USA
| | - Andrew Stacey
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, USA.,Department of Ophthalmology, Seattle Children's Hospital, Seattlees, WA, USA
| | - Debarshi Mustafi
- Department of Ophthalmology and Roger and Karalis Johnson Retina Center, University of Washington, Seattle, WA, USA.,Department of Ophthalmology, Seattle Children's Hospital, Seattlees, WA, USA.,Brotman Baty Institute for Precision Medicine, Seattle, WA, USA
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2
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Chen JL, Miller DT, Schmidt LS, Malkin D, Korf BR, Eng C, Kwiatkowski DJ, Giannikou K. Mosaicism in Tumor Suppressor Gene Syndromes: Prevalence, Diagnostic Strategies, and Transmission Risk. Annu Rev Genomics Hum Genet 2022; 23:331-361. [PMID: 36044908 DOI: 10.1146/annurev-genom-120121-105450] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
A mosaic state arises when pathogenic variants are acquired in certain cell lineages during postzygotic development, and mosaic individuals may present with a generalized or localized phenotype. Here, we review the current state of knowledge regarding mosaicism for eight common tumor suppressor genes-NF1, NF2, TSC1, TSC2, PTEN, VHL, RB1, and TP53-and their related genetic syndromes/entities. We compare and discuss approaches for comprehensive diagnostic genetic testing, the spectrum of variant allele frequency, and disease severity. We also review affected individuals who have no mutation identified after conventional genetic analysis, as well as genotype-phenotype correlations and transmission risk for each tumor suppressor gene in full heterozygous and mosaic patients. This review provides new insight into similarities as well as marked differences regarding the appreciation of mosaicism in these tumor suppressor syndromes.
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Affiliation(s)
- Jillian L Chen
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Boston University School of Medicine, Boston, Massachusetts, USA
| | - David T Miller
- Division of Genetics and Genomics, Boston Children's Hospital and Harvard Medical School, Boston, Massachusetts, USA
| | - Laura S Schmidt
- Urologic Oncology Branch, National Cancer Institute, National Institutes of Health, Bethesda, Maryland, USA.,Basic Science Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland, USA
| | - David Malkin
- Division of Haematology/Oncology, The Hospital for Sick Children, Toronto, Ontario, Canada.,Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada
| | - Bruce R Korf
- Department of Genetics, University of Alabama at Birmingham, Birmingham, Alabama, USA
| | - Charis Eng
- Genomic Medicine Institute, Lerner Research Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Taussig Cancer Institute, Cleveland Clinic, Cleveland, Ohio, USA.,Department of Genetics and Genome Sciences, Case Western Reserve University School of Medicine, Cleveland, Ohio, USA.,Germline High Risk Cancer Focus Group, Case Comprehensive Cancer Center, Case Western Reserve University, Cleveland, Ohio, USA
| | - David J Kwiatkowski
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA;
| | - Krinio Giannikou
- Cancer Genetics Laboratory, Division of Pulmonary and Critical Care Medicine and Division of Genetics, Brigham and Women's Hospital and Harvard Medical School, Boston, Massachusetts, USA; .,Division of Hematology and Oncology, Cancer and Blood Disease Institute, Children's Hospital Los Angeles, Los Angeles, California, USA;
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3
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Zaletaev DV, Nemtsova MV, Strelnikov VV. Epigenetic Regulation Disturbances on Gene Expression in Imprinting Diseases. Mol Biol 2022. [DOI: 10.1134/s0026893321050149] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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4
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Le Gall J, Dehainault C, Benoist C, Matet A, Lumbroso-Le Rouic L, Aerts I, Jiménez I, Schleiermacher G, Houdayer C, Radvanyi F, Frouin E, Renault V, Doz F, Stoppa-Lyonnet D, Gauthier-Villars M, Cassoux N, Golmard L. Highly Sensitive Detection Method of Retinoblastoma Genetic Predisposition and Biomarkers. J Mol Diagn 2021; 23:1714-1721. [PMID: 34656762 DOI: 10.1016/j.jmoldx.2021.08.014] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2021] [Revised: 07/15/2021] [Accepted: 08/18/2021] [Indexed: 12/14/2022] Open
Abstract
Retinoblastoma is a malignant tumor of the infant retina. Nearly half of patients are predisposed to retinoblastoma by a germline RB1 pathogenic variant. Nonhereditary retinoblastoma is mainly caused by inactivation of both RB1 alleles at a somatic level. Several polymorphisms have been reported as biomarkers of retinoblastoma risk, aggressiveness, or invasion. The most informative genetic testing is obtained from tumor DNA. Historically, access to tumor DNA has been warranted by the frequent indication of enucleation, which has decreased because of advances in conservative approaches. Recent studies showed that tumor cell-free DNA can be analyzed in aqueous humor from retinoblastoma patients. This report describes a next-generation sequencing method relying on unique molecular identifiers for a highly sensitive detection of retinoblastoma genetic predisposition and biomarkers in a single analysis. It is the first use of unique molecular identifiers for retinoblastoma genetics. This gene panel enables the detection of RB1 point variants, large genome rearrangements, and loss of heterozygosity. It is adapted for genomic DNA extracted from blood or tumor DNA extracted from tumor fragment, aqueous humor, or plasma. The access to tumor cell-free DNA improves the diagnosis of genetic predisposition in case of conservative ocular therapy and provides access to biomarkers guiding the treatment strategy. The analysis of a gene panel is cost-effective and can be easily implemented in diagnostic laboratories.
