1
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Fahiminiya S, Oikonomopoulos S, Rivard GE, Gandhi M, Scott P, Montpetit A, Chen SH, Park K, Vezina C, Ragoussis J, Carvalho CMB, Mitchell GA, Soucy JF, Gauthier J. Deciphering a novel complex inversion affecting F8 in a family with severe haemophilia A by optical genome mapping. Haemophilia 2023; 29:921-924. [PMID: 36897533 DOI: 10.1111/hae.14771] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2023] [Revised: 01/29/2023] [Accepted: 02/13/2023] [Indexed: 03/11/2023]
Affiliation(s)
- Somayyeh Fahiminiya
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montréal, Québec, Canada
- Division of Hematology-Oncology, Department of Pathology, Dalhousie University; Queen Elizabeth II Health Sciences Centre, Nova Scotia Health, Halifax, Nova Scotia, Canada
| | - Spyros Oikonomopoulos
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - Georges-Etienne Rivard
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montréal, Québec, Canada
- Division of Hematology-Oncology, Department of Pediatrics, Université de Montréal, CHU Sainte-Justine, Montréal, Québec, Canada
| | - Mira Gandhi
- Pacific Northwest Research Institute (PNRI), Seattle, Washington, USA
| | - Patrick Scott
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montréal, Québec, Canada
| | | | - Shu-Huang Chen
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada
| | - KyungHee Park
- Pacific Northwest Research Institute (PNRI), Seattle, Washington, USA
| | - Catherine Vezina
- Montreal Children's Hospital, McGill University Health Center, Montréal, Québec, Canada
| | - Jiannis Ragoussis
- McGill Genome Centre, Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Department of Bioengineering, McGill University, Montréal, Québec, Canada
| | | | - Grant A Mitchell
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montréal, Québec, Canada
- Division of Medical Genetics, Department of Pediatrics, Université de Montréal, CHU Sainte-Justine, Montréal, Québec, Canada
| | - Jean-Francois Soucy
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montréal, Québec, Canada
- Division of Medical Genetics, Department of Pediatrics, Université de Montréal, CHU Sainte-Justine, Montréal, Québec, Canada
| | - Julie Gauthier
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montréal, Québec, Canada
- Division of Medical Genetics, Department of Pediatrics, Université de Montréal, CHU Sainte-Justine, Montréal, Québec, Canada
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2
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Fahiminiya S, Rivard GE, Scott P, Montpetit A, Bacot F, St-Louis J, Mitchell GA, Foulkes WD, Soucy JF, Gauthier J. A full molecular picture of F8 intron 1 inversion created with optical genome mapping. Haemophilia 2021; 27:e638-e640. [PMID: 34232555 DOI: 10.1111/hae.14375] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 05/17/2021] [Accepted: 06/26/2021] [Indexed: 11/30/2022]
Affiliation(s)
- Somayyeh Fahiminiya
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada.,Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - Georges-Etienne Rivard
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada.,Division of Hematology-Oncology, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - Patrick Scott
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada
| | | | - François Bacot
- Centre d'expertise et de services Génome Québec, Montreal, Québec, Canada
| | - Jean St-Louis
- Division of Hematology-Oncology, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - Grant A Mitchell
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada.,Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Québec, Canada
| | - Jean-Francois Soucy
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada.,Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
| | - Julie Gauthier
- Molecular Diagnostic Laboratory, CHU Sainte-Justine, Montreal, Québec, Canada.,Division of Medical Genetics, Department of Pediatrics, CHU Sainte-Justine and Université de Montréal, Montreal, Québec, Canada
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3
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Tremblay K, Rousseau S, Zawati MH, Auld D, Chassé M, Coderre D, Falcone EL, Gauthier N, Grandvaux N, Gros-Louis F, Jabet C, Joly Y, Kaufmann DE, Laprise C, Larochelle C, Maltais F, Mes-Masson AM, Montpetit A, Piché A, Richards JB, Tse SM, Turgeon AF, Turecki G, Vinh DC, Wang HT, Mooser V. The Biobanque québécoise de la COVID-19 (BQC19)-A cohort to prospectively study the clinical and biological determinants of COVID-19 clinical trajectories. PLoS One 2021; 16:e0245031. [PMID: 34010280 PMCID: PMC8133500 DOI: 10.1371/journal.pone.0245031] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 04/03/2021] [Indexed: 11/30/2022] Open
Abstract
SARS-CoV-2 infection causing the novel coronavirus disease 2019 (COVID–19) has been responsible for more than 2.8 million deaths and nearly 125 million infections worldwide as of March 2021. In March 2020, the World Health Organization determined that the COVID–19 outbreak is a global pandemic. The urgency and magnitude of this pandemic demanded immediate action and coordination between local, regional, national, and international actors. In that mission, researchers require access to high-quality biological materials and data from SARS-CoV-2 infected and uninfected patients, covering the spectrum of disease manifestations. The “Biobanque québécoise de la COVID-19” (BQC19) is a pan–provincial initiative undertaken in Québec, Canada to enable the collection, storage and sharing of samples and data related to the COVID-19 crisis. As a disease-oriented biobank based on high-quality biosamples and clinical data of hospitalized and non-hospitalized SARS-CoV-2 PCR positive and negative individuals. The BQC19 follows a legal and ethical management framework approved by local health authorities. The biosamples include plasma, serum, peripheral blood mononuclear cells and DNA and RNA isolated from whole blood. In addition to the clinical variables, BQC19 will provide in-depth analytical data derived from the biosamples including whole genome and transcriptome sequencing, proteome and metabolome analyses, multiplex measurements of key circulating markers as well as anti-SARS-CoV-2 antibody responses. BQC19 will provide the scientific and medical communities access to data and samples to better understand, manage and ultimately limit, the impact of COVID-19. In this paper we present BQC19, describe the process according to which it is governed and organized, and address opportunities for future research collaborations. BQC19 aims to be a part of a global communal effort addressing the challenges of COVID–19.
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Affiliation(s)
- Karine Tremblay
- Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay–Lac-Saint-Jean, Saguenay, QC, Canada
- Department of Pharmacology-Physiology, Medicine and Health Sciences Faculty, Université de Sherbrooke, Sherbrooke, QC, Canada
- * E-mail: (KT); (SR); (MHZ)
| | - Simon Rousseau
- The Meakins-Christie Laboratories at the Research Institute of the McGill University Heath Centre Research Institute, Montréal, QC, Canada
- Department of Medicine, Faculty of Medicine, McGill University, Montréal, QC, Canada
- * E-mail: (KT); (SR); (MHZ)
| | - Ma’n H. Zawati
- Centre of Genomics and Policy, McGill University, Montréal, QC, Canada
- * E-mail: (KT); (SR); (MHZ)
| | - Daniel Auld
- McGill Genome Centre and Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Michaël Chassé
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Centre Hospitalier de l’Université de Montréal (CHUM), Montréal, QC, Canada
| | | | - Emilia Liana Falcone
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Department of Immunity and Viral Infections, Montreal Clinical Research Institute (IRCM), Montreal, Quebec, Canada
| | - Nicolas Gauthier
- CIUSSS du Nord-de-l’Ile-de-Montréal—Hôpital du Sacré-Cœur-de-Montréal, Montreal, QC, Canada
| | - Nathalie Grandvaux
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, Université de Montréal, Montreal, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - François Gros-Louis
- Centre de Recherche du Centre Hospitalier Universitaire de Québec, Regenerative Medicine Division, Québec, QC, Canada
- Department of Surgery, Faculty of Medicine, Université Laval, Quebec, QC, Canada
| | - Carole Jabet
- Fonds de Recherche du Québec Santé, Montreal, QC, Canada
| | - Yann Joly
- Centre of Genomics and Policy, McGill University, Montréal, QC, Canada
| | - Daniel E. Kaufmann
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
| | - Catherine Laprise
- Centre Intégré Universitaire de Santé et de Services Sociaux (CIUSSS) du Saguenay–Lac-Saint-Jean, Saguenay, QC, Canada
- Département des Sciences Fondamentales, Centre Intersectoriel en Santé Durable, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Catherine Larochelle
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Department of Neurosciences, Université de Montréal, Montreal, QC, Canada
| | | | - Anne-Marie Mes-Masson
- Centre de Recherche du Centre Hospitalier de l’Université de Montréal (CRCHUM), Montreal, QC, Canada
- Institut du Cancer de Montréal, Montreal, QC, Canada
| | | | - Alain Piché
- Département de Microbiologie et Infectiologie, Université de Sherbrooke, Sherbrooke, Quebec, Canada
- Département de Médecine, Service d’Infectiologie, Centre de Recherche Clinique du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, Quebec, Canada
| | - J. Brent Richards
- Lady Davis Institute, Jewish General Hospital, McGill University, Montréal, QC, Canada
- Department of Epidemiology and Department of Human Genetics, Biostatistics and Occupational Health, McGill University, Montréal, QC, Canada
| | - Sze Man Tse
- Division of Respiratory Medicine, Department of Pediatrics, CHU Sainte-Justine, Université de Montréal, Montreal, QC, Canada
| | - Alexis F. Turgeon
- Centre Hospitalier Universitaire de Québec–Université Laval Research Center, Population Health and Optimal Health Practices Research Unit, Trauma-Emergency-Critical Care Medicine, Québec City, QC, Canada
- Division of Critical Care Medicine, Department of Anesthesiology and Critical Care Medicine, Faculty of Medicine, Université Laval, Québec City, QC, Canada
| | - Gustavo Turecki
- CIUSSS de l’Ouest-de-l’Ile-de-Montréal, Montreal, QC, Canada
- Department of Psychiatry, Douglas Mental Health University Institute, McGill University, Montreal, QC, Canada
| | - Donald C. Vinh
- Division of Infectious Diseases, Department of Medicine, McGill University Health Centre, Montreal, QC, Canada
- Division of Medical Microbiology, Department of Laboratory Medicine, McGill University Health Centre, Montreal, QC, Canada
| | - Han Ting Wang
- Division of Critical Care Medicine, Department of Medicine, Universite de Montreal, Montreal, QC, Canada
- CIUSSS de l’Est-de-l’Ile-de-Montréal, Hôpital Maisonneuve-Rosemont Research Centre, Montreal, QC, Canada
| | - Vincent Mooser
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC, Canada
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4
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Negri GL, Grande BM, Delaidelli A, El-Naggar A, Cochrane D, Lau CC, Triche TJ, Moore RA, Jones SJ, Montpetit A, Marra MA, Malkin D, Morin RD, Sorensen PH. Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma. J Pathol 2019; 249:319-331. [PMID: 31236944 DOI: 10.1002/path.5319] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 05/23/2019] [Accepted: 06/20/2019] [Indexed: 01/14/2023]
Abstract
Despite being the most common childhood bone tumor, the genomic characterization of osteosarcoma remains incomplete. In particular, very few osteosarcoma metastases have been sequenced to date, critical to better understand mechanisms of progression and evolution in this tumor. We performed an integrated whole genome and exome sequencing analysis of paired primary and metastatic pediatric osteosarcoma specimens to identify recurrent genomic alterations. Sequencing of 13 osteosarcoma patients including 13 primary, 10 metastatic, and 3 locally recurring tumors revealed a highly heterogeneous mutational landscape, including cases of hypermutation and microsatellite instability positivity, but with virtually no recurrent alterations except for mutations involving the tumor suppressor genes RB1 and TP53. At the germline level, we detected alterations in multiple cancer related genes in the majority of the cohort, including those potentially disrupting DNA damage response pathways. Metastases retained only a minimal number of short variants from their corresponding primary tumors, while copy number alterations showed higher conservation. One recurrently amplified gene, KDR, was highly expressed in advanced cases and associated with poor prognosis. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Gian Luca Negri
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Amal El-Naggar
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology, Faculty of Medicine, Menoufia University, Shebeen El-Kom, Egypt
| | - Dawn Cochrane
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Ching C Lau
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Timothy J Triche
- Department of Pathology and Laboratory Medicine, Childrens Hospital Los Angeles, Los Angeles, CA, USA.,Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Alexandre Montpetit
- Department of Human Genetics, McGill University and Research Institute, McGill University Health Centre, Montreal, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - David Malkin
- Division of Haematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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5
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Harutyunyan AS, Krug B, Chen H, Papillon-Cavanagh S, Zeinieh M, De Jay N, Deshmukh S, Chen CCL, Belle J, Mikael LG, Marchione DM, Li R, Nikbakht H, Hu B, Cagnone G, Cheung WA, Mohammadnia A, Bechet D, Faury D, McConechy MK, Pathania M, Jain SU, Ellezam B, Weil AG, Montpetit A, Salomoni P, Pastinen T, Lu C, Lewis PW, Garcia BA, Kleinman CL, Jabado N, Majewski J. H3K27M induces defective chromatin spread of PRC2-mediated repressive H3K27me2/me3 and is essential for glioma tumorigenesis. Nat Commun 2019; 10:1262. [PMID: 30890717 PMCID: PMC6425035 DOI: 10.1038/s41467-019-09140-x] [Citation(s) in RCA: 185] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2018] [Accepted: 02/18/2019] [Indexed: 01/16/2023] Open
Abstract
Lys-27-Met mutations in histone 3 genes (H3K27M) characterize a subgroup of deadly gliomas and decrease genome-wide H3K27 trimethylation. Here we use primary H3K27M tumor lines and isogenic CRISPR-edited controls to assess H3K27M effects in vitro and in vivo. We find that whereas H3K27me3 and H3K27me2 are normally deposited by PRC2 across broad regions, their deposition is severely reduced in H3.3K27M cells. H3K27me3 is unable to spread from large unmethylated CpG islands, while H3K27me2 can be deposited outside these PRC2 high-affinity sites but to levels corresponding to H3K27me3 deposition in wild-type cells. Our findings indicate that PRC2 recruitment and propagation on chromatin are seemingly unaffected by K27M, which mostly impairs spread of the repressive marks it catalyzes, especially H3K27me3. Genome-wide loss of H3K27me3 and me2 deposition has limited transcriptomic consequences, preferentially affecting lowly-expressed genes regulating neurogenesis. Removal of H3K27M restores H3K27me2/me3 spread, impairs cell proliferation, and completely abolishes their capacity to form tumors in mice. Lysine27-to-methionine mutations in histone H3 genes (H3K27M) occur in a subgroup of gliomas and decrease genome-wide H3K27 trimethylation. Here the authors utilise primary H3K27M tumour lines and isogenic CRISPR-edited controls and show that H3K27M induces defective chromatin spread of PRC2-mediated repressive H3K27me2/me3.