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Affiliation(s)
- Jessica Le Gall
- Department of Genetics, Institut Curie, Paris, France; PSL Research University, Paris, France
| | - Catherine Dehainault
- Department of Genetics, Institut Curie, Paris, France; PSL Research University, Paris, France
| | - Camille Benoist
- PSL Research University, Paris, France; Bioinformatics Unit, Institut Curie, Paris, France
| | - Alexandre Matet
- Department of Ocular Oncology, Institut Curie, Paris, France; Université de Paris, Paris, France
| | - Livia Lumbroso-Le Rouic
- PSL Research University, Paris, France; Department of Ophthalmology, Institut Curie, Paris, France
| | - Isabelle Aerts
- PSL Research University, Paris, France; Oncology Center SIREDO, Institut Curie, Paris, France
| | - Irene Jiménez
- PSL Research University, Paris, France; Oncology Center SIREDO, Institut Curie, Paris, France; INSERM U830, Institut Curie, Paris, France
| | - Gudrun Schleiermacher
- PSL Research University, Paris, France; Oncology Center SIREDO, Institut Curie, Paris, France; INSERM U830, Institut Curie, Paris, France
| | - Claude Houdayer
- Department of Genetics, Rouen University Hospital and Inserm U1245, Rouen University (UNIROUEN), Normandie University, Normandy Center for Genomic and Personalized Medicine, Rouen, France
| | - François Radvanyi
- PSL Research University, Paris, France; Molecular Oncology Team, CNRS, UMR144, Institut Curie, Paris, France
| | - Eleonore Frouin
- PSL Research University, Paris, France; Bioinformatics Unit, Institut Curie, Paris, France
| | - Victor Renault
- PSL Research University, Paris, France; Bioinformatics Unit, Institut Curie, Paris, France
| | - François Doz
- Université de Paris, Paris, France; Oncology Center SIREDO, Institut Curie, Paris, France; Centre National de la Recherche Scientifique (CNRS), UMR144, Equipe Labellisée Ligue Contre le Cancer, Institut Curie, Paris, France
| | - Dominique Stoppa-Lyonnet
- Department of Genetics, Institut Curie, Paris, France; Université de Paris, Paris, France; INSERM U830, Institut Curie, Paris, France
| | - Marion Gauthier-Villars
- Department of Genetics, Institut Curie, Paris, France; PSL Research University, Paris, France
| | - Nathalie Cassoux
- Department of Ocular Oncology, Institut Curie, Paris, France; Université de Paris, Paris, France
| | - Lisa Golmard
- Department of Genetics, Institut Curie, Paris, France; PSL Research University, Paris, France.
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5
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Ruiz de la Cruz M, de la Cruz Montoya AH, Rojas Jiménez EA, Martínez Gregorio H, Díaz Velásquez CE, Paredes de la Vega J, de la Cruz Hernández-Hernández F, Vaca Paniagua F. Cis-Acting Factors Causing Secondary Epimutations: Impact on the Risk for Cancer and Other Diseases. Cancers (Basel) 2021; 13:cancers13194807. [PMID: 34638292 PMCID: PMC8508567 DOI: 10.3390/cancers13194807] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Revised: 08/09/2021] [Accepted: 08/15/2021] [Indexed: 12/25/2022] Open
Abstract
Epigenetics affects gene expression and contributes to disease development by alterations known as epimutations. Hypermethylation that results in transcriptional silencing of tumor suppressor genes has been described in patients with hereditary cancers and without pathogenic variants in the coding region of cancer susceptibility genes. Although somatic promoter hypermethylation of these genes can occur in later stages of the carcinogenic process, constitutional methylation can be a crucial event during the first steps of tumorigenesis, accelerating tumor development. Primary epimutations originate independently of changes in the DNA sequence, while secondary epimutations are a consequence of a mutation in a cis or trans-acting factor. Secondary epimutations have a genetic basis in cis of the promoter regions of genes involved in familial cancers. This highlights epimutations as a novel carcinogenic mechanism whose contribution to human diseases is underestimated by the scarcity of the variants described. In this review, we provide an overview of secondary epimutations and present evidence of their impact on cancer. We propose the necessity for genetic screening of loci associated with secondary epimutations in familial cancer as part of prevention programs to improve molecular diagnosis, secondary prevention, and reduce the mortality of these diseases.
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Affiliation(s)
- Miguel Ruiz de la Cruz
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | | | - Ernesto Arturo Rojas Jiménez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Héctor Martínez Gregorio
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Clara Estela Díaz Velásquez
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
| | - Jimena Paredes de la Vega
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
| | - Fidel de la Cruz Hernández-Hernández
- Avenida Instituto Politécnico Nacional # 2508, Colonia San Pedro Zacatenco, Delegación Gustavo A. Madero, C.P. Departamento de Infectómica y Patogénesis Molecular, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Mexico City 07360, Mexico;
| | - Felipe Vaca Paniagua
- Laboratorio Nacional en Salud, Diagnóstico Molecular y Efecto Ambiental en Enfermedades Crónico-Degenerativas, Facultad de Estudios Superiores Iztacala, Tlalnepantla 54090, Mexico; (M.R.d.l.C.); (E.A.R.J.); (H.M.G.); (C.E.D.V.); (J.P.d.l.V.)
- Unidad de Biomedicina, Facultad de Estudios Superiores Iztacala, UNAM, Tlalnepantla 54090, Mexico;
- Subdirección de Investigación Básica, Instituto Nacional de Cancerología, Ciudad de México 14080, Mexico
- Correspondence: ; Tel.: +52-55-5623-1333 (ext. 39788)
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6
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Miracco C, Toti P, Gelmi MC, Aversa S, Baldino G, Galluzzi P, De Francesco S, Petrelli F, Sorrentino E, Belmonte G, Galimberti D, Bracco S, Hadjistilianou T. Retinoblastoma Is Characterized by a Cold, CD8+ Cell Poor, PD-L1- Microenvironment, Which Turns Into Hot, CD8+ Cell Rich, PD-L1+ After Chemotherapy. Invest Ophthalmol Vis Sci 2021; 62:6. [PMID: 33538768 PMCID: PMC7862737 DOI: 10.1167/iovs.62.2.6] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023] Open
Abstract
Purpose To investigate the impact of chemotherapy (CHT) on human retinoblastoma (RB) tumor microenvironment (TME). Cases and Methods Ninety-four RBs were studied, including 44 primary RBs treated by upfront surgery (Group 1) and 50 primary RBs enucleated after CHT (CHT), either intra-arterial (IAC; Group 2, 33 cases) or systemic (S-CHT; Group 3, 17 cases). Conventional and multiplexed immunohistochemistry were performed to make quantitative comparisons among the three groups, for the following parameters: tumor-infiltrating inflammatory cells (TI-ICs); programmed cell death protein 1 (PD-1) positive TI-ICs; Ki67 proliferation index; gliosis; PD-1 ligand (PD-L1) protein expression; vessel number. We also correlated these TME factors with the presence of histological high-risk factors (HHRF+) and RB anaplasia grade (AG). Results After CHT, a decrease in both RB burden and Ki67 positivity was observed. In parallel, most subsets of TI-ICs, PD-1+ TI-ICs, gliosis, and PD-L1 protein expression significantly increased (P < 0.001, P = 0.02, P < 0.001, respectively). Vessel number did not significantly vary. Age, HHRFs+ and AG were significantly different between primary and chemoreduced RBs (P < 0.001, P = 0.006, P = 0.001, respectively) and were correlated with most TME factors. Conclusions CHT modulates host antitumor immunity by reorienting the RB TME from anergic into an active, CD8+, PD-L1+ hot state. Furthermore, some clinicopathological characteristics of RB correlate with several factors of TME. Our study adds data in favor of the possibility of a new therapeutic scenario in human RB.