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Affiliation(s)
- Ashot S Harutyunyan
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Brian Krug
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Haifen Chen
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | | | - Michele Zeinieh
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Nicolas De Jay
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada.,Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada
| | - Shriya Deshmukh
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Carol C L Chen
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Jad Belle
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Leonie G Mikael
- Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Center, Montreal, QC, H4A 3J1, Canada
| | - Dylan M Marchione
- Department of Biochemistry and Biophysics, and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Rui Li
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Hamid Nikbakht
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Bo Hu
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Gael Cagnone
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Warren A Cheung
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada.,Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | | | - Denise Bechet
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Damien Faury
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Melissa K McConechy
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada
| | - Manav Pathania
- Samantha Dickson Brain Cancer Unit, University College London Cancer Institute, London, WCE1 6DD, United Kingdom
| | - Siddhant U Jain
- Department of Biomolecular Chemistry, School of Medicine and Public Health and Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI, 53715, USA
| | - Benjamin Ellezam
- Department of Pathology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC, H3T 1C5, Canada
| | - Alexander G Weil
- Department of Pediatric Neurosurgery, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, QC, H3T 1C5, Canada
| | - Alexandre Montpetit
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Paolo Salomoni
- Samantha Dickson Brain Cancer Unit, University College London Cancer Institute, London, WCE1 6DD, United Kingdom.,Nuclear Function in CNS pathophysiology, German Center for Neurodegenerative Diseases, 53127, Bonn, Germany
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada.,Center for Pediatric Genomic Medicine, Children's Mercy Kansas City, Kansas City, MO, 64108, USA
| | - Chao Lu
- Department of Genetics and Development, Columbia University Irving Medical Center, New York, NY, 10032, USA
| | - Peter W Lewis
- Department of Biomolecular Chemistry, School of Medicine and Public Health and Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI, 53715, USA
| | - Benjamin A Garcia
- Department of Biochemistry and Biophysics, and Penn Epigenetics Institute, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, 19104, USA
| | - Claudia L Kleinman
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada.,Lady Davis Research Institute, Jewish General Hospital, Montreal, QC, H3T 1E2, Canada
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada. .,Department of Pediatrics, McGill University, and The Research Institute of the McGill University Health Center, Montreal, QC, H4A 3J1, Canada.
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC, H3A 1B1, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada.
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6
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Guéant JL, Chéry C, Oussalah A, Nadaf J, Coelho D, Josse T, Flayac J, Robert A, Koscinski I, Gastin I, Filhine-Tresarrieu P, Pupavac M, Brebner A, Watkins D, Pastinen T, Montpetit A, Hariri F, Tregouët D, Raby BA, Chung WK, Morange PE, Froese DS, Baumgartner MR, Benoist JF, Ficicioglu C, Marchand V, Motorin Y, Bonnemains C, Feillet F, Majewski J, Rosenblatt DS. Publisher Correction: A PRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients. Nat Commun 2018; 9:554. [PMID: 29396438 PMCID: PMC5797229 DOI: 10.1038/s41467-018-03054-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
Abstract
The original version of this Article contained an error in the title, which was incorrectly given as 'APRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients'. This has now been corrected in both the PDF and HTML versions of the Article to read 'A PRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients'.
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Affiliation(s)
- Jean-Louis Guéant
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France.
| | - Céline Chéry
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Abderrahim Oussalah
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Javad Nadaf
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, H4A 3J1, Montreal, Quebec, Canada
| | - David Coelho
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Thomas Josse
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Justine Flayac
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Aurélie Robert
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Isabelle Koscinski
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Isabelle Gastin
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Pierre Filhine-Tresarrieu
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Mihaela Pupavac
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, H4A 3J1, Montreal, Quebec, Canada
| | - Alison Brebner
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, H4A 3J1, Montreal, Quebec, Canada
| | - David Watkins
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, H4A 3J1, Montreal, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, H4A 3J1, Montreal, Quebec, Canada
| | - Alexandre Montpetit
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, H4A 3J1, Montreal, Quebec, Canada
| | - Fadi Hariri
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, H4A 3J1, Montreal, Quebec, Canada
| | - David Tregouët
- Sorbonne Universités, UPMC University Paris 06, Institut National pour la Santé et la Recherche Médicale (INSERM), ICAN Institute for Cardiometabolism and Nutrition, Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, 75013, Paris, France
| | - Benjamin A Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, 02115, Boston, MA, United States of America
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, 10032, New York, NY, United States of America
| | - Pierre-Emmanuel Morange
- INSERM, UMR_S1062, Nutrition Obesity and Risk of Thrombosis, Aix-Marseille University, 13005, Marseille, France
| | - D Sean Froese
- Division of Metabolism and Children's Research Centre (CRC), University Children's Hospital, CH-8032, Zürich, Switzerland
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Centre (CRC), University Children's Hospital, CH-8032, Zürich, Switzerland
| | | | - Can Ficicioglu
- Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, 19104, Philadelphia, PA, United States of America
| | - Virginie Marchand
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR7365 CNRS - Université, de Lorraine and FR3209 CNRS- Université de Lorraine, 54505, Nancy, France
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR7365 CNRS - Université, de Lorraine and FR3209 CNRS- Université de Lorraine, 54505, Nancy, France
| | - Chrystèle Bonnemains
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - François Feillet
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Jacek Majewski
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, H4A 3J1, Montreal, Quebec, Canada
| | - David S Rosenblatt
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, H4A 3J1, Montreal, Quebec, Canada
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7
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Guéant JL, Chéry C, Oussalah A, Nadaf J, Coelho D, Josse T, Flayac J, Robert A, Koscinski I, Gastin I, Filhine-Tresarrieu P, Pupavac M, Brebner A, Watkins D, Pastinen T, Montpetit A, Hariri F, Tregouët D, Raby BA, Chung WK, Morange PE, Froese DS, Baumgartner MR, Benoist JF, Ficicioglu C, Marchand V, Motorin Y, Bonnemains C, Feillet F, Majewski J, Rosenblatt DS. APRDX1 mutant allele causes a MMACHC secondary epimutation in cblC patients. Nat Commun 2018; 9:67. [PMID: 29302025 PMCID: PMC5754367 DOI: 10.1038/s41467-017-02306-5] [Citation(s) in RCA: 53] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2017] [Accepted: 11/17/2017] [Indexed: 12/17/2022] Open
Abstract
To date, epimutations reported in man have been somatic and erased in germlines. Here, we identify a cause of the autosomal recessive cblC class of inborn errors of vitamin B12 metabolism that we name “epi-cblC”. The subjects are compound heterozygotes for a genetic mutation and for a promoter epimutation, detected in blood, fibroblasts, and sperm, at the MMACHC locus; 5-azacytidine restores the expression of MMACHC in fibroblasts. MMACHC is flanked by CCDC163P and PRDX1, which are in the opposite orientation. The epimutation is present in three generations and results from PRDX1 mutations that force antisense transcription of MMACHC thereby possibly generating a H3K36me3 mark. The silencing of PRDX1 transcription leads to partial hypomethylation of the epiallele and restores the expression of MMACHC. This example of epi-cblC demonstrates the need to search for compound epigenetic-genetic heterozygosity in patients with typical disease manifestation and genetic heterozygosity in disease-causing genes located in other gene trios. Inborn errors of vitamin B12 metabolism of the cblC class are caused by mutations in the MMACHC gene. Here, Guéant et al. report epi-cblC, a class of cblC in which patients are compound heterozygous for a genetic mutation and a secondary epimutation at the MMACHC locus.
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Affiliation(s)
- Jean-Louis Guéant
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France.
| | - Céline Chéry
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Abderrahim Oussalah
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Javad Nadaf
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, Montreal, H4A 3J1, Quebec, Canada
| | - David Coelho
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Thomas Josse
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Justine Flayac
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Aurélie Robert
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Isabelle Koscinski
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Isabelle Gastin
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Pierre Filhine-Tresarrieu
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Mihaela Pupavac
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, Montreal, H4A 3J1, Quebec, Canada
| | - Alison Brebner
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, Montreal, H4A 3J1, Quebec, Canada
| | - David Watkins
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, Montreal, H4A 3J1, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, Montreal, H4A 3J1, Quebec, Canada
| | - Alexandre Montpetit
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, Montreal, H4A 3J1, Quebec, Canada
| | - Fadi Hariri
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, Montreal, H4A 3J1, Quebec, Canada
| | - David Tregouët
- Sorbonne Universités, UPMC University Paris 06, Institut National pour la Santé et la Recherche Médicale (INSERM), ICAN Institute for Cardiometabolism and Nutrition, Unité Mixte de Recherche en Santé (UMR_S) 1166, Team Genomics & Pathophysiology of Cardiovascular Diseases, 75013 Paris, France
| | - Benjamin A Raby
- Channing Division of Network Medicine, Department of Medicine, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, 02115, United States of America
| | - Wendy K Chung
- Departments of Pediatrics and Medicine, Columbia University, New York, NY, 10032, United States of America
| | - Pierre-Emmanuel Morange
- INSERM, UMR_S1062, Nutrition Obesity and Risk of Thrombosis, Aix-Marseille University, 13005, Marseille, France
| | - D Sean Froese
- Division of Metabolism and Children's Research Centre (CRC), University Children's Hospital, CH-8032, Zürich, Switzerland
| | - Matthias R Baumgartner
- Division of Metabolism and Children's Research Centre (CRC), University Children's Hospital, CH-8032, Zürich, Switzerland
| | | | - Can Ficicioglu
- Children's Hospital of Philadelphia, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA, 19104, United States of America
| | - Virginie Marchand
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR7365 CNRS - Université de Lorraine and FR3209 CNRS- Université de Lorraine, 54505, Nancy, France
| | - Yuri Motorin
- Laboratoire Ingénierie Moléculaire et Physiopathologie Articulaire (IMoPA), UMR7365 CNRS - Université de Lorraine and FR3209 CNRS- Université de Lorraine, 54505, Nancy, France
| | - Chrystèle Bonnemains
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - François Feillet
- INSERM, UMR_S954 Nutrition-Genetics-Environmental Risk Exposure and Reference Centre of Inborn Metabolism Diseases, University of Lorraine and University Hospital Centre of Nancy (CHRU Nancy), 54505, Nancy, France
| | - Jacek Majewski
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, Montreal, H4A 3J1, Quebec, Canada
| | - David S Rosenblatt
- Department of Human Genetics, McGill University and Research Institute McGill University Health Centre, Montreal, H4A 3J1, Quebec, Canada
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8
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Ngô HM, Zhou Y, Lorenzi H, Wang K, Kim TK, Zhou Y, El Bissati K, Mui E, Fraczek L, Rajagopala SV, Roberts CW, Henriquez FL, Montpetit A, Blackwell JM, Jamieson SE, Wheeler K, Begeman IJ, Naranjo-Galvis C, Alliey-Rodriguez N, Davis RG, Soroceanu L, Cobbs C, Steindler DA, Boyer K, Noble AG, Swisher CN, Heydemann PT, Rabiah P, Withers S, Soteropoulos P, Hood L, McLeod R. Toxoplasma Modulates Signature Pathways of Human Epilepsy, Neurodegeneration & Cancer. Sci Rep 2017; 7:11496. [PMID: 28904337 PMCID: PMC5597608 DOI: 10.1038/s41598-017-10675-6] [Citation(s) in RCA: 76] [Impact Index Per Article: 10.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2016] [Accepted: 08/14/2017] [Indexed: 12/27/2022] Open
Abstract
One third of humans are infected lifelong with the brain-dwelling, protozoan parasite, Toxoplasma gondii. Approximately fifteen million of these have congenital toxoplasmosis. Although neurobehavioral disease is associated with seropositivity, causality is unproven. To better understand what this parasite does to human brains, we performed a comprehensive systems analysis of the infected brain: We identified susceptibility genes for congenital toxoplasmosis in our cohort of infected humans and found these genes are expressed in human brain. Transcriptomic and quantitative proteomic analyses of infected human, primary, neuronal stem and monocytic cells revealed effects on neurodevelopment and plasticity in neural, immune, and endocrine networks. These findings were supported by identification of protein and miRNA biomarkers in sera of ill children reflecting brain damage and T. gondii infection. These data were deconvoluted using three systems biology approaches: "Orbital-deconvolution" elucidated upstream, regulatory pathways interconnecting human susceptibility genes, biomarkers, proteomes, and transcriptomes. "Cluster-deconvolution" revealed visual protein-protein interaction clusters involved in processes affecting brain functions and circuitry, including lipid metabolism, leukocyte migration and olfaction. Finally, "disease-deconvolution" identified associations between the parasite-brain interactions and epilepsy, movement disorders, Alzheimer's disease, and cancer. This "reconstruction-deconvolution" logic provides templates of progenitor cells' potentiating effects, and components affecting human brain parasitism and diseases.
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Affiliation(s)
- Huân M Ngô
- The University of Chicago, Chicago, IL, 60637, USA.,Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA.,BrainMicro LLC, New Haven, CT, 06511, USA
| | - Ying Zhou
- The University of Chicago, Chicago, IL, 60637, USA
| | | | - Kai Wang
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Taek-Kyun Kim
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Yong Zhou
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | | | - Ernest Mui
- The University of Chicago, Chicago, IL, 60637, USA
| | | | | | | | - Fiona L Henriquez
- The University of Chicago, Chicago, IL, 60637, USA.,FLH, IBEHR School of Science and Sport, University of the West of Scotland, Paisley, PA1 2BE, UK
| | - Alexandre Montpetit
- Genome Quebec, Montréal, QC H3B 1S6, Canada; McGill University, Montréal, QC H3A 0G4, Canada
| | - Jenefer M Blackwell
- Department of Pathology, University of Cambridge, Cambridge, CB2 1QP, United Kingdom.,Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | - Sarra E Jamieson
- Telethon Kids Institute, The University of Western Australia, Perth, Australia
| | | | | | | | | | | | | | - Charles Cobbs
- California Pacific Medical Center, San Francisco, CA, 94114, USA
| | - Dennis A Steindler
- JM USDA Human Nutrition Research Center on Aging, Tufts University, Boston, MA, 02111, USA
| | - Kenneth Boyer
- Rush University Medical Center, Chicago, IL, 60612, USA
| | - A Gwendolyn Noble
- Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | - Charles N Swisher
- Northwestern University, Feinberg School of Medicine, Chicago, IL, 60611, USA
| | | | - Peter Rabiah
- Northshore University Health System, Evanston, IL, 60201, USA
| | | | | | - Leroy Hood
- Institute for Systems Biology, Seattle, WA, 98109, USA
| | - Rima McLeod
- The University of Chicago, Chicago, IL, 60637, USA.
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9
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Torchia J, Golbourn B, Feng S, Ho KC, Sin-Chan P, Vasiljevic A, Norman JD, Guilhamon P, Garzia L, Agamez NR, Lu M, Chan TS, Picard D, de Antonellis P, Khuong-Quang DA, Planello AC, Zeller C, Barsyte-Lovejoy D, Lafay-Cousin L, Letourneau L, Bourgey M, Yu M, Gendoo DMA, Dzamba M, Barszczyk M, Medina T, Riemenschneider AN, Morrissy AS, Ra YS, Ramaswamy V, Remke M, Dunham CP, Yip S, Ng HK, Lu JQ, Mehta V, Albrecht S, Pimentel J, Chan JA, Somers GR, Faria CC, Roque L, Fouladi M, Hoffman LM, Moore AS, Wang Y, Choi SA, Hansford JR, Catchpoole D, Birks DK, Foreman NK, Strother D, Klekner A, Bognár L, Garami M, Hauser P, Hortobágyi T, Wilson B, Hukin J, Carret AS, Van Meter TE, Hwang EI, Gajjar A, Chiou SH, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheinemann K, Fleming AJ, Johnston DL, Michaud J, Zelcer S, Hammond R, Afzal S, Ramsay DA, Sirachainan N, Hongeng S, Larbcharoensub N, Grundy RG, Lulla RR, Fangusaro JR, Druker H, Bartels U, Grant R, Malkin D, McGlade CJ, Nicolaides T, Tihan T, Phillips J, Majewski J, Montpetit A, Bourque G, Bader GD, Reddy AT, Gillespie GY, Warmuth-Metz M, Rutkowski S, Tabori U, Lupien M, Brudno M, Schüller U, Pietsch T, Judkins AR, Hawkins CE, Bouffet E, Kim SK, Dirks PB, Taylor MD, Erdreich-Epstein A, Arrowsmith CH, De Carvalho DD, Rutka JT, Jabado N, Huang A. Integrated (epi)-Genomic Analyses Identify Subgroup-Specific Therapeutic Targets in CNS Rhabdoid Tumors. Cancer Cell 2016; 30:891-908. [PMID: 27960086 PMCID: PMC5500911 DOI: 10.1016/j.ccell.2016.11.003] [Citation(s) in RCA: 164] [Impact Index Per Article: 20.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 09/19/2016] [Accepted: 10/31/2016] [Indexed: 02/07/2023]
Abstract
We recently reported that atypical teratoid rhabdoid tumors (ATRTs) comprise at least two transcriptional subtypes with different clinical outcomes; however, the mechanisms underlying therapeutic heterogeneity remained unclear. In this study, we analyzed 191 primary ATRTs and 10 ATRT cell lines to define the genomic and epigenomic landscape of ATRTs and identify subgroup-specific therapeutic targets. We found ATRTs segregated into three epigenetic subgroups with distinct genomic profiles, SMARCB1 genotypes, and chromatin landscape that correlated with differential cellular responses to a panel of signaling and epigenetic inhibitors. Significantly, we discovered that differential methylation of a PDGFRB-associated enhancer confers specific sensitivity of group 2 ATRT cells to dasatinib and nilotinib, and suggest that these are promising therapies for this highly lethal ATRT subtype.