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Affiliation(s)
- Clelia Miracco
- Department of Medicine, Surgery and Neuroscience, Pathological Anatomy Section, University Hospital of Siena, Siena, Italy
| | - Paolo Toti
- Department of Medicine, Surgery and Neuroscience, Pathological Anatomy Section, University Hospital of Siena, Siena, Italy
| | - Maria Chiara Gelmi
- Department of Medicine, Surgery and Neuroscience, Ophthalmology Unit, University Hospital of Siena, Siena, Italy
| | - Sara Aversa
- Department of Medicine, Surgery and Neuroscience, Pathological Anatomy Section, University Hospital of Siena, Siena, Italy
| | - Gennaro Baldino
- Department of Health Promotion Sciences, Maternal and Infant Care, Internal Medicine and Medical Specialties (PROMISE), University of Palermo, Palermo, Italy
| | - Paolo Galluzzi
- Department of Medicine, Surgery and Neuroscience, Unit of Neuroimaging and Neurointervention, University Hospital of Siena, Siena, Italy
| | - Sonia De Francesco
- Department of Medicine, Surgery and Neuroscience, Ophthalmology Unit, University Hospital of Siena, Siena, Italy
| | - Federica Petrelli
- Department of Medicine, Surgery and Neuroscience, Pathological Anatomy Section, University Hospital of Siena, Siena, Italy
| | - Ester Sorrentino
- Department of Medicine, Surgery and Neuroscience, Pathological Anatomy Section, University Hospital of Siena, Siena, Italy
| | - Giuseppe Belmonte
- Department of Medicine, Surgery and Neuroscience, Pathological Anatomy Section, University Hospital of Siena, Siena, Italy
| | - Daniela Galimberti
- Department of Maternal, Newborn and Child Health, Unit of Pediatrics, University Hospital of Siena, Siena, Italy
| | - Sandra Bracco
- Department of Medicine, Surgery and Neuroscience, Unit of Neuroimaging and Neurointervention, University Hospital of Siena, Siena, Italy
| | - Theodora Hadjistilianou
- Department of Medicine, Surgery and Neuroscience, Ophthalmology Unit, University Hospital of Siena, Siena, Italy
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7
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Jiménez I, Frouin É, Chicard M, Dehainault C, Le Gall J, Benoist C, Gauthier A, Lapouble E, Houdayer C, Radvanyi F, Bernard V, Brisse HJ, Gauthier-Villars M, Stoppa-Lyonnet D, Baulande S, Cassoux N, Lumbroso L, Matet A, Aerts I, Renault V, Doz F, Golmard L, Delattre O, Schleiermacher G. Molecular diagnosis of retinoblastoma by circulating tumor DNA analysis. Eur J Cancer 2021; 154:277-287. [PMID: 34298378 DOI: 10.1016/j.ejca.2021.05.039] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2021] [Revised: 05/11/2021] [Accepted: 05/27/2021] [Indexed: 12/21/2022]
Abstract
PURPOSE The analysis of circulating tumor DNA (ctDNA), a fraction of total cell-free DNA (cfDNA), might be of special interest in retinoblastoma patients. Because the accessibility to tumor tissue is very limited in these patients, either for histopathological diagnosis of suspicious intraocular masses (biopsies are proscribed) or for somatic RB1 studies and genetic counseling (due to current successful conservative approaches), we aim to validate the detection of ctDNA in plasma of non-hereditary retinoblastoma patients by molecular analysis of RB1 gene. EXPERIMENTAL DESIGN In a cohort of 19 intraocular unilateral non-hereditary retinoblastoma patients for whom a plasma sample was available at diagnosis, we performed high-deep next-generation sequencing (NGS) of RB1 in cfDNA. Two different bioinformatics/statistics approaches were applied depending on whether the somatic RB1 status was available or not. RESULTS Median plasma sample volume was 600 μL [100-1000]; median cfDNA plasma concentration was 119 [38-1980] and 27 [11-653] ng/mL at diagnosis and after complete remission, respectively. In the subgroup of patients with known somatic RB1 alterations (n = 11), seven of nine somatic mutations were detected (median allele fraction: 6.7%). In patients without identified somatic RB1 alterations (n = 8), six candidate variants were identified for seven patients. CONCLUSIONS Despite small tumor size, blood-ocular barrier, poor ctDNA blood release and limited plasma sample volumes, we confirm that it is possible to detect ctDNA with high-deep NGS in plasma from patients with intraocular non-hereditary retinoblastoma. This may aid in diagnosis of suspicious cases, family genetic counseling or follow-up of residual intraocular disease.