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Affiliation(s)
- Jonathon Torchia
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Brian Golbourn
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Shengrui Feng
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G0A4, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - King Ching Ho
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Patrick Sin-Chan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Alexandre Vasiljevic
- Department of Pathology, Groupement Hospitalier Est, CHU de Lyon, Lyon-Bron 69677, France
| | - Joseph D Norman
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Paul Guilhamon
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Livia Garzia
- Program in Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Natalia R Agamez
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Mei Lu
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Tiffany S Chan
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Daniel Picard
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Pasqualino de Antonellis
- Program in Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Dong-Anh Khuong-Quang
- Department of Pediatrics, McGill University, Montreal, QC H3Z2Z3, Canada; Department of Human Genetics, McGill University, Montreal, QC H3Z2Z3, Canada
| | - Aline C Planello
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Constanze Zeller
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Dalia Barsyte-Lovejoy
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Lucie Lafay-Cousin
- Division of Pediatric Hematology/Oncology, Alberta Children's Hospital, AB T3B6A8, Canada
| | - Louis Letourneau
- Genome Quebec Innovation Centre, McGill University, Montreal, QC H3A1A4, Canada
| | - Mathieu Bourgey
- Genome Quebec Innovation Centre, McGill University, Montreal, QC H3A1A4, Canada
| | - Man Yu
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Deena M A Gendoo
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Misko Dzamba
- Department of Computer Science, University of Toronto, Toronto, ON M5G0A4, Canada
| | - Mark Barszczyk
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Tiago Medina
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Alexandra N Riemenschneider
- Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - A Sorana Morrissy
- Program in Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Young-Shin Ra
- Department of Neurosurgery, Asan Medical Center, Seoul 138-736, Korea
| | - Vijay Ramaswamy
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Marc Remke
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Christopher P Dunham
- Division of Anatomic Pathology, Children's and Women's Health Centre of B.C, University of British Columbia, Vancouver, BC V6H3N1, Canada
| | - Stephen Yip
- Department of Pathology & Laboratory Medicine, University of British Columbia, V6T1Z3, Canada
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Qiang Lu
- Laboratory Medicine and Pathology, Stollery Children's Hospital, University of Alberta, Edmonton, AB T2W3N2, Canada
| | - Vivek Mehta
- Division of Neurosurgery, Stollery Children's Hospital, University of Alberta, Edmonton, AB T2W3N2, Canada
| | - Steffen Albrecht
- Department of Pathology, McGill University, Montreal, QC H3Z2Z3, Canada
| | - Jose Pimentel
- Divison of Pathology, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon 1649-035, Portugal
| | - Jennifer A Chan
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB T2N1N4, Canada
| | - Gino R Somers
- Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Claudia C Faria
- Department of Neurosurgery, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon 1649-035, Portugal
| | - Lucia Roque
- Cytometry and Cytogenetic Laboratory, CIPM, Portuguese Cancer Institute, Lisbon 1099-023, Portugal
| | - Maryam Fouladi
- Division of Oncology, Department of Cancer and Blood Diseases, Cincinnati Children's Hospital, Cincinnati, OH 45229, USA
| | - Lindsey M Hoffman
- Department of Pediatrics, University of Colorado, Denver, CO 80045, USA
| | - Andrew S Moore
- Oncology Service, Children's Health Queensland Hospital; University of Queensland Diamantina Institute, Brisbane, QLD 4102, Australia
| | - Yin Wang
- Research Institute of Health Development Strategies, Fudan University, Shanghai 200032, China
| | - Seung Ah Choi
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 03080, Korea
| | - Jordan R Hansford
- Royal Children's Hospital, Murdoch Children's Research Institute, Melbourne, VIC 3052, Australia
| | - Daniel Catchpoole
- Children's Cancer Research Unit, Children's Hospital at Westmead, Westmead, NSW 2145, Australia
| | - Diane K Birks
- Department of Pediatrics, University of Colorado, Denver, CO 80045, USA
| | | | - Doug Strother
- Division of Pediatric Hematology/Oncology, Stollery Children's Hospital, University of Alberta, Edmonton, AB T2W3N2, Canada
| | - Almos Klekner
- Department of Neurosurgery, University of Debrecen, Debrecen 4032, Hungary
| | - Laszló Bognár
- Department of Neurosurgery, University of Debrecen, Debrecen 4032, Hungary
| | - Miklós Garami
- Second Department of Pediatrics, Semmelweis University, Budapest 1094, Hungary
| | - Péter Hauser
- Second Department of Pediatrics, Semmelweis University, Budapest 1094, Hungary
| | - Tibor Hortobágyi
- Department of Histopathology, University of Szeged, Szeged 6720, Hungary
| | - Beverly Wilson
- Division of Pediatric Hematology/Oncology, Stollery Children's Hospital, University of Alberta, Edmonton, AB T2W3N2, Canada
| | - Juliette Hukin
- Division of Hematology and Oncology, Children's and Women's Health Centre of B.C, University of British Columbia, Vancouver, BC V6H3N1, Canada
| | - Anne-Sophie Carret
- Department of Pediatrics, Division of Hematology-Oncology, Université de Montréal/CHU Sainte-Justine, Montreal, QC H3T1C5, Canada
| | - Timothy E Van Meter
- Department of Neurosurgery, Virginia Commonwealth University, Richmond, VA 23298-0631, USA
| | - Eugene I Hwang
- Department of Oncology, Children's National Medical Center, Washington, DC 20010, USA
| | - Amar Gajjar
- Division of Neuro-Oncology, St. Jude Children's Research Hospital, Memphis, TN 38105, USA
| | - Shih-Hwa Chiou
- Department of Medical Research, Taipei Veterans General Hospital and National Yang-Ming University, Taipei 112, Taiwan
| | - Hideo Nakamura
- Department of Neurosurgery, Kumamoto University, Kumamoto 860-8556, Japan
| | - Helen Toledano
- Department of Pediatric Hematology Oncology, Children's Medical Center of Israel, Petach Tikva 49202, Isreal
| | - Iris Fried
- Department of Pediatric Hematology-Oncology, Hadassah Hebrew University Medical Center, Jerusalem 91120, Israel
| | - Daniel Fults
- Department of Neurosurgery, University of Utah, School of Medicine, Salt Lake City, UT 84132, USA
| | - Takafumi Wataya
- Department of Neurosurgery, Shizuoka Children's Hospital, Shizuoka 420-8660, Japan
| | - Chris Fryer
- Division of Hematology and Oncology, Children's and Women's Health Centre of B.C, University of British Columbia, Vancouver, BC V6H3N1, Canada
| | - David D Eisenstat
- Division of Pediatric Hematology/Oncology, Stollery Children's Hospital, University of Alberta, Edmonton, AB T2W3N2, Canada
| | - Katrin Scheinemann
- Department of Pediatrics, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Adam J Fleming
- Department of Pediatrics, McMaster University, Hamilton, ON L8S4K1, Canada
| | - Donna L Johnston
- Department of Pediatrics, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON K1H8L1, Canada
| | - Jean Michaud
- Pathology and Laboratory Medicine, Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, ON K1H8L1, Canada
| | - Shayna Zelcer
- Division of Pediatric Hematology/Oncology, Children's Hospital, London Health Sciences Center, London, ON N6A5A5, Canada
| | - Robert Hammond
- Department of Pathology and Laboratory Medicine, Children's Hospital of Western Ontario, University of Western Ontario, London, ON N6A5W9, Canada
| | - Samina Afzal
- Department of Pediatrics, Dalhousie University, Halifax, NS B3H4R2, Canada
| | - David A Ramsay
- Department of Pathology and Laboratory Medicine, Children's Hospital of Western Ontario, University of Western Ontario, London, ON N6A5W9, Canada
| | - Nongnuch Sirachainan
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10300, Thailand
| | - Suradej Hongeng
- Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10300, Thailand
| | - Noppadol Larbcharoensub
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok 10400, Thailand
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, University of Nottingham, Nottingham NG72RD, England
| | - Rishi R Lulla
- Division of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Jason R Fangusaro
- Division of Pediatric Hematology-Oncology and Stem Cell Transplantation, Ann and Robert H. Lurie Children's Hospital of Chicago, Chicago, IL 60611, USA
| | - Harriet Druker
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Ute Bartels
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Ronald Grant
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - David Malkin
- Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Program in Genetics & Genome Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - C Jane McGlade
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G0A4, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Theodore Nicolaides
- Department of Pediatrics (Hematology/Oncology), University of California, San Francisco, San Francisco, CA 94143-0112, USA
| | - Tarik Tihan
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94143-0112, USA
| | - Joanna Phillips
- Department of Neurosurgery, University of California, San Francisco, San Francisco, CA 94143-0112, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC H3Z2Z3, Canada; Genome Quebec Innovation Centre, McGill University, Montreal, QC H3A1A4, Canada
| | - Alexandre Montpetit
- Genome Quebec Innovation Centre, McGill University, Montreal, QC H3A1A4, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H3Z2Z3, Canada; Genome Quebec Innovation Centre, McGill University, Montreal, QC H3A1A4, Canada
| | - Gary D Bader
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5G0A4, Canada
| | - Alyssa T Reddy
- Department of Pediatric Hematology and Oncology, University of Alabama, Birmingham, AL 35233, USA
| | - G Yancey Gillespie
- Department of Neurosurgery, University of Alabama, Birmingham, AL 35233, USA
| | - Monika Warmuth-Metz
- Department of Neuroradiology, University of Würzburg, Würzburg 97070, Germany
| | - Stefan Rutkowski
- Department of Pediatric Hematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Uri Tabori
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Program in Genetics & Genome Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Mathieu Lupien
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G0A4, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Michael Brudno
- Department of Computer Science, University of Toronto, Toronto, ON M5G0A4, Canada; Program in Genetics & Genome Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Ulrich Schüller
- Department of Neuropathology, University Medical Center Hamburg-Eppendorf, Hamburg 20246, Germany
| | - Torsten Pietsch
- Institute for Neuropathology, University of Bonn Medical Center, Bonn 53105, Germany
| | - Alexander R Judkins
- Department of Pathology & Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA 90027, USA
| | - Cynthia E Hawkins
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Pathology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Eric Bouffet
- Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Seung-Ki Kim
- Division of Pediatric Neurosurgery, Seoul National University Children's Hospital, Seoul 03080, Korea
| | - Peter B Dirks
- Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Program in Developmental & Stem Cell Biology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada
| | - Anat Erdreich-Epstein
- Department of Pediatrics, Children's Hospital Los Angeles, Keck School of Medicine, University of Southern California, Los Angeles, CA 90027, USA
| | - Cheryl H Arrowsmith
- Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada
| | - Daniel D De Carvalho
- Department of Medical Biophysics, University of Toronto, Toronto, ON M5G0A4, Canada; Princess Margaret Cancer Center, University Health Network, Toronto, ON M5G1L7, Canada.
| | - James T Rutka
- Department of Surgery, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Neurosurgery, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada.
| | - Nada Jabado
- Department of Pediatrics, McGill University, Montreal, QC H3Z2Z3, Canada; Department of Human Genetics, McGill University, Montreal, QC H3Z2Z3, Canada.
| | - Annie Huang
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON M5G0A4, Canada; Department of Paediatrics, University of Toronto, Toronto, ON M5G0A4, Canada; Division of Hematology/Oncology, Hospital for Sick Children, Toronto, ON M5G1X8, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, Toronto, ON M5G1X8, Canada.
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10
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Morin A, Kwan T, Ge B, Letourneau L, Ban M, Tandre K, Caron M, Sandling JK, Carlsson J, Bourque G, Laprise C, Montpetit A, Syvanen AC, Ronnblom L, Sawcer SJ, Lathrop MG, Pastinen T. Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells. BMC Med Genomics 2016; 9:59. [PMID: 27624058 PMCID: PMC5022205 DOI: 10.1186/s12920-016-0220-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 09/01/2016] [Indexed: 12/14/2022] Open
Abstract
Background The observation that the genetic variants identified in genome-wide association studies (GWAS) frequently lie in non-coding regions of the genome that contain cis-regulatory elements suggests that altered gene expression underlies the development of many complex traits. In order to efficiently make a comprehensive assessment of the impact of non-coding genetic variation in immune related diseases we emulated the whole-exome sequencing paradigm and developed a custom capture panel for the known DNase I hypersensitive site (DHS) in immune cells – “Immunoseq”. Results We performed Immunoseq in 30 healthy individuals where we had existing transcriptome data from T cells. We identified a large number of novel non-coding variants in these samples. Relying on allele specific expression measurements, we also showed that our selected capture regions are enriched for functional variants that have an impact on differential allelic gene expression. The results from a replication set with 180 samples confirmed our observations. Conclusions We show that Immunoseq is a powerful approach to detect novel rare variants in regulatory regions. We also demonstrate that these novel variants have a potential functional role in immune cells. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0220-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andréanne Morin
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Bing Ge
- McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Louis Letourneau
- McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Maria Ban
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Karolina Tandre
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
| | - Maxime Caron
- McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Johanna K Sandling
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden.,Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonas Carlsson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Quebec, Canada
| | - Alexandre Montpetit
- McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Ann-Christine Syvanen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Ronnblom
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
| | - Stephen J Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mark G Lathrop
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada. .,McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada.
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11
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Fontebasso AM, Shirinian M, Khuong-Quang DA, Bechet D, Gayden T, Kool M, De Jay N, Jacob K, Gerges N, Hutter B, Şeker-Cin H, Witt H, Montpetit A, Brunet S, Lepage P, Bourret G, Klekner A, Bognár L, Hauser P, Garami M, Farmer JP, Montes JL, Atkinson J, Lambert S, Kwan T, Korshunov A, Tabori U, Collins VP, Albrecht S, Faury D, Pfister SM, Paulus W, Hasselblatt M, Jones DTW, Jabado N. Non-random aneuploidy specifies subgroups of pilocytic astrocytoma and correlates with older age. Oncotarget 2016; 6:31844-56. [PMID: 26378811 PMCID: PMC4741644 DOI: 10.18632/oncotarget.5571] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2015] [Accepted: 08/15/2015] [Indexed: 11/25/2022] Open
Abstract
Pilocytic astrocytoma (PA) is the most common brain tumor in children but is rare in adults, and hence poorly studied in this age group. We investigated 222 PA and report increased aneuploidy in older patients. Aneuploid genomes were identified in 45% of adult compared with 17% of pediatric PA. Gains were non-random, favoring chromosomes 5, 7, 6 and 11 in order of frequency, and preferentially affecting non-cerebellar PA and tumors with BRAF V600E mutations and not with KIAA1549-BRAF fusions or FGFR1 mutations. Aneuploid PA differentially expressed genes involved in CNS development, the unfolded protein response, and regulators of genomic stability and the cell cycle (MDM2, PLK2),whose correlated programs were overexpressed specifically in aneuploid PA compared to other glial tumors. Thus, convergence of pathways affecting the cell cycle and genomic stability may favor aneuploidy in PA, possibly representing an additional molecular driver in older patients with this brain tumor.
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Affiliation(s)
- Adam M Fontebasso
- Division of Experimental Medicine, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Margret Shirinian
- Department of Experimental Pathology, Immunology and Microbiology, American University Of Beirut, Beirut, Lebanon
| | - Dong-Anh Khuong-Quang
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Denise Bechet
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Tenzin Gayden
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Marcel Kool
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Nicolas De Jay
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Karine Jacob
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Noha Gerges
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Barbara Hutter
- Division of Theoretical Bioinformatics, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Huriye Şeker-Cin
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Hendrik Witt
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Alexandre Montpetit
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Sébastien Brunet
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Pierre Lepage
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Geneviève Bourret
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Almos Klekner
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - László Bognár
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Peter Hauser
- 2nd Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Miklós Garami
- 2nd Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Jean-Pierre Farmer
- Department of Neurosurgery, Montreal Children's Hospital and McGill University Health Centre, Montreal, Canada
| | - Jose-Luis Montes
- Department of Neurosurgery, Montreal Children's Hospital and McGill University Health Centre, Montreal, Canada
| | - Jeffrey Atkinson
- Department of Neurosurgery, Montreal Children's Hospital and McGill University Health Centre, Montreal, Canada
| | - Sally Lambert
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Tony Kwan
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Uri Tabori
- Division of Pediatric Hematology-Oncology and The Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Canada
| | - V Peter Collins
- Division of Molecular Histopathology, Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Steffen Albrecht
- Department of Pathology, Montreal Children's Hospital and McGill University Health Centre, Montreal, Canada
| | - Damien Faury
- Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany.,Department of Pediatric Oncology, Hematology and Immunology, University of Heidelberg, Heidelberg, Germany
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Centre (DKFZ), Heidelberg, Germany
| | - Nada Jabado
- Division of Experimental Medicine, McGill University and McGill University Health Centre, Montreal, Quebec, Canada.,Departments of Pediatrics and Human Genetics, McGill University and McGill University Health Centre, Montreal, Quebec, Canada
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12
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Abstract
The transcriptome is composed of different types of RNA molecules including mRNAs, tRNAs, rRNAs, and other noncoding RNAs that are found inside a cell at a given time. Analyzing transcriptome patterns can shed light on the functional state of the cell as well as on the dynamics of cellular behavior associated with genomic and environmental changes. Likewise, transcriptome analysis has been a major help in solving biological issues and understanding the molecular basis of many diseases including human cancers. Specifically, since targeted and whole genome sequencing studies are becoming more common in identifying the driving factors of cancer, a comprehensive and high-resolution analysis of the transcriptome, as provided by RNA-Sequencing (RNA-Seq), plays a key role in investigating the functional relevance of the identified genomic aberrations. Here, we describe experimental procedures of RNA-Seq and downstream data processing and analysis, with a focus on the identification of abnormally expressed transcripts and genes.
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Affiliation(s)
- Pudchalaluck Panichnantakul
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Mathieu Bourgey
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | | | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Yasser Riazalhosseini
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada.
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13
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Nicolas G, Wallon D, Charbonnier C, Quenez O, Rousseau S, Richard AC, Rovelet-Lecrux A, Coutant S, Le Guennec K, Bacq D, Garnier JG, Olaso R, Boland A, Meyer V, Deleuze JF, Munter HM, Bourque G, Auld D, Montpetit A, Lathrop M, Guyant-Maréchal L, Martinaud O, Pariente J, Rollin-Sillaire A, Pasquier F, Le Ber I, Sarazin M, Croisile B, Boutoleau-Bretonnière C, Thomas-Antérion C, Paquet C, Sauvée M, Moreaud O, Gabelle A, Sellal F, Ceccaldi M, Chamard L, Blanc F, Frebourg T, Campion D, Hannequin D. Screening of dementia genes by whole-exome sequencing in early-onset Alzheimer disease: input and lessons. Eur J Hum Genet 2015; 24:710-6. [PMID: 26242991 DOI: 10.1038/ejhg.2015.173] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2015] [Revised: 06/10/2015] [Accepted: 06/30/2015] [Indexed: 12/11/2022] Open
Abstract
Causative variants in APP, PSEN1 or PSEN2 account for a majority of cases of autosomal dominant early-onset Alzheimer disease (ADEOAD, onset before 65 years). Variant detection rates in other EOAD patients, that is, with family history of late-onset AD (LOAD) (and no incidence of EOAD) and sporadic cases might be much lower. We analyzed the genomes from 264 patients using whole-exome sequencing (WES) with high depth of coverage: 90 EOAD patients with family history of LOAD and no incidence of EOAD in the family and 174 patients with sporadic AD starting between 51 and 65 years. We found three PSEN1 and one PSEN2 causative, probably or possibly causative variants in four patients (1.5%). Given the absence of PSEN1, PSEN2 and APP causative variants, we investigated whether these 260 patients might be burdened with protein-modifying variants in 20 genes that were previously shown to cause other types of dementia when mutated. For this analysis, we included an additional set of 160 patients who were previously shown to be free of causative variants in PSEN1, PSEN2 and APP: 107 ADEOAD patients and 53 sporadic EOAD patients with an age of onset before 51 years. In these 420 patients, we detected no variant that might modify the function of the 20 dementia-causing genes. We conclude that EOAD patients with family history of LOAD and no incidence of EOAD in the family or patients with sporadic AD starting between 51 and 65 years have a low variant-detection rate in AD genes.
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Affiliation(s)
- Gaël Nicolas
- Department of Genetics, Rouen University Hospital, Rouen, France.,Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - David Wallon
- Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
| | - Camille Charbonnier
- Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | - Olivier Quenez
- Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France
| | | | | | | | - Sophie Coutant
- Department of Genetics, Rouen University Hospital, Rouen, France.,Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France
| | - Kilan Le Guennec
- Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France
| | | | | | | | | | | | | | | | - Guillaume Bourque
- McGill University and Génome Québec Innovation Centre, Montréal, Canada
| | - Daniel Auld
- McGill University and Génome Québec Innovation Centre, Montréal, Canada
| | | | - Mark Lathrop
- McGill University and Génome Québec Innovation Centre, Montréal, Canada
| | | | | | - Jérémie Pariente
- Department of Neurology, CMRR and INSERM U825, Purpan University Hospital, Toulouse, France
| | - Adeline Rollin-Sillaire
- CNR-MAJ; and Department of Neurology, Université de Lille, CHU, Inserm UMR-S 1171, Lille, France
| | - Florence Pasquier
- CNR-MAJ; and Department of Neurology, Université de Lille, CHU, Inserm UMR-S 1171, Lille, France
| | - Isabelle Le Ber
- CNR-MAJ, Pitié-Salpêtrière; and CRICM, IM2A, UMR-S975 AP-HP, University Hospital Pitié-Salpêtrière, Paris, France
| | - Marie Sarazin
- Department of Neurology, AP-HP, University Hospital Saint-Anne, Paris, France
| | - Bernard Croisile
- Department of Neuropsychology, CMRR, University Hospital, Groupe Hospitalier Est, Bron, France
| | | | | | - Claire Paquet
- CMRR Paris Nord AP-HP, Hôpital Lariboisière, INSERM, U942, Université Paris Diderot, Sorbonne Paris Cité, UMRS 942, Paris, France
| | | | | | - Audrey Gabelle
- CMRR, Gui de Chauliac Hospital, Montpellier University Hospital, Montpellier, France
| | - François Sellal
- Department of Neurology, CMRR Hôpitaux Civils de Colmar and Unité INSERM U-1118, Université de Strasbourg, Strasbourg, France
| | - Mathieu Ceccaldi
- Department of Neurology and Neuropsychology, CMRR, Timone Hospital and INSERM UMR1106, Aix-Marseille University, Marseille, France
| | - Ludivine Chamard
- Department of Neurology, CMRR, Besançon University Hospital, Besançon, France
| | - Frédéric Blanc
- CMRR Alsace, Department of Neurology, University Hospital of Strasbourg, Strasbourg, France
| | - Thierry Frebourg
- Department of Genetics, Rouen University Hospital, Rouen, France.,Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France
| | - Dominique Campion
- Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Research, Rouvray Psychiatric Hospital, Sotteville-lès-Rouen, France
| | - Didier Hannequin
- Department of Genetics, Rouen University Hospital, Rouen, France.,Inserm U1079, Rouen University, IRIB, Normandy University, Rouen, France.,CNR-MAJ, Rouen University Hospital, Rouen, France.,Department of Neurology, Rouen University Hospital, Rouen, France
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14
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Torchia J, Picard D, Lafay-Cousin L, Hawkins CE, Kim SK, Letourneau L, Ra YS, Ho KC, Chan TSY, Sin-Chan P, Dunham CP, Yip S, Ng HK, Lu JQ, Albrecht S, Pimentel J, Chan JA, Somers GR, Zielenska M, Faria CC, Roque L, Baskin B, Birks D, Foreman N, Strother D, Klekner A, Garami M, Hauser P, Hortobágyi T, Bognár L, Wilson B, Hukin J, Carret AS, Van Meter TE, Nakamura H, Toledano H, Fried I, Fults D, Wataya T, Fryer C, Eisenstat DD, Scheineman K, Johnston D, Michaud J, Zelcer S, Hammond R, Ramsay DA, Fleming AJ, Lulla RR, Fangusaro JR, Sirachainan N, Larbcharoensub N, Hongeng S, Barakzai MA, Montpetit A, Stephens D, Grundy RG, Schüller U, Nicolaides T, Tihan T, Phillips J, Taylor MD, Rutka JT, Dirks P, Bader GD, Warmuth-Metz M, Rutkowski S, Pietsch T, Judkins AR, Jabado N, Bouffet E, Huang A. Molecular subgroups of atypical teratoid rhabdoid tumours in children: an integrated genomic and clinicopathological analysis. Lancet Oncol 2015; 16:569-82. [PMID: 25882982 DOI: 10.1016/s1470-2045(15)70114-2] [Citation(s) in RCA: 105] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
BACKGROUND Rhabdoid brain tumours, also called atypical teratoid rhabdoid tumours, are lethal childhood cancers with characteristic genetic alterations of SMARCB1/hSNF5. Lack of biological understanding of the substantial clinical heterogeneity of these tumours restricts therapeutic advances. We integrated genomic and clinicopathological analyses of a cohort of patients with atypical teratoid rhabdoid tumours to find out the molecular basis for clinical heterogeneity in these tumours. METHODS We obtained 259 rhabdoid tumours from 37 international institutions and assessed transcriptional profiles in 43 primary tumours and copy number profiles in 38 primary tumours to discover molecular subgroups of atypical teratoid rhabdoid tumours. We used gene and pathway enrichment analyses to discover group-specific molecular markers and did immunohistochemical analyses on 125 primary tumours to evaluate clinicopathological significance of molecular subgroup and ASCL1-NOTCH signalling. FINDINGS Transcriptional analyses identified two atypical teratoid rhabdoid tumour subgroups with differential enrichment of genetic pathways, and distinct clinicopathological and survival features. Expression of ASCL1, a regulator of NOTCH signalling, correlated with supratentorial location (p=0·004) and superior 5-year overall survival (35%, 95% CI 13-57, and 20%, 6-34, for ASCL1-positive and ASCL1-negative tumours, respectively; p=0·033) in 70 patients who received multimodal treatment. ASCL1 expression also correlated with superior 5-year overall survival (34%, 7-61, and 9%, 0-21, for ASCL1-positive and ASCL1-negative tumours, respectively; p=0·001) in 39 patients who received only chemotherapy without radiation. Cox hazard ratios for overall survival in patients with differential ASCL1 enrichment treated with chemotherapy with or without radiation were 2·02 (95% CI 1·04-3·85; p=0·038) and 3·98 (1·71-9·26; p=0·001). Integrated analyses of molecular subgroupings with clinical prognostic factors showed three distinct clinical risk groups of tumours with different therapeutic outcomes. INTERPRETATION An integration of clinical risk factors and tumour molecular groups can be used to identify patients who are likely to have improved long-term radiation-free survival and might help therapeutic stratification of patients with atypical teratoid rhabdoid tumours. FUNDING C17 Research Network, Genome Canada, b.r.a.i.n.child, Mitchell Duckman, Tal Doron and Suri Boon foundations.