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Affiliation(s)
- Irene Jiménez
- SiRIC RTOP « Recherche Translationelle en Oncologie Pédiatrique », Translational Research Department, PSL Research University, Institut Curie Research Center, Paris, France; INSERM U830, Equipe Labellisée Ligue Contre le Cancer, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, Institut Curie Research Center, Paris, France; SIREDO Center: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Éléonore Frouin
- Clinical Bioinformatics, PSL Research University, Institut Curie, Paris, France
| | - Mathieu Chicard
- SiRIC RTOP « Recherche Translationelle en Oncologie Pédiatrique », Translational Research Department, PSL Research University, Institut Curie Research Center, Paris, France; INSERM U830, Equipe Labellisée Ligue Contre le Cancer, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, Institut Curie Research Center, Paris, France; SIREDO Center: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | | | - Jessica Le Gall
- Department of Genetics, PSL Research University, Institut Curie, Paris, France
| | - Camille Benoist
- Clinical Bioinformatics, PSL Research University, Institut Curie, Paris, France
| | - Arnaud Gauthier
- Pathology Department, PSL Research University, Institut Curie, Paris, France
| | - Eve Lapouble
- Somatic Genetics Unit, PSL Research University, Institut Curie, Paris, France
| | - Claude Houdayer
- INSERM U1245, Normandie University, UNIROUEN, Normandy Centre for Genomic and Personalized Medicine and Rouen University Hospital, Department of Genetics, Rouen, France
| | - François Radvanyi
- CNRS, UMR144, Equipe Labellisée Ligue Contre le Cancer, Institut Curie, PSL Research University, Paris, France
| | - Virginie Bernard
- Centre Hospitalier Universitaire Grenoble-Alpes, Grenoble, France
| | - Hervé J Brisse
- Imaging Department, PSL Research University, Institut Curie, Paris, France
| | | | | | - Sylvain Baulande
- Institut Curie Genomics of Excellence (ICGex) Platform, PSL Research University, Research Center, Institut Curie, Paris, France
| | - Nathalie Cassoux
- SiRIC RTOP « Recherche Translationelle en Oncologie Pédiatrique », Translational Research Department, PSL Research University, Institut Curie Research Center, Paris, France; SIREDO Center: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France; Université de Paris, Paris, France
| | | | - Alexandre Matet
- Ocular Oncology Service, Institut Curie, Paris, France; Université de Paris, Paris, France
| | - Isabelle Aerts
- SIREDO Center: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Victor Renault
- Clinical Bioinformatics, PSL Research University, Institut Curie, Paris, France
| | - François Doz
- SIREDO Center: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France; Université de Paris, Paris, France
| | - Lisa Golmard
- Department of Genetics, PSL Research University, Institut Curie, Paris, France
| | - Olivier Delattre
- INSERM U830, Equipe Labellisée Ligue Contre le Cancer, PSL Research University, Institut Curie Research Center, Paris, France; SIREDO Center: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France
| | - Gudrun Schleiermacher
- SiRIC RTOP « Recherche Translationelle en Oncologie Pédiatrique », Translational Research Department, PSL Research University, Institut Curie Research Center, Paris, France; INSERM U830, Equipe Labellisée Ligue Contre le Cancer, PSL Research University, Institut Curie Research Center, Paris, France; Department of Translational Research, Institut Curie Research Center, Paris, France; SIREDO Center: Care, Innovation and Research for Children, Adolescents and Young Adults with Cancer, Institut Curie, Paris, France.
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8
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Pettini F, Visibelli A, Cicaloni V, Iovinelli D, Spiga O. Multi-Omics Model Applied to Cancer Genetics. Int J Mol Sci 2021; 22:ijms22115751. [PMID: 34072237 PMCID: PMC8199287 DOI: 10.3390/ijms22115751] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/18/2021] [Accepted: 05/26/2021] [Indexed: 12/29/2022] Open
Abstract
In this review, we focus on bioinformatic oncology as an integrative discipline that incorporates knowledge from the mathematical, physical, and computational fields to further the biomedical understanding of cancer. Before providing a deeper insight into the bioinformatics approach and utilities involved in oncology, we must understand what is a system biology framework and the genetic connection, because of the high heterogenicity of the backgrounds of people approaching precision medicine. In fact, it is essential to providing general theoretical information on genomics, epigenomics, and transcriptomics to understand the phases of multi-omics approach. We consider how to create a multi-omics model. In the last section, we describe the new frontiers and future perspectives of this field.
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Affiliation(s)
- Francesco Pettini
- Department of Medical Biotechnology, University of Siena, Via M. Bracci 2, 53100 Siena, Italy
- Correspondence: ; Tel.: +39-3755461426
| | - Anna Visibelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; (A.V.); (D.I.); (O.S.)
| | - Vittoria Cicaloni
- Toscana Life Sciences Foundation, Via Fiorentina 1, 53100 Siena, Italy;
| | - Daniele Iovinelli
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; (A.V.); (D.I.); (O.S.)
| | - Ottavia Spiga
- Department of Biotechnology, Chemistry and Pharmacy, University of Siena, Via A. Moro 2, 53100 Siena, Italy; (A.V.); (D.I.); (O.S.)