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Affiliation(s)
- Jonathon Torchia
- Division of Hematology-Oncology, University of Toronto, Toronto, ON, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Daniel Picard
- Division of Hematology-Oncology, University of Toronto, Toronto, ON, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Lucie Lafay-Cousin
- Alberta Children's Hospital, and Departments of Oncology and Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Cynthia E Hawkins
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Pathology, Hospital for Sick Children, Toronto, ON, Canada
| | - Seung-Ki Kim
- Department of Neurosurgery, Seoul National University Children's Hospital, Seoul, South Korea
| | - Louis Letourneau
- Genome Quebec Innovation Centre, McGill University, Montreal, QC, Canada
| | - Young-Shin Ra
- Department of Neurosurgery, Asan Medical Center, Songpa-gu, Seoul, South Korea
| | - King Ching Ho
- Division of Hematology-Oncology, University of Toronto, Toronto, ON, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada
| | - Tiffany Sin Yu Chan
- Division of Hematology-Oncology, University of Toronto, Toronto, ON, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Patrick Sin-Chan
- Division of Hematology-Oncology, University of Toronto, Toronto, ON, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Christopher P Dunham
- Division of Anatomic Pathology, Children's and Women's Health Centre of British Columbia, Vancouver, BC, Canada
| | - Stephen Yip
- Department of Neuropathology, Vancouver General Hospital, Vancouver, BC, Canada
| | - Ho-Keung Ng
- Department of Anatomical and Cellular Pathology, Chinese University of Hong Kong, Hong Kong, China
| | - Jian-Qiang Lu
- Department of Laboratory Medicine and Pathology, University of Alberta Hospital, Edmonton, AB, Canada
| | - Steffen Albrecht
- Department of Pathology, Montreal Children's Hospital, McGill University Health Center Research Institute, Montreal, QC, Canada
| | - José Pimentel
- Department of Neurology, Hospital de Santa Maria, Centro Hospitalar Lisboa Norte, Lisbon, Portugal
| | - Jennifer A Chan
- Department of Pathology and Laboratory Medicine, University of Calgary, Calgary, AB, Canada
| | - Gino R Somers
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Maria Zielenska
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Paediatric Laboratory Medicine, Hospital for Sick Children, Toronto, ON, Canada
| | - Claudia C Faria
- Instituto de Medicina Molecular, Faculdade de Medicina, Universidade de Lisboa, Lisbon, Portugal
| | - Lucia Roque
- Cytogenetic Laboratory, Centro de Investigação em Patobiologia Molecular, Portuguese Cancer Institute, Lisbon, Portugal
| | - Berivan Baskin
- Department of Immunology, Genetics and Pathology, Uppsala University Hospital, Uppsala, Sweden
| | - Diane Birks
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Nick Foreman
- Department of Pediatrics, University of Colorado Denver, Aurora, CO, USA
| | - Douglas Strother
- Alberta Children's Hospital, and Departments of Oncology and Pediatrics, Cumming School of Medicine, University of Calgary, Calgary, AB, Canada
| | - Almos Klekner
- Department of Neurosurgery, University of Debrecen, Debrecen, Hungary
| | - Miklos Garami
- Second Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Peter Hauser
- Second Department of Pediatrics, Semmelweis University, Budapest, Hungary
| | - Tibor Hortobágyi
- Department of Histopathology, Faculty of Medicine, University of Szeged, Hungary
| | - Laszló Bognár
- Department of Neurosurgery, University of Debrecen, Debrecen, Hungary
| | - Beverly Wilson
- Division of Pediatric Hematology/Oncology, Department of Pediatrics, University of Alberta, Edmonton, AB, Canada
| | - Juliette Hukin
- Division of Neurology and Oncology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - Anne-Sophie Carret
- Division of Hematology-Oncology, Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montreal, QC, Canada
| | - Timothy E Van Meter
- Pediatric Hematology-Oncology, Department of Pediatrics, Virginia Commonwealth University School of Medicine, Richmond, VA, USA
| | - Hideo Nakamura
- Department of Neurosurgery, Kumamoto University, Kumamoto, Japan
| | - Helen Toledano
- Oncology Department, Schneider Hospital, Petach Tikva, Israel
| | - Iris Fried
- Pediatric Hematology Oncology Department, Hadassah Hebrew University Hospital, Jerusalem, Israel
| | - Daniel Fults
- Department of Neurosurgery, University of Utah, School of Medicine, Salt Lake City, UT, USA
| | - Takafumi Wataya
- Department of Neurosurgery, Shizuoka Children's Hospital, Aoi-ku, Shizuoka, Japan
| | - Chris Fryer
- Division of Hematology and Oncology, Department of Pediatrics, University of British Columbia, Vancouver, BC, Canada
| | - David D Eisenstat
- Departments of Pediatrics and Medical Genetics, University of Alberta, Edmonton, AB, Canada
| | | | - Donna Johnston
- Department of Pediatrics, Faculty of Medicine, University of Ottawa, Ottawa, ON, Canada
| | - Jean Michaud
- Department of Pathology and Laboratory Medicine, Ottawa Hospital and Children's Hospital of Eastern Ontario, Ottawa, ON, Canada
| | - Shayna Zelcer
- Division of Children's Health and Therapeutics, Children's Health Research Institute, London, ON, Canada
| | - Robert Hammond
- Department of Pathology, University of Western Ontario, London, ON, Canada
| | - David A Ramsay
- Department of Pathology, London Health Sciences Centre, London, ON, Canada
| | - Adam J Fleming
- Division of Pediatric Hematology/Oncology, McMaster University, Hamilton, ON, Canada
| | - Rishi R Lulla
- Division of Pediatrics-Hematology, Oncology and Stem Cell Transplantation, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Jason R Fangusaro
- Division of Pediatrics-Hematology, Oncology and Stem Cell Transplantation, Ann and Robert H Lurie Children's Hospital of Chicago, Chicago, IL, USA
| | - Nongnuch Sirachainan
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Noppadol Larbcharoensub
- Department of Pathology, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | - Suradej Hongeng
- Division of Hematology and Oncology, Department of Pediatrics, Faculty of Medicine, Ramathibodi Hospital, Mahidol University, Bangkok, Thailand
| | | | | | - Derek Stephens
- Department of Clinical Research Services, Hospital for Sick Children, Toronto, ON, Canada
| | - Richard G Grundy
- Children's Brain Tumour Research Centre, School of Clinical Sciences, Queen's Medical Centre, University of Nottingham, Nottingham, UK
| | - Ulrich Schüller
- Center for Neuropathology, Ludwig-Maximilians-University, Munich, Germany
| | - Theodore Nicolaides
- Department of Pediatrics Hematology/Oncology, University of California, San Francisco, CA, USA
| | - Tarik Tihan
- Department of Pathology and Laboratory Medicine, University of California, San Francisco, CA, USA
| | - Joanna Phillips
- Department of Neurological Surgery, University of California, San Francisco, CA, USA
| | - Michael D Taylor
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Neurosurgery, Hospital for Sick Children, Toronto, ON, Canada
| | - James T Rutka
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Neurosurgery, Hospital for Sick Children, Toronto, ON, Canada
| | - Peter Dirks
- Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Division of Neurosurgery, Hospital for Sick Children, Toronto, ON, Canada
| | - Gary D Bader
- Department of Computer Science, Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, ON, Canada; Department of Molecular Genetics, University of Toronto, ON, Canada
| | | | - Stefan Rutkowski
- Department of Paediatric Haematology and Oncology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Torsten Pietsch
- Department of Neuropathology, University of Bonn Medical Center, Bonn, Germany
| | - Alexander R Judkins
- Department of Pathology and Laboratory Medicine at Children's Hospital Los Angeles, Los Angeles, CA, USA
| | - Nada Jabado
- Department of Pediatrics, McGill University, Montreal, QC, Canada; Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Eric Bouffet
- Division of Hematology-Oncology, University of Toronto, Toronto, ON, Canada; Department of Pediatrics, University of Toronto, Toronto, ON, Canada
| | - Annie Huang
- Division of Hematology-Oncology, University of Toronto, Toronto, ON, Canada; Arthur and Sonia Labatt Brain Tumour Research Centre, Hospital for Sick Children, University of Toronto, Toronto, ON, Canada; Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada; Department of Pediatrics, University of Toronto, Toronto, ON, Canada.
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Kaminska M, Montpetit A, Mathieu A, Jobin V, Morisson F, Mayer P. Higher effective oronasal versus nasal continuous positive airway pressure in obstructive sleep apnea: effect of mandibular stabilization. Can Respir J 2014; 21:234-8. [PMID: 24791252 PMCID: PMC4173891 DOI: 10.1155/2014/408073] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND In some individuals with obstructive sleep apnea (OSA), oronasal continuous positive airway pressure (CPAP) leads to poorer OSA correction than nasal CPAP. The authors hypothesized that this results from posterior mandibular displacement caused by the oronasal mask. OBJECTIVE To test this hypothesis using a mandibular advancement device (MAD) for mandibular stabilization. METHODS Subjects whose OSA was not adequately corrected by oronasal CPAP at pressures for which nasal CPAP was effective were identified. These subjects underwent polysomnography (PSG) CPAP titration with each nasal and oronasal mask consecutively, with esophageal pressure and leak monitoring, to obtain the effective pressure (Peff) of CPAP for correcting obstructive events with each mask (maximum 20 cmH2O). PSG titration was repeated using a MAD in the neutral position. Cephalometry was performed. RESULTS Six subjects with mean (± SD) nasal Peff 10.4±3.0 cmH2O were studied. Oronasal Peff was greater than nasal Peff in all subjects, with obstructive events persisting at 20 cmH2O by oronasal mask in four cases. This was not due to excessive leak. With the MAD, oronasal Peff was reduced in three subjects, and Peff <20 cmH2O could be obtained in two of the four subjects with Peff >20 cmH2O by oronasal mask alone. Subjects' cephalometric variables were similar to published norms. CONCLUSION In subjects with OSA with higher oronasal than nasal Peff, this is partially explained by posterior mandibular displacement caused by the oronasal mask. Combination treatment with oronasal mask and MAD may be useful in some individuals if a nasal mask is not tolerated.
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Affiliation(s)
- M Kaminska
- Respiratory Epidemiology and Clinical Research Unit, McGill University, and Respiratory Division, McGill University Health Centre
| | - A Montpetit
- Clinique d’Orthodontie, Université de Montréal
| | - A Mathieu
- Sleep Laboratory, Centre Hospitalier Universitaire de Montreal – Hotel-Dieu, Montreal
| | - V Jobin
- Sleep Laboratory, Centre Hospitalier Universitaire de Montreal – Hotel-Dieu, Montreal
| | | | - P Mayer
- Sleep Laboratory, Centre Hospitalier Universitaire de Montreal – Hotel-Dieu, Montreal
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16
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Wang J, Pritchard JR, Kreitmann L, Montpetit A, Behr MA. Disruption of Mycobacterium avium subsp. paratuberculosis-specific genes impairs in vivo fitness. BMC Genomics 2014; 15:415. [PMID: 24885784 PMCID: PMC4058006 DOI: 10.1186/1471-2164-15-415] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 05/27/2014] [Indexed: 01/08/2023] Open
Abstract
Background Mycobacterium avium subsp. paratuberculosis (MAP) is an obligate intracellular pathogen that infects many ruminant species. The acquisition of foreign genes via horizontal gene transfer has been postulated to contribute to its pathogenesis, as these genetic elements are absent from its putative ancestor, M. avium subsp. hominissuis (MAH), an environmental organism with lesser pathogenicity. In this study, high-throughput sequencing of MAP transposon libraries were analyzed to qualitatively and quantitatively determine the contribution of individual genes to bacterial survival during infection. Results Out of 52384 TA dinucleotides present in the MAP K-10 genome, 12607 had a MycoMarT7 transposon in the input pool, interrupting 2443 of the 4350 genes in the MAP genome (56%). Of 96 genes situated in MAP-specific genomic islands, 82 were disrupted in the input pool, indicating that MAP-specific genomic regions are dispensable for in vitro growth (odds ratio = 0.21). Following 5 independent in vivo infections with this pool of mutants, the correlation between output pools was high for 4 of 5 (R = 0.49 to 0.61) enabling us to define genes whose disruption reproducibly reduced bacterial fitness in vivo. At three different thresholds for reduced fitness in vivo, MAP-specific genes were over-represented in the list of predicted essential genes. We also identified additional genes that were severely depleted after infection, and several of them have orthologues that are essential genes in M. tuberculosis. Conclusions This work indicates that the genetic elements required for the in vivo survival of MAP represent a combination of conserved mycobacterial virulence genes and MAP-specific genes acquired via horizontal gene transfer. In addition, the in vitro and in vivo essential genes identified in this study may be further characterized to offer a better understanding of MAP pathogenesis, and potentially contribute to the discovery of novel therapeutic and vaccine targets. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-415) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | | | | | | | - Marcel A Behr
- Department of Microbiology and Immunology, McGill University, 3775 University Street, Montreal, QC H3A 2B4, Canada.
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17
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Bailey SD, Xie C, Paré G, Montpetit A, Mohan V, Yusuf S, Gerstein H, Engert JC, Anand SS. Variation at the DPP4 locus influences apolipoprotein B levels in South Asians and exhibits heterogeneity in Europeans related to BMI. Diabetologia 2014; 57:738-45. [PMID: 24362726 DOI: 10.1007/s00125-013-3142-3] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/26/2012] [Accepted: 11/12/2013] [Indexed: 12/31/2022]
Abstract
AIMS/HYPOTHESIS Dyslipidaemia, a common feature of type 2 diabetes, is characterised by an increase in atherogenic particles, quantifiable through apolipoprotein B (ApoB) levels. Genetic studies of lipid levels have focused on Europeans; a study in South Asians could identify novel genes. METHODS We tested 31,739 single nucleotide polymorphisms (SNPs) from ∼ 2,000 genes in 2,573 South Asians from the epidemiological arm of the Diabetes Reduction Assessment with Ramipril and Rosiglitazone Medication (DREAM) study (EpiDREAM) for association with ApoB and we tested two novel associations for replication in 1,181 South Asians from the INTERHEART case-control study. RESULTS The SNP, rs4664443, within DPP4 was associated with ApoB (p = 7.98 × 10(-5)) in EpiDREAM. The observed association was replicated in the INTERHEART South Asians (one-sided p = 9.65 × 10(-3); combined two-sided p = 4.68 × 10(-6)). The rs4664443 SNP was not associated with ApoB among five other EpiDREAM ethnicities. However, because South Asians had a significantly lower mean BMI compared with other EpiDREAM ethnicities, we tested for and found an interaction between rs4664443 and BMI for ApoB among the Europeans, the largest subgroup in EpiDREAM (p = 4.14 × 10(-3) for interaction), observing an association with ApoB in Europeans with a BMI <25 kg/m(2) (p = 2.35 × 10(-3)), but not with a BMI ≥ 25 kg/m(2) (p = 0.21). The association between rs4664443 and ApoB among all EpiDREAM individuals with BMI <25 kg/m(2) was significant (n = 2,972; p = 1.44 × 10(-5)) compared with those with a BMI ≥ 25 kg/m(2) (n = 11,559; p = 0.81), and there was evidence of association among all genotyped individuals with a BMI <25 kg/m(2), including the INTERHEART South Asians (n = 3,601; p = 9.52 × 10(-7)). CONCLUSION/INTERPRETATION Variation at the DPP4 locus is associated with ApoB in South Asians and displays heterogeneity related to BMI in other ethnicities.
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Affiliation(s)
- Swneke D Bailey
- Department of Human Genetics, McGill University, Montreal, QC, Canada
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18
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Kleinman CL, Gerges N, Papillon-Cavanagh S, Sin-Chan P, Pramatarova A, Quang DAK, Adoue V, Busche S, Caron M, Djambazian H, Bemmo A, Fontebasso AM, Spence T, Schwartzentruber J, Albrecht S, Hauser P, Garami M, Klekner A, Bognar L, Montes JL, Staffa A, Montpetit A, Berube P, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel PM, Duchaine T, Perotti C, Fleming A, Faury D, Remke M, Gallo M, Dirks P, Taylor MD, Sladek R, Pastinen T, Chan JA, Huang A, Majewski J, Jabado N. Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. Nat Genet 2014; 46:39-44. [PMID: 24316981 DOI: 10.1038/ng.2849] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 11/13/2013] [Indexed: 12/20/2022]
Abstract
Embryonal tumors with multilayered rosettes (ETMRs) are rare, deadly pediatric brain tumors characterized by high-level amplification of the microRNA cluster C19MC. We performed integrated genetic and epigenetic analyses of 12 ETMR samples and identified, in all cases, C19MC fusions to TTYH1 driving expression of the microRNAs. ETMR tumors, cell lines and xenografts showed a specific DNA methylation pattern distinct from those of other tumors and normal tissues. We detected extreme overexpression of a previously uncharacterized isoform of DNMT3B originating at an alternative promoter that is active only in the first weeks of neural tube development. Transcriptional and immunohistochemical analyses suggest that C19MC-dependent DNMT3B deregulation is mediated by RBL2, a known repressor of DNMT3B. Transfection with individual C19MC microRNAs resulted in DNMT3B upregulation and RBL2 downregulation in cultured cells. Our data suggest a potential oncogenic re-engagement of an early developmental program in ETMR via epigenetic alteration mediated by an embryonic, brain-specific DNMT3B isoform.
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Affiliation(s)
- Claudia L Kleinman
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [3]
| | - Noha Gerges
- 1] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [2]
| | | | - Patrick Sin-Chan
- Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Albena Pramatarova
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | | | - Véronique Adoue
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Stephan Busche
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Maxime Caron
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Haig Djambazian
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Amandine Bemmo
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Adam M Fontebasso
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Tara Spence
- Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Steffen Albrecht
- Department of Pathology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Peter Hauser
- Second Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Miklos Garami
- Second Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Almos Klekner
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Laszlo Bognar
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Jose-Luis Montes
- Division of Neurosurgery, Department of Surgery, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Alfredo Staffa
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Alexandre Montpetit
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Pierre Berube
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Magdalena Zakrzewska
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Krzysztof Zakrzewski
- Department of Neurosurgery, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Pawel P Liberski
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Zhifeng Dong
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Peter M Siegel
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Thomas Duchaine
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Christian Perotti
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Adam Fleming
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, McGill University and the McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Damien Faury
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, McGill University and the McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Marc Remke
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marco Gallo
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Dirks
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Robert Sladek
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tomi Pastinen
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Jennifer A Chan
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Annie Huang
- 1] Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada. [2] Program in Cell Biology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada. [3]
| | - Jacek Majewski
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [3]
| | - Nada Jabado
- 1] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [2] Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada. [3]
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Li R, Montpetit A, Rousseau M, Wu SYM, Greenwood CMT, Spector TD, Pollak M, Polychronakos C, Richards JB. Somatic point mutations occurring early in development: a monozygotic twin study. J Med Genet 2013; 51:28-34. [DOI: 10.1136/jmedgenet-2013-101712] [Citation(s) in RCA: 58] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Pryce G, Visintin C, Ramagopalan SV, Al-Izki S, De Faveri LE, Nuamah RA, Mein CA, Montpetit A, Hardcastle AJ, Kooij G, de Vries HE, Amor S, Thomas SA, Ledent C, Marsicano G, Lutz B, Thompson AJ, Selwood DL, Giovannoni G, Baker D. Control of spasticity in a multiple sclerosis model using central nervous system-excluded CB1 cannabinoid receptor agonists. FASEB J 2013; 28:117-30. [PMID: 24121462 DOI: 10.1096/fj.13-239442] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The purpose of this study was the generation of central nervous system (CNS)-excluded cannabinoid receptor agonists to test the hypothesis that inhibition of spasticity, due to CNS autoimmunity, could be controlled by affecting neurotransmission within the periphery. Procedures included identification of chemicals and modeling to predict the mode of exclusion; induction and control of spasticity in the ABH mouse model of multiple sclerosis; conditional deletion of CB1 receptor in peripheral nerves; side-effect profiling to demonstrate the mechanism of CNS-exclusion via drug pumps; genome-wide association study in N2(129×ABH) backcross to map polymorphic cannabinoid drug pump; and sequencing and detection of cannabinoid drug-pump activity in human brain endothelial cell lines. Three drugs (CT3, SAB378 and SAD448) were identified that control spasticity via action on the peripheral nerve CB1 receptor. These were peripherally restricted via drug pumps that limit the CNS side effects (hypothermia) of cannabinoids to increase the therapeutic window. A cannabinoid drug pump is polymorphic and functionally lacking in many laboratory (C57BL/6, 129, CD-1) mice used for transgenesis, pharmacology, and toxicology studies. This phenotype was mapped and controlled by 1-3 genetic loci. ABCC1 within a cluster showing linkage is a cannabinoid CNS-drug pump. Global and conditional CB1 receptor-knockout mice were used as controls. In summary, CNS-excluded CB1 receptor agonists are a novel class of therapeutic agent for spasticity.
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Affiliation(s)
- Gareth Pryce
- 1Blizard Institute, Barts and the London School of Medicine and Dentistry, Queen Mary University of London, 4 Newark St., London E1 2AT, UK.
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21
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Anand SS, Meyre D, Pare G, Bailey SD, Xie C, Zhang X, Montpetit A, Desai D, Bosch J, Mohan V, Diaz R, McQueen MJ, Cordell HJ, Keavney B, Yusuf S, Gaudet D, Gerstein H, Engert JC. Genetic information and the prediction of incident type 2 diabetes in a high-risk multiethnic population: the EpiDREAM genetic study. Diabetes Care 2013; 36:2836-42. [PMID: 23603917 PMCID: PMC3747911 DOI: 10.2337/dc12-2553] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE To determine if 16 single nucleotide polymorphisms (SNPs) associated with type 2 diabetes (T2DM) in Europeans are also associated with T2DM in South Asians and Latinos and if they can add to the prediction of incident T2DM in a high-risk population. RESEARCH DESIGN AND METHODS In the EpiDREAM prospective cohort study, physical measures, questionnaires, and blood samples were collected from 25,063 individuals at risk for dysglycemia. Sixteen SNPs that have been robustly associated with T2DM in Europeans were genotyped. Among 15,466 European, South Asian, and Latino subjects, we examined the association of these 16 SNPs alone and combined in a gene score with incident cases of T2DM (n = 1,016) that developed during 3.3 years of follow-up. RESULTS Nine of the 16 SNPs were significantly associated with T2DM, and their direction of effect was consistent across the three ethnic groups. The gene score was significantly higher among subjects who developed incident T2DM (cases vs. noncases: 16.47 [2.50] vs. 15.99 [2.56]; P = 0.00001). The gene score remained an independent predictor of incident T2DM, with an odds ratio of 1.08 (95% CI 1.05-1.11) per additional risk allele after adjustment for T2DM risk factors. The gene score in those with no family history of T2DM was 16.02, whereas it was 16.19 in those with one parent with T2DM and it was 16.32 in those with two parents with T2DM (P trend = 0.0004). The C statistic of T2DM risk factors was 0.708 (0.691-0.725) and increased only marginally to 0.714 (0.698-0.731) with the addition of the gene score (P for C statistic change = 0.0052). CONCLUSIONS T2DM genetic associations are generally consistent across ethnic groups, and a gene score only adds marginal information to clinical factors for T2DM prediction.
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Affiliation(s)
- Sonia S Anand
- Population Health Research Institute, McMaster University and Hamilton Health Sciences, Hamilton General Hospital, Hamilton, Ontario, Canada.
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22
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Fontebasso AM, Schwartzentruber J, Khuong-Quang DA, Liu XY, Sturm D, Korshunov A, Jones DTW, Witt H, Kool M, Albrecht S, Fleming A, Hadjadj D, Busche S, Lepage P, Montpetit A, Staffa A, Gerges N, Zakrzewska M, Zakrzewski K, Liberski PP, Hauser P, Garami M, Klekner A, Bognar L, Zadeh G, Faury D, Pfister SM, Jabado N, Majewski J. Mutations in SETD2 and genes affecting histone H3K36 methylation target hemispheric high-grade gliomas. Acta Neuropathol 2013; 125:659-69. [PMID: 23417712 PMCID: PMC3631313 DOI: 10.1007/s00401-013-1095-8] [Citation(s) in RCA: 216] [Impact Index Per Article: 19.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2013] [Revised: 01/28/2013] [Accepted: 01/30/2013] [Indexed: 12/16/2022]
Abstract
Recurrent mutations affecting the histone H3.3 residues Lys27 or indirectly Lys36 are frequent drivers of pediatric high-grade gliomas (over 30% of HGGs). To identify additional driver mutations in HGGs, we investigated a cohort of 60 pediatric HGGs using whole-exome sequencing (WES) and compared them to 543 exomes from non-cancer control samples. We identified mutations in SETD2, a H3K36 trimethyltransferase, in 15% of pediatric HGGs, a result that was genome-wide significant (FDR = 0.029). Most SETD2 alterations were truncating mutations. Sequencing the gene in this cohort and another validation cohort (123 gliomas from all ages and grades) showed SETD2 mutations to be specific to high-grade tumors affecting 15% of pediatric HGGs (11/73) and 8% of adult HGGs (5/65) while no SETD2 mutations were identified in low-grade diffuse gliomas (0/45). Furthermore, SETD2 mutations were mutually exclusive with H3F3A mutations in HGGs (P = 0.0492) while they partly overlapped with IDH1 mutations (4/14), and SETD2-mutant tumors were found exclusively in the cerebral hemispheres (P = 0.0055). SETD2 is the only H3K36 trimethyltransferase in humans, and SETD2-mutant tumors showed a substantial decrease in H3K36me3 levels (P < 0.001), indicating that the mutations are loss-of-function. These data suggest that loss-of-function SETD2 mutations occur in older children and young adults and are specific to HGG of the cerebral cortex, similar to the H3.3 G34R/V and IDH mutations. Taken together, our results suggest that mutations disrupting the histone code at H3K36, including H3.3 G34R/V, IDH1 and/or SETD2 mutations, are central to the genesis of hemispheric HGGs in older children and young adults.
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Affiliation(s)
- Adam M. Fontebasso
- Division of Experimental Medicine, McGill University and McGill University Health Centre, Montreal, QC Canada
| | | | - Dong-Anh Khuong-Quang
- Department of Human Genetics, McGill University and McGill University Health Centre, Montreal, QC Canada
| | - Xiao-Yang Liu
- Department of Human Genetics, McGill University and McGill University Health Centre, Montreal, QC Canada
| | - Dominik Sturm
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - David T. W. Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Hendrik Witt
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Paediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Steffen Albrecht
- Department of Pathology, Montreal Children’s Hospital, McGill University Health Centre, Montreal, QC Canada
| | - Adam Fleming
- Division of Hemato-Oncology, Montreal Children’s Hospital, McGill University Health Centre, Montreal, QC Canada
| | - Djihad Hadjadj
- Department of Human Genetics, McGill University and McGill University Health Centre, Montreal, QC Canada
| | - Stephan Busche
- Department of Human Genetics, McGill University and McGill University Health Centre, Montreal, QC Canada
| | - Pierre Lepage
- McGill University and Genome Quebec Innovation Centre, Montreal, QC Canada
| | | | - Alfredo Staffa
- McGill University and Genome Quebec Innovation Centre, Montreal, QC Canada
| | - Noha Gerges
- Department of Human Genetics, McGill University and McGill University Health Centre, Montreal, QC Canada
| | - Magdalena Zakrzewska
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Krzystof Zakrzewski
- Department of Neurosurgery, Polish Mother’s Memorial Hospital Research Institute, Lodz, Poland
| | - Pawel P. Liberski
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Peter Hauser
- 2nd Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Miklos Garami
- 2nd Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Almos Klekner
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Laszlo Bognar
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Gelareh Zadeh
- Division of Neurosurgery, Toronto Western Hospital, Ontario, Canada
| | - Damien Faury
- Department of Human Genetics, McGill University and McGill University Health Centre, Montreal, QC Canada
| | - Stefan M. Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Paediatric Oncology, Hematology and Immunology, Heidelberg University Hospital, Heidelberg, Germany
| | - Nada Jabado
- Division of Experimental Medicine, McGill University and McGill University Health Centre, Montreal, QC Canada
- Department of Human Genetics, McGill University and McGill University Health Centre, Montreal, QC Canada
- Division of Hemato-Oncology, Montreal Children’s Hospital, McGill University Health Centre, Montreal, QC Canada
- Department of Paediatrics, The Research Institute of the McGill University Health Centre, McGill University, Montreal, QC Canada
| | - Jacek Majewski
- McGill University and Genome Quebec Innovation Centre, Montreal, QC Canada
- Department of Human Genetics, McGill University and McGill University Health Centre, Montreal, QC Canada
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23
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Lowe R, Gemma C, Beyan H, Hawa MI, Bazeos A, Leslie RD, Montpetit A, Rakyan VK, Ramagopalan SV. Buccals are likely to be a more informative surrogate tissue than blood for epigenome-wide association studies. Epigenetics 2013; 8:445-54. [PMID: 23538714 DOI: 10.4161/epi.24362] [Citation(s) in RCA: 126] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
There is increasing evidence that interindividual epigenetic variation is an etiological factor in common human diseases. Such epigenetic variation could be genetic or non-genetic in origin, and epigenome-wide association studies (EWASs) are underway for a wide variety of diseases/phenotypes. However, performing an EWAS is associated with a range of issues not typically encountered in genome-wide association studies (GWASs), such as the tissue to be analyzed. In many EWASs, it is not possible to analyze the target tissue in large numbers of live humans, and consequently surrogate tissues are employed, most commonly blood. But there is as yet no evidence demonstrating that blood is more informative than buccal cells, the other easily accessible tissue. To assess the potential of buccal cells for use in EWASs, we performed a comprehensive analysis of a buccal cell methylome using whole-genome bisulfite sequencing. Strikingly, a buccal vs. blood comparison reveals>6X as many hypomethylated regions in buccal. These tissue-specific differentially methylated regions (tDMRs) are strongly enriched for DNaseI hotspots. Almost 75% of these tDMRs are not captured by commonly used DNA methylome profiling platforms such as Reduced Representational Bisulfite Sequencing and the Illumina Infinium HumanMethylation450 BeadChip, and they also display distinct genomic properties. Buccal hypo-tDMRs show a statistically significant enrichment near SNPs associated to disease identified through GWASs. Finally, we find that, compared with blood, buccal hypo-tDMRs show significantly greater overlap with hypomethylated regions in other tissues. We propose that for non-blood based diseases/phenotypes, buccal will be a more informative tissue for EWASs.
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Affiliation(s)
- Robert Lowe
- The Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London, UK
| | - Carolina Gemma
- The Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London, UK
| | - Huriya Beyan
- The Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London, UK
| | - Mohammed I Hawa
- The Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London, UK
| | - Alexandra Bazeos
- The Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London, UK; Department of Haematology; Imperial College London; Hammersmith Hospital; London, UK
| | - R David Leslie
- The Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London, UK
| | | | - Vardhman K Rakyan
- The Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London, UK
| | - Sreeram V Ramagopalan
- The Blizard Institute; Barts and The London School of Medicine and Dentistry; Queen Mary University of London; London, UK
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24
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Martinelli D, Travaglini L, Drouin CA, Ceballos-Picot I, Rizza T, Bertini E, Carrozzo R, Petrini S, de Lonlay P, El Hachem M, Hubert L, Montpetit A, Torre G, Dionisi-Vici C. MEDNIK syndrome: a novel defect of copper metabolism treatable by zinc acetate therapy. Brain 2013; 136:872-81. [PMID: 23423674 DOI: 10.1093/brain/awt012] [Citation(s) in RCA: 91] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
MEDNIK syndrome-acronym for mental retardation, enteropathy, deafness, neuropathy, ichthyosis, keratodermia-is caused by AP1S1 gene mutations, encoding σ1A, the small subunit of the adaptor protein 1 complex, which plays a crucial role in clathrin coat assembly and mediates trafficking between trans-Golgi network, endosomes and the plasma membrane. MEDNIK syndrome was first reported in a few French-Canadian families sharing common ancestors, presenting a complex neurocutaneous phenotype, but its pathogenesis is not completely understood. A Sephardic-Jewish patient, carrying a new AP1S1 homozygous mutation, showed severe perturbations of copper metabolism with hypocupremia, hypoceruloplasminemia and liver copper accumulation, along with intrahepatic cholestasis. Zinc acetate treatment strikingly improved clinical conditions, as well as liver copper and bile-acid overload. We evaluated copper-related metabolites and liver function retrospectively in the original French-Canadian patient series. Intracellular copper metabolism and subcellular localization and function of copper pump ATP7A were investigated in patient fibroblasts. Copper metabolism perturbation and hepatopathy were confirmed in all patients. Studies in mutant fibroblasts showed abnormal copper incorporation and retention, reduced expression of copper-dependent enzymes cytochrome-c-oxidase and Cu/Zn superoxide dismutase, and aberrant intracellular trafficking of Menkes protein ATP7A, which normalized after rescue experiments expressing wild-type AP1S1 gene. We solved the pathogenetic mechanism of MEDNIK syndrome, demonstrating that AP1S1 regulates intracellular copper machinery mediated by copper-pump proteins. This multisystem disease is characterized by a unique picture, combining clinical and biochemical signs of both Menkes and Wilson's diseases, in which liver copper overload is treatable by zinc acetate therapy, and can now be listed as a copper metabolism defect in humans. Our results may also contribute to understand the mechanism(s) of intracellular trafficking of copper pumps.