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9
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Oleksiewicz U, Machnik M. Causes, effects, and clinical implications of perturbed patterns within the cancer epigenome. Semin Cancer Biol 2020; 83:15-35. [PMID: 33359485 DOI: 10.1016/j.semcancer.2020.12.014] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 12/18/2020] [Accepted: 12/18/2020] [Indexed: 02/06/2023]
Abstract
Somatic mutations accumulating over a patient's lifetime are well-defined causative factors that fuel carcinogenesis. It is now clear, however, that epigenomic signature is also largely perturbed in many malignancies. These alterations support the transcriptional program crucial for the acquisition and maintenance of cancer hallmarks. Epigenetic instability may arise due to the genetic mutations or transcriptional deregulation of the proteins implicated in epigenetic signaling. Moreover, external stimulation and physiological aging may also participate in this phenomenon. The epigenomic signature is frequently associated with a cell of origin, as well as with tumor stage and differentiation, which all reflect its high heterogeneity across and within various tumors. Here, we will overview the current understanding of the causes and effects of the altered and heterogeneous epigenomic landscape in cancer. We will focus mainly on DNA methylation and post-translational histone modifications as the key regulatory epigenetic signaling marks. In addition, we will describe how this knowledge is translated into the clinic. We will particularly concentrate on the applicability of epigenetic alterations as biomarkers for improved diagnosis, prognosis, and prediction. Finally, we will also review current developments regarding epi-drug usage in clinical and experimental settings.
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Affiliation(s)
- Urszula Oleksiewicz
- Department of Cancer Immunology, Poznan University of Medical Sciences, Poznan, Poland; Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Poznan, Poland.
| | - Marta Machnik
- Department of Cancer Immunology, Poznan University of Medical Sciences, Poznan, Poland; Department of Cancer Diagnostics and Immunology, Greater Poland Cancer Centre, Poznan, Poland
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10
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Fiala EM, Ortiz MV, Kennedy JA, Glodzik D, Fleischut MH, Duffy KA, Hathaway ER, Heaton T, Gerstle JT, Steinherz P, Shukla N, McNeer N, Tkachuk K, Bouvier N, Cadoo K, Carlo MI, Latham A, Dubard Gault M, Joseph V, Kemel Y, Kentsis A, Stadler Z, La Quaglia M, Papaemmanuil E, Friedman D, Ganguly A, Kung A, Offit K, Kalish JM, Walsh MF. 11p15.5 epimutations in children with Wilms tumor and hepatoblastoma detected in peripheral blood. Cancer 2020; 126:3114-3121. [PMID: 32320050 PMCID: PMC7383476 DOI: 10.1002/cncr.32907] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2019] [Revised: 02/18/2020] [Accepted: 03/17/2020] [Indexed: 01/14/2023]
Abstract
Background Constitutional or somatic mosaic epimutations are increasingly recognized as a mechanism of gene dysregulation resulting in cancer susceptibility. Beckwith‐Wiedemann syndrome is the cancer predisposition syndrome most commonly associated with epimutation and is extremely variable in its phenotypic presentation, which can include isolated tumors. Because to the authors' knowledge large‐scale germline DNA sequencing studies have not included methylation analysis, the percentage of pediatric cancer predisposition that is due to epimutations is unknown. Methods Germline methylation testing at the 11p15.5 locus was performed in blood for 24 consecutive patients presenting with hepatoblastoma (3 patients) or Wilms tumor (21 patients). Results Six individuals with Wilms tumor and 1 patient with hepatoblastoma were found to have low‐level gain of methylation at imprinting control 1, and a child with hepatoblastoma was found to have loss of methylation at imprinting control 2. The loss of methylation at imprinting control 2 was found to be maternally inherited, despite not being associated with any detectable genomic alteration. Conclusions Overall, 33% of patients (8 of 24 patients) with Wilms tumor or hepatoblastoma were found to have an epigenetic susceptibility that was detectable in the blood. It is interesting to note that low‐level gain of methylation at imprinting control 1 predominantly was detected in females with bilateral Wilms tumors. Further studies in larger cohorts are needed to determine the efficacy of testing all patients with Wilms tumor or hepatoblastoma for 11p15.5 epimutations in the blood as part of DNA analysis because this hallmark of predisposition will not be detected by sequencing‐based approaches and detecting a cancer predisposition may modify treatment. In the current study, all patients presenting with Wilms tumor or hepatoblastoma undergo 11p15.5 methylation analysis. Approximately one‐third are found to have an epimutation at this locus that is detectable in peripheral blood.