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Affiliation(s)
- Diego Martinelli
- Unit of Metabolism, Bambino Gesù Children's Hospital, IRCCS, Piazza Sant'Onofrio, 4 - 00165 Rome, Italy
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25
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Ebers G, Ramagopalan SV, Dyment DA, Cader ZM, Disanto G, Handel A, DeLuca GC, Sadovnick AD, Lepage P, Montpetit A. RARE VARIANTS IN THE CYP27B1 GENE ARE ASSOCIATED WITH MULTIPLE SCLEROSIS. J Neurol Psychiatry 2012. [DOI: 10.1136/jnnp-2012-304200a.128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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26
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Hitz MP, Lemieux-Perreault LP, Marshall C, Feroz-Zada Y, Davies R, Yang SW, Lionel AC, D'Amours G, Lemyre E, Cullum R, Bigras JL, Thibeault M, Chetaille P, Montpetit A, Khairy P, Overduin B, Klaassen S, Hoodless P, Nemer M, Stewart AFR, Boerkoel C, Scherer SW, Richter A, Dubé MP, Andelfinger G. Rare copy number variants contribute to congenital left-sided heart disease. PLoS Genet 2012; 8:e1002903. [PMID: 22969434 PMCID: PMC3435243 DOI: 10.1371/journal.pgen.1002903] [Citation(s) in RCA: 108] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2011] [Accepted: 07/03/2012] [Indexed: 12/13/2022] Open
Abstract
Left-sided congenital heart disease (CHD) encompasses a spectrum of malformations that range from bicuspid aortic valve to hypoplastic left heart syndrome. It contributes significantly to infant mortality and has serious implications in adult cardiology. Although left-sided CHD is known to be highly heritable, the underlying genetic determinants are largely unidentified. In this study, we sought to determine the impact of structural genomic variation on left-sided CHD and compared multiplex families (464 individuals with 174 affecteds (37.5%) in 59 multiplex families and 8 trios) to 1,582 well-phenotyped controls. 73 unique inherited or de novo CNVs in 54 individuals were identified in the left-sided CHD cohort. After stringent filtering, our gene inventory reveals 25 new candidates for LS-CHD pathogenesis, such as SMC1A, MFAP4, and CTHRC1, and overlaps with several known syndromic loci. Conservative estimation examining the overlap of the prioritized gene content with CNVs present only in affected individuals in our cohort implies a strong effect for unique CNVs in at least 10% of left-sided CHD cases. Enrichment testing of gene content in all identified CNVs showed a significant association with angiogenesis. In this first family-based CNV study of left-sided CHD, we found that both co-segregating and de novo events associate with disease in a complex fashion at structural genomic level. Often viewed as an anatomically circumscript disease, a subset of left-sided CHD may in fact reflect more general genetic perturbations of angiogenesis and/or vascular biology.
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Affiliation(s)
- Marc-Phillip Hitz
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine, Université de Montréal, Montréal, Québec, Canada
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | | | - Christian Marshall
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Yassamin Feroz-Zada
- Adult Congenital Heart Centre, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Robbie Davies
- University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Shi Wei Yang
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine, Université de Montréal, Montréal, Québec, Canada
| | - Anath Christopher Lionel
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Guylaine D'Amours
- Service of Medical Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine, Université de Montréal, Montréal, Québec, Canada
| | - Emmanuelle Lemyre
- Service of Medical Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine, Université de Montréal, Montréal, Québec, Canada
| | - Rebecca Cullum
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Jean-Luc Bigras
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine, Université de Montréal, Montréal, Québec, Canada
| | - Maryse Thibeault
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine, Université de Montréal, Montréal, Québec, Canada
| | - Philippe Chetaille
- Cardiology Service, Centre Mère-Enfants, Centre Hospitalier Universitaire de Québec, Université de Laval, Québec City, Québec, Canada
| | - Alexandre Montpetit
- Genome Quebec Innovation Centre, McGill University, Montréal, Québec, Canada
| | - Paul Khairy
- Adult Congenital Heart Centre, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Bert Overduin
- European Molecular Biology Laboratory–European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, United Kingdom
| | - Sabine Klaassen
- Experimental and Clinical Research Center, Max-Delbrück-Center for Molecular Medicine, Berlin, Germany
| | - Pamela Hoodless
- Terry Fox Laboratory, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Mona Nemer
- Department of Biochemistry, Microbiology, and Immunology, University of Ottawa, Ottawa, Ontario, Canada
| | - Alexandre F. R. Stewart
- Ruddy Canadian Cardiovascular Genetics Centre, University of Ottawa Heart Institute, Ottawa, Ontario, Canada
| | - Cornelius Boerkoel
- Child and Family Research Institute, Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Stephen W. Scherer
- The Centre for Applied Genomics and Program in Genetics and Genome Biology, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Andrea Richter
- Service of Medical Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine, Université de Montréal, Montréal, Québec, Canada
| | - Marie-Pierre Dubé
- Adult Congenital Heart Centre, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine, Université de Montréal, Montréal, Québec, Canada
- * E-mail:
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27
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Khuong-Quang DA, Buczkowicz P, Rakopoulos P, Liu XY, Fontebasso AM, Bouffet E, Bartels U, Albrecht S, Schwartzentruber J, Letourneau L, Bourgey M, Bourque G, Montpetit A, Bourret G, Lepage P, Fleming A, Lichter P, Kool M, von Deimling A, Sturm D, Korshunov A, Faury D, Jones DT, Majewski J, Pfister SM, Jabado N, Hawkins C. K27M mutation in histone H3.3 defines clinically and biologically distinct subgroups of pediatric diffuse intrinsic pontine gliomas. Acta Neuropathol 2012; 124:439-47. [PMID: 22661320 PMCID: PMC3422615 DOI: 10.1007/s00401-012-0998-0] [Citation(s) in RCA: 686] [Impact Index Per Article: 57.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2012] [Revised: 05/18/2012] [Accepted: 05/19/2012] [Indexed: 11/28/2022]
Abstract
Pediatric glioblastomas (GBM) including diffuse intrinsic pontine gliomas (DIPG) are devastating brain tumors with no effective therapy. Here, we investigated clinical and biological impacts of histone H3.3 mutations. Forty-two DIPGs were tested for H3.3 mutations. Wild-type versus mutated (K27M-H3.3) subgroups were compared for HIST1H3B, IDH, ATRX and TP53 mutations, copy number alterations and clinical outcome. K27M-H3.3 occurred in 71 %, TP53 mutations in 77 % and ATRX mutations in 9 % of DIPGs. ATRX mutations were more frequent in older children (p < 0.0001). No G34V/R-H3.3, IDH1/2 or H3.1 mutations were identified. K27M-H3.3 DIPGs showed specific copy number changes, including all gains/amplifications of PDGFRA and MYC/PVT1 loci. Notably, all long-term survivors were H3.3 wild type and this group of patients had better overall survival. K27M-H3.3 mutation defines clinically and biologically distinct subgroups and is prevalent in DIPG, which will impact future therapeutic trial design. K27M- and G34V-H3.3 have location-based incidence (brainstem/cortex) and potentially play distinct roles in pediatric GBM pathogenesis. K27M-H3.3 is universally associated with short survival in DIPG, while patients wild-type for H3.3 show improved survival. Based on prognostic and therapeutic implications, our findings argue for H3.3-mutation testing at diagnosis, which should be rapidly integrated into the clinical decision-making algorithm, particularly in atypical DIPG.
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Affiliation(s)
| | - Pawel Buczkowicz
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8 Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
- Division of Pathology, The Hospital for Sick Children, Toronto, Canada
| | - Patricia Rakopoulos
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8 Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
| | - Xiao-Yang Liu
- Department of Human Genetics, McGill University, Montreal, QC Canada
| | | | - Eric Bouffet
- Division of Haematology–Oncology, The Hospital for Sick Children, Toronto, Canada
| | - Ute Bartels
- Division of Haematology–Oncology, The Hospital for Sick Children, Toronto, Canada
| | - Steffen Albrecht
- Department of Pathology, Montreal Children’s Hospital, McGill University Health Center, Montreal, QC H1P 2P3 Canada
| | | | - Louis Letourneau
- McGill University and Genome Quebec Innovation Center, Montreal, Canada
| | - Mathieu Bourgey
- McGill University and Genome Quebec Innovation Center, Montreal, Canada
| | - Guillaume Bourque
- McGill University and Genome Quebec Innovation Center, Montreal, Canada
| | | | - Genevieve Bourret
- McGill University and Genome Quebec Innovation Center, Montreal, Canada
| | - Pierre Lepage
- McGill University and Genome Quebec Innovation Center, Montreal, Canada
| | - Adam Fleming
- Department of Paediatrics, Montreal Children’s Hospital, McGill University Health Center, Montreal, QC H1P 2P3 Canada
| | - Peter Lichter
- Division of Molecular Genetics, The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neuro-oncology, The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andreas von Deimling
- Clinical Cooperation Unit Neuropathology, The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Dominik Sturm
- Division of Pediatric Neuro-oncology, The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Andrey Korshunov
- Clinical Cooperation Unit Neuropathology, The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Damien Faury
- Department of Paediatrics, Montreal Children’s Hospital, McGill University Health Center, Montreal, QC H1P 2P3 Canada
| | - David T. Jones
- Division of Pediatric Neuro-oncology, The German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, QC Canada
- McGill University and Genome Quebec Innovation Center, Montreal, Canada
| | - Stefan M. Pfister
- Division of Pediatric Neuro-oncology, The German Cancer Research Center (DKFZ), Heidelberg, Germany
- Department of Hematology and Oncology, Heidelberg University Hospital, Heidelberg, Germany
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, QC Canada
- Division of Experimental Medicine, McGill University, Montreal, Canada
- Department of Paediatrics, Montreal Children’s Hospital, McGill University Health Center, Montreal, QC H1P 2P3 Canada
| | - Cynthia Hawkins
- The Arthur and Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, 555 University Avenue, Toronto, ON M5G 1X8 Canada
- Department of Laboratory Medicine and Pathobiology, Faculty of Medicine, University of Toronto, Toronto, Canada
- Division of Pathology, The Hospital for Sick Children, Toronto, Canada
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Yauk CL, Lucas Argueso J, Auerbach SS, Awadalla P, Davis SR, DeMarini DM, Douglas GR, Dubrova YE, Elespuru RK, Glover TW, Hales BF, Hurles ME, Klein CB, Lupski JR, Manchester DK, Marchetti F, Montpetit A, Mulvihill JJ, Robaire B, Robbins WA, Rouleau GA, Shaughnessy DT, Somers CM, Taylor JG, Trasler J, Waters MD, Wilson TE, Witt KL, Bishop JB. Harnessing genomics to identify environmental determinants of heritable disease. Mutat Res 2012; 752:6-9. [PMID: 22935230 DOI: 10.1016/j.mrrev.2012.08.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2012] [Revised: 08/17/2012] [Accepted: 08/19/2012] [Indexed: 12/27/2022]
Abstract
Next-generation sequencing technologies can now be used to directly measure heritable de novo DNA sequence mutations in humans. However, these techniques have not been used to examine environmental factors that induce such mutations and their associated diseases. To address this issue, a working group on environmentally induced germline mutation analysis (ENIGMA) met in October 2011 to propose the necessary foundational studies, which include sequencing of parent-offspring trios from highly exposed human populations, and controlled dose-response experiments in animals. These studies will establish background levels of variability in germline mutation rates and identify environmental agents that influence these rates and heritable disease. Guidance for the types of exposures to examine come from rodent studies that have identified agents such as cancer chemotherapeutic drugs, ionizing radiation, cigarette smoke, and air pollution as germ-cell mutagens. Research is urgently needed to establish the health consequences of parental exposures on subsequent generations.
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Affiliation(s)
| | | | - Scott S Auerbach
- National Institute of Environmental Health Sciences, United States
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Kristine L Witt
- National Institute of Environmental Health Sciences, United States
| | - Jack B Bishop
- National Institute of Environmental Health Sciences, United States
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Dyment DA, Cader MZ, Chao MJ, Lincoln MR, Morrison KM, Disanto G, Morahan JM, De Luca GC, Sadovnick AD, Lepage P, Montpetit A, Ebers GC, Ramagopalan SV. Exome sequencing identifies a novel multiple sclerosis susceptibility variant in the TYK2 gene. Neurology 2012; 79:406-11. [PMID: 22744673 DOI: 10.1212/wnl.0b013e3182616fc4] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE To identify rare variants contributing to multiple sclerosis (MS) susceptibility in a family we have previously reported with up to 15 individuals affected across 4 generations. METHODS We performed exome sequencing in a subset of affected individuals to identify novel variants contributing to MS risk within this unique family. The candidate variant was genotyped in a validation cohort of 2,104 MS trio families. RESULTS Four family members with MS were sequenced and 21,583 variants were found to be shared among these individuals. Refining the variants to those with 1) a predicted loss of function and 2) present within regions of modest haplotype sharing identified 1 novel mutation (rs55762744) in the tyrosine kinase 2 (TYK2) gene. A different polymorphism within this gene has been shown to be protective in genome-wide association studies. In contrast, the TYK2 variant identified here is a novel, missense mutation and was found to be present in 10/14 (72%) cases and 28/60 (47%) of the unaffected family members. Genotyping additional 2,104 trio families showed the variant to be transmitted preferentially from heterozygous parents (transmitted 16: not transmitted 5; χ(2) = 5.76, p = 0.016). CONCLUSIONS Rs55762744 is a rare variant of modest effect on MS risk affecting a subset of patients (0.8%). Within this pedigree, rs55762744 is common and appears to be a modifier of modest risk effect. Exome sequencing is a quick and cost-effective method and we show here the utility of sequencing a few cases from a single, unique family to identify a novel variant. The sequencing of additional family members or other families may help identify other variants important in MS.
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Affiliation(s)
- David A Dyment
- The Department of Medical Genetics, University of Ottawa, Ottawa, Canada
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Shih CS, Ekoma S, Ho C, Pradhan K, Hwang E, Jakacki R, Fisher M, Kilburn L, Horn M, Vezina G, Rood B, Packer R, Mittal R, Omar S, Khalifa N, Bedir R, Avery R, Hwang E, Acosta M, Hutcheson K, Santos D, Zand D, Kilburn L, Rosenbaum K, Rood B, Packer R, Kalin-Hajdu E, Ospina L, Carret AS, Marzouki M, Decarie JC, Freeman E, Hershon L, Warmuth-Metz M, Zurakowski D, Bison B, Falkenstein F, Gnekow A, Ehrstedt C, Laurencikas E, Bjorklund AC, Stromberg B, Hedborg F, Pfeifer S, Bertin D, Packer RJ, Vallero S, Basso ME, Romano E, Peretta P, Morra I, D'Alonzo G, Fagioli F, Toledano H, Laviv Y, Dratviman-Storobinsky O, Michowiz S, Yaniv I, Cohen IJ, Goldenberg-Cohen N, Muller K, Gnekow A, Warmuth-Metz M, Pietsch T, Zwiener I, Falkenstein F, Meyer FM, Micke O, Hoffmann W, Kortmann RD, Shofty B, Ben-Sira L, Roth J, Constantini S, Shofty B, Weizmann L, Joskowicz L, Kesler A, Ben-Bashat D, Yalon M, Dvir R, Freedman S, Roth J, Ben-Sira L, Constantini S, Bandopadhayay P, Dagi L, Robison N, Goumnerova L, Ullrich N, Opocher E, De Salvo GL, De Paoli A, Simmons I, Sehested A, Walker DA, Picton SV, Gnekow A, Grill J, Driever PH, Azizi AA, Viscardi E, Perilongo G, Cappellano AM, Bouffet E, Silva F, Paiva P, Cavalheiro S, Seixas MT, Silva NS, Antony R, Fraser K, Lin J, Falkenstein F, Kwiecien R, Mirow C, Thieme B, von Hornstein S, Pietsch T, Faldum A, Warmuth-Metz M, Kortmann RD, Gnekow AK, Shofty B, Bokshtein F, Kesler A, Ben-Sira L, Freedman S, Constantini S, Panandiker AP, Klimo P, Thompson C, Armstrong G, Kun L, Boop F, Sanford A, Orge F, Laschinger K, Gold D, Bangert B, Stearns D, Cappellano AM, Senerchia A, Paiva P, Cavalheiro S, Silva F, Silva NS, Gnekow AK, Falkenstein F, Walker D, Perilongo G, Picton S, Grill J, Kortmann RD, Stokland T, van Meeteren AS, Slavc I, Faldum A, de Salvo GL, Fernandez KS, Antony R, Lulla RR, Flores M, Benavides VC, Mitchell C, AlKofide A, Hassonah M, Khafagh Y, Ayas MA, AlFawaz I, Anas M, Barria M, Siddiqui K, Al-Shail E, Fisher MJ, Ullrich NJ, Ferner RE, Gutmann DH, Listernick R, Packer RJ, Tabori U, Hoffman RO, Ardern-Holmes SL, Hummel TR, Hargrave DR, Charrow J, Loguidice M, Balcer LJ, Liu GT, Fisher MJ, Listernick R, Gutmann DH, Ferner RE, Packer RJ, Ullrich NJ, Tabori U, Hoffman RO, Ardern-Holmes SL, Hummel TR, Hargrave DR, Loguidice M, Balcer LJ, Liu GT, Jeeva I, Nelson O, Guy D, Damani A, Gogi D, Picton S, Simmons I, Jeeva I, Picton S, Guy D, Nelson O, Dewsbery S, Gogi D, Simmons I, Sievert AJ, Lang SS, Boucher K, Slaunwhite E, Brewington D, Madsen P, Storm PB, Resnick AC, Hemenway M, Madden J, Macy M, Foreman N, Rush S, Mascelli S, Raso A, Barla A, Nozza P, Biassoni R, Pignatelli S, Cama A, Verri A, Capra V, Garre M, Bergthold G, Piette C, Raquin MA, Dufour C, Varlet P, Dhermain F, Puget S, Sainte-Rose C, Abely M, Canale S, Grill J, Terashima K, Chow K, Jones J, Ahern C, Jo E, Ellezam B, Paulino A, Okcu MF, Su J, Adesina A, Mahajan A, Dauser R, Whitehead W, Lau C, Chintagumpala M, Kebudi R, Tuncer S, Cakir FB, Gorgun O, Agaoglu FY, Ayan I, Darendeliler E, Wolf D, Cohen K, Jeyapalan JN, Morley ICF, Hill AA, Tatevossian RG, Qaddoumi I, Ellison DW, Sheer D, Donson A, Barton V, Birks D, Kleinschmidt-DeMasters BK, Hemenway M, Handler M, Foreman N, Rush S, Tatevossian R, Qaddoumi I, Tang B, Dalton J, Shurtleff S, Punchihewa C, Orisme W, Neale G, Gajjar A, Baker S, Sheer D, Ellison D, Gilheeney S, Jamzadeh A, Winchester M, Yataghene K, De Braganca K, Khakoo Y, Lyden D, Dunkel I, Terasaki M, Eto T, Morioka M, Ho CY, Bar E, Giannini C, Karajannis MA, Zagzag D, Eberhart CG, Rodriguez FJ, Lee Y, Bartels U, Tabori U, Huang A, Bouffet E, Zaky W, Bluml S, Grimm J, Wong K, McComb G, Gilles F, Finlay J, Dhall G, Chen HH, Chen YW, Chang FC, Lin SC, Chang KP, Ho DM, Wong TT, Lee CC, Azizi AA, Fox R, Grill J, Mirow C, Gnekow A, Walker D, Perilongo G, Opocher E, Wheatley K, van Meeteren AYS, Phuakpet K, Tabori U, Bartels U, Huang A, Kulkarni A, Laperriere N, Bouffet E, Epari S, Nair V, Gupta T, Patil P, Moiyadi A, Shetty P, Kane S, Jalali R, Dorris K, Nadi M, Sutton M, Wang L, Stogner K, Li D, Hurwitz B, Stevenson C, Miles L, Kim MO, Fuller C, Hawkins C, Bouffet E, Jones B, Drake J, Fouladi M, Fontebasso AM, Shirinian M, Jones DTW, Quang DAK, Jacob K, Cin H, Witt H, Gerges N, Montpetit A, Brunet S, Lepage P, Klekner A, Lambert S, Kwan T, Hawkins C, Tabori U, Collins VP, Albrecht S, Pfister SM, Jabado N, Arrington D, Manley P, Kieran M, Chi S, Robison N, Chordas C, Ullrich N. LOW GRADE GLIOMAS. Neuro Oncol 2012; 14:i69-i81. [PMCID: PMC3483338 DOI: 10.1093/neuonc/nos092] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023] Open
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Lanktree M, Guo Y, Murtaza M, Glessner J, Bailey S, Onland-Moret N, Lettre G, Ongen H, Rajagopalan R, Johnson T, Shen H, Nelson C, Klopp N, Baumert J, Padmanabhan S, Pankratz N, Pankow J, Shah S, Taylor K, Barnard J, Peters B, Maloney C, Lobmeyer M, Stanton A, Zafarmand M, Romaine S, Mehta A, van Iperen E, Gong Y, Price T, Smith E, Kim C, Li Y, Asselbergs F, Atwood L, Bailey K, Bhatt D, Bauer F, Behr E, Bhangale T, Boer J, Boehm B, Bradfield J, Brown M, Braund P, Burton P, Carty C, Chandrupatla H, Chen W, Connell J, Dalgeorgou C, de Boer A, Drenos F, Elbers C, Fang J, Fox C, Frackelton E, Fuchs B, Furlong C, Gibson Q, Gieger C, Goel A, Grobbee D, Hastie C, Howard P, Huang GH, Johnson W, Li Q, Kleber M, Klein B, Klein R, Kooperberg C, Ky B, LaCroix A, Lanken P, Lathrop M, Li M, Marshall V, Melander O, Mentch F, Meyer N, Monda K, Montpetit A, Murugesan G, Nakayama K, Nondahl D, Onipinla A, Rafelt S, Newhouse S, Otieno F, Patel S, Putt M, Rodriguez S, Safa R, Sawyer D, Schreiner P, Simpson C, Sivapalaratnam S, Srinivasan S, Suver C, Swergold G, Sweitzer N, Thomas K, Thorand B, Timpson N, Tischfield S, Tobin M, Tomaszewski M, Verschuren W, Wallace C, Winkelmann B, Zhang H, Zheng D, Zhang L, Zmuda J, Clarke R, Balmforth A, Danesh J, Day I, Schork N, de Bakker P, Delles C, Duggan D, Hingorani A, Hirschhorn J, Hofker M, Humphries S, Kivimaki M, Lawlor D, Kottke-Marchant K, Mega J, Mitchell B, Morrow D, Palmen J, Redline S, Shields D, Shuldiner A, Sleiman P, Smith G, Farrall M, Jamshidi Y, Christiani D, Casas J, Hall A, Doevendans P, Christie J, Berenson G, Murray S, Illig T, Dorn G, Cappola T, Boerwinkle E, Sever P, Rader D, Reilly M, Caulfield M, Talmud P, Topol E, Engert J, Wang K, Dominiczak A, Hamsten A, Curtis S, Silverstein R, Lange L, Sabatine M, Trip M, Saleheen D, Peden J, Cruickshanks K, März W, O'Connell J, Klungel O, Wijmenga C, Maitland-van der Zee A, Schadt E, Johnson J, Jarvik G, Papanicolaou G, Grant S, Munroe P, North K, Samani N, Koenig W, Gaunt T, Anand S, van der Schouw Y, Soranzo N, FitzGerald G, Reiner A, Hegele R, Hakonarson H, Keating B. Meta-analysis of Dense Genecentric Association Studies Reveals Common and Uncommon Variants Associated with Height. Am J Hum Genet 2012. [DOI: 10.1016/j.ajhg.2012.05.017] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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Spinella JF, Saillour V, Richer C, Ouimet M, Cassart P, Healy J, Bareke E, Larivière M, St-Onge P, Busche S, Ge B, Montpetit A, Pastinen T, Sinnett D. Abstract 4335: The genomic landscape of childhood pre-B acute lymphoblastic leukemia. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-4335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Precursor B-cell acute lymphoblastic leukemia (pre-B ALL) is the most frequent pediatric cancer. Increased understanding of the pathobiology of B-cell ALL has led to risk-targeted treatment regimens and increased survival rates. However, the underlying causes of this pediatric cancer are still unclear. We are using next-generation sequencing technology to better understand the genomic landscape of pre-B ALL and to build a catalogue of variations involved in pediatric ALL onset and/or progression. Using a unique “quartet” design that involves matched tumor (at diagnosis) and normal (remission) samples, as well as DNA from both parents, we will be able to identify somatic mutations driving the leukemic process. Here, we report the deep-sequencing of the whole exomes, and the partial miRNomes, of over 60 childhood B-cell ALL quartets. Using ABI SOLiD technology, we captured over 4.0 Gb of sequence on average per sample with a mean coverage of 40X. Genome-wide genotyping (Illumina's Omni 2.5 array) was also for quality control and structural variant identification. For each individual, approximately 97% of the targeted region was covered α1X and 80% of the targeted bases passed our thresholds for variant calling (≥ 5X coverage, MQV ≤ 20). According to these criteria, about 25,000 SNPs were found per individual. Using this quartet design we were able to incorporate parental sequence information to reduce sequencing errors and facilitate the identification of true variants within a given family, and of leukemia-specific variants within the ALL cohort. We investigated the somatic mutation profiles of the ALL genomes and identified both recurrent and private leukemia-specific mutations, and highlighted genes/pathways with an increased burden of somatic loss of function variants. Our goal now is to validate potential driver mutations that could play a direct role in leukemogenesis through functional assessment. Ultimately, this work will provide invaluable insights to understand the genetic mechanisms underlying pediatric ALL which could lead to the development of powerful clinical tools to improve detection, diagnosis and treatment of this childhood cancer.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 4335. doi:1538-7445.AM2012-4335
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Affiliation(s)
| | - Virginie Saillour
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Chantal Richer
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Manon Ouimet
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Pauline Cassart
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Jasmine Healy
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Eric Bareke
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Mathieu Larivière
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Pascal St-Onge
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Stephan Busche
- 2McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Bing Ge
- 2McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Alexandre Montpetit
- 2McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Tomi Pastinen
- 3Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Daniel Sinnett
- 4Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
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Healy J, Saillour V, Spinella JF, Vidal R, Bareke E, Richer C, Larivière M, Busche S, Ge B, Montpetit A, Pastinen T, Sinnett D. Abstract 2484: Whole-exome sequencing of a rare case of familial childhood acute lymphoblastic leukemia. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-2484] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Acute lymphoblastic leukemia (ALL) is the most common cancer in children, accounting for approximately 25% of all pediatric cancer cases. However, familial childhood ALL is extremely rare. Few families with multiple non-twinned siblings diagnosed with childhood ALL have been reported, and to date no highly penetrant leukemia susceptibility gene(s) has been identified to explain this uncommon occurrence. We postulated that pure (nonsyndromic) familial childhood ALL could result from the accumulation of disadvantaging rare DNA variants in predisposing genes or biological pathways. To address this hypothesis, we used next-generation sequencing technologies to capture and re-sequence the whole-exomes of a family comprising the mother, father and two male non-twinned affected siblings (sibling A and sibling B). Both brothers were diagnosed with the identical ALL subtype, pre-B hyperdiploid childhood ALL, three years apart. The similar clinical and molecular characteristics of the siblings suggest shared etiologic factors. Using the Agilent SureSelect All Human Exon 38 Mb Kit and the SOLiD 3 Plus system, we captured and sequenced a total of 17.5 Gb of sequence for the entire family, with a mean coverage of 47X. For each individual, approximately 96% or 36.4 Mb of the targeted bases were covered α1X and 70% of the targeted bases or 26.4 Mb passed our thresholds for variant calling. We identified 52,038 positions at which the called allele(s) differed from the reference genome in at least one of the four family members. In total, we identified 19,096 germline variants in sibling A and 28,061 in sibling B, of which 2,355 (12.3%) and 2,125 (7.6%), respectively, were previously undiscovered in dbSNP. We investigated non-synonymous homozygous variant and compound heterozygous positions shared between the siblings, as well as genes/pathways with increased burden of rare non-synonymous variants. Based on several criteria (PolyPhen annotation, known allele frequency, etc.), we identified variants that are strong functional candidates to explain this case of pure familial childhood ALL. In parallel, high-density genotyping was also performed (Illumina Omni 2.5M) for quality control and structural variant detection, allowing the identification of putatively shared copy number variants that may also be involved in leukemogenesis. Though independent validation and functional assessment is required, this is the first study to identify genetic factors involved in pure familial childhood ALL.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 2484. doi:1538-7445.AM2012-2484
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Affiliation(s)
- Jasmine Healy
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Virginie Saillour
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | | | - Ramon Vidal
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Eric Bareke
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Chantal Richer
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Mathieu Larivière
- 1Sainte-Justine UHC Research Center, University of Montreal, Montreal, Quebec, Canada
| | - Stephan Busche
- 2McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Bing Ge
- 2McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Alexandre Montpetit
- 2McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
| | - Tomi Pastinen
- 3Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Daniel Sinnett
- 4Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada
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Rousseau J, Chapdelaine P, Boisvert S, Almeida LP, Corbeil J, Montpetit A, Tremblay JP. Endonucleases: tools to correct the dystrophin gene. J Gene Med 2012; 13:522-37. [PMID: 21954090 DOI: 10.1002/jgm.1611] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
BACKGROUND Various endonucleases can be engineered to induce double-strand breaks (DSBs) in chosen DNA sequences. These DSBs are spontaneously repaired by nonhomologous-end-joining, resulting in micro-insertions or micro-deletions (INDELs). We detected, characterized and quantified the frequency of INDELs produced by one meganuclease (MGN) targeting the RAG1 gene, six MGNs targeting three introns of the human dystrophin gene and one pair of zinc finger nucleases (ZFNs) targeting exon 50 of the human dystrophin gene. The experiments were performed in human cells (i.e. 293 T cells, myoblasts and myotubes). METHODS To analyse the INDELs produced by the endonucleases the targeted region was polymerase chain reaction amplified and the amplicons were digested with the Surveyor enzyme, cloned in bacteria or deep sequenced. RESULTS Endonucleases targeting the dystrophin gene produced INDELs of different sizes but there were clear peaks in the size distributions. The positions of these peaks were similar for MGNs but not for ZFNs in 293 T cells and in myoblasts. The size of the INDELs produced by these endonucleases in the dystrophin gene would have permitted a change in the reading frame. In a subsequent experiment, we observed that the frequency of INDELs was increased by re-exposition of the cells to the same endonuclease. CONCLUSIONS Endonucleases are able to: (i) restore the normal reading of a gene with a frame shift