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Affiliation(s)
- Elise M Fiala
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael V Ortiz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Jennifer A Kennedy
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Dominik Glodzik
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Megan Harlan Fleischut
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kelly A Duffy
- Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Evan R Hathaway
- Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Todd Heaton
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Justin T Gerstle
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Peter Steinherz
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Neerav Shukla
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Nicole McNeer
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Kaitlyn Tkachuk
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Nancy Bouvier
- Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Karen Cadoo
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Maria I Carlo
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alicia Latham
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Division of Long Term Follow-Up, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Marianne Dubard Gault
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Vijai Joseph
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Yelena Kemel
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Alex Kentsis
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Zsofia Stadler
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Michael La Quaglia
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Surgery, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Elli Papaemmanuil
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Danielle Friedman
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, New York.,Division of Long Term Follow-Up, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Arupa Ganguly
- Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Andrew Kung
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York
| | - Kenneth Offit
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | - Jennifer M Kalish
- Human Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Center for Childhood Cancer Research, Children's Hospital of Philadelphia, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Genetics, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania.,Department of Pediatrics, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Michael F Walsh
- Division of Clinical Genetics, Memorial Sloan Kettering Cancer Center, New York, New York.,Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, New York.,Weill Cornell Medical College, New York, New York.,Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
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11
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DNA Methylation in the Diagnosis of Monogenic Diseases. Genes (Basel) 2020; 11:genes11040355. [PMID: 32224912 PMCID: PMC7231024 DOI: 10.3390/genes11040355] [Citation(s) in RCA: 23] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2020] [Revised: 03/13/2020] [Accepted: 03/24/2020] [Indexed: 02/08/2023] Open
Abstract
DNA methylation in the human genome is largely programmed and shaped by transcription factor binding and interaction between DNA methyltransferases and histone marks during gamete and embryo development. Normal methylation profiles can be modified at single or multiple loci, more frequently as consequences of genetic variants acting in cis or in trans, or in some cases stochastically or through interaction with environmental factors. For many developmental disorders, specific methylation patterns or signatures can be detected in blood DNA. The recent use of high-throughput assays investigating the whole genome has largely increased the number of diseases for which DNA methylation analysis provides information for their diagnosis. Here, we review the methylation abnormalities that have been associated with mono/oligogenic diseases, their relationship with genotype and phenotype and relevance for diagnosis, as well as the limitations in their use and interpretation of results.
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12
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Dámaso E, Canet-Hermida J, Vargas-Parra G, Velasco À, Marín F, Darder E, Del Valle J, Fernández A, Izquierdo À, Mateu G, Oliveras G, Escribano C, Piñol V, Uchima HI, Soto JL, Hitchins M, Farrés R, Lázaro C, Queralt B, Brunet J, Capellá G, Pineda M. Highly sensitive MLH1 methylation analysis in blood identifies a cancer patient with low-level mosaic MLH1 epimutation. Clin Epigenetics 2019; 11:171. [PMID: 31779681 PMCID: PMC6883525 DOI: 10.1186/s13148-019-0762-6] [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: 05/23/2019] [Accepted: 10/09/2019] [Indexed: 12/15/2022] Open
Abstract
Constitutional MLH1 methylation (epimutation) is a rare cause of Lynch syndrome. Low-level methylation (≤ 10%) has occasionally been described. This study aimed to identify low-level constitutional MLH1 epimutations and determine its causal role in patients with MLH1-hypermethylated colorectal cancer. Eighteen patients with MLH1-hypermethylated colorectal tumors in whom MLH1 methylation was previously undetected in blood by methylation-specific multiplex ligation-dependent probe amplification (MS-MLPA) were screened for MLH1 methylation using highly sensitive MS-melting curve analysis (MS-MCA). Constitutional methylation was characterized by different approaches. MS-MCA identified one patient (5.6%) with low-level MLH1 methylation (~ 1%) in blood and other normal tissues, which was confirmed by clonal bisulfite sequencing in blood. The patient had developed three clonally related gastrointestinal MLH1-methylated tumor lesions at 22, 24, and 25 years of age. The methylated region in normal tissues overlapped with that reported for other carriers of constitutional MLH1 epimutations. Low-level MLH1 methylation and reduced allelic expression were linked to the same genetic haplotype, whereas the opposite allele was lost in patient’s tumors. Mutation screening of MLH1 and other hereditary cancer genes was negative. Herein, a highly sensitive MS-MCA-based approach has demonstrated its utility for the identification of low-level constitutional MLH1 epigenetic mosaicism. The eventual identification and characterization of additional cases will be critical to ascertain the cancer risks associated with constitutional MLH1 epigenetic mosaicism.
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Affiliation(s)
- Estela Dámaso
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain
| | - Júlia Canet-Hermida
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain
| | - Gardenia Vargas-Parra
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Àngela Velasco
- Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Fátima Marín
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Esther Darder
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Jesús Del Valle
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Anna Fernández
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain
| | - Àngel Izquierdo
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain
| | - Gemma Mateu
- Pathology Department, Dr Josep Trueta University Hospital, Girona, Spain
| | - Glòria Oliveras
- Pathology Department, Dr Josep Trueta University Hospital, Girona, Spain
| | | | - Virgínia Piñol
- Department of Gastroenterology, Dr Josep Trueta University Hospital, Girona, Spain
| | - Hugo-Ikuo Uchima
- Department of Gastroenterology, Dr Josep Trueta University Hospital, Girona, Spain
| | - José Luis Soto
- Hereditary Cancer Program Valencian Region, Molecular Genetics Laboratory, Elche University Hospital, Elche, Alicante, Spain
| | - Megan Hitchins
- Department of Biomedical Sciences, Cedars-Sinai Medical Center, CA, Los Angeles, USA
| | - Ramon Farrés
- Department of General and Digestive Surgery, Dr Josep Trueta University Hospital, Girona, Spain
| | - Conxi Lázaro
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain
| | - Bernat Queralt
- Department of Medical Oncology, Catalan Institute of Oncology, Girona, Spain
| | - Joan Brunet
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain.,Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Girona (IDIBGI), Girona, Spain.,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.,Department of Medical Sciences Department, School of Medicine, University of Girona, Girona, Spain
| | - Gabriel Capellá
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
| | - Marta Pineda
- Hereditary Cancer Program, Catalan Institute of Oncology, Institut d'Investigació Biomèdica de Bellvitge (IDIBELL), ONCOBELL Program, Av. Gran Via de l'Hospitalet, 199-203, 08908 L' Hospitalet de Llobregat, Barcelona, Spain. .,Centro de Investigación Biomédica en Red de Cáncer (CIBERONC), Madrid, Spain.
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13
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Borchiellini M, Ummarino S, Di Ruscio A. The Bright and Dark Side of DNA Methylation: A Matter of Balance. Cells 2019; 8:cells8101243. [PMID: 31614870 PMCID: PMC6830319 DOI: 10.3390/cells8101243] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2019] [Revised: 10/06/2019] [Accepted: 10/10/2019] [Indexed: 12/11/2022] Open
Abstract
DNA methylation controls several cellular processes, from early development to old age, including biological responses to endogenous or exogenous stimuli contributing to disease transition. As a result, minimal DNA methylation changes during developmental stages drive severe phenotypes, as observed in germ-line imprinting disorders, while genome-wide alterations occurring in somatic cells are linked to cancer onset and progression. By summarizing the molecular events governing DNA methylation, we focus on the methods that have facilitated mapping and understanding of this epigenetic mark in healthy conditions and diseases. Overall, we review the bright (health-related) and dark (disease-related) side of DNA methylation changes, outlining how bulk and single-cell genomic analyses are moving toward the identification of new molecular targets and driving the development of more specific and less toxic demethylating agents.
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Affiliation(s)
- Marta Borchiellini
- Department of Health Sciences, University of Eastern Piedmont, 28100 Novara, Italy.
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
| | - Simone Ummarino
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
| | - Annalisa Di Ruscio
- Department of Translational Medicine, University of Eastern Piedmont, 28100 Novara, Italy.
- Harvard Medical School Initiative for RNA Medicine, Harvard Medical School, Boston, MA 02115, USA.
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14
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Lee MP. Understanding Cancer Through the Lens of Epigenetic Inheritance, Allele-Specific Gene Expression, and High-Throughput Technology. Front Oncol 2019; 9:794. [PMID: 31497535 PMCID: PMC6712412 DOI: 10.3389/fonc.2019.00794] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Accepted: 08/06/2019] [Indexed: 02/06/2023] Open
Abstract
Epigenetic information is characterized by its stable transmission during mitotic cell divisions and plasticity during development and differentiation. This duality is in contrast to genetic information, which is stable and identical in all cells in an organism with exception of immunoglobulin gene rearrangements in lymphocytes and somatic mutations in cancer cells. Allele-specific analysis of gene expression and epigenetic modifications provides a unique approach to studying epigenetic regulation in normal and cancer cells. Extension of Knudson's two-hits theory to include epigenetic alteration as a means to inactivate tumor suppressor genes provides better understanding of how genetic mutations and epigenetic alterations jointly contribute to cancer development. High-throughput technology has greatly accelerated cancer discovery. Large initiatives such as TCGA have shown that epigenetic components are frequent targets of mutations in cancer and these discoveries provide new insights into understanding cancer etiology and generate new opportunities for cancer therapeutics.
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Affiliation(s)
- Maxwell P Lee
- High Dimension Data Analysis Group, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD, United States
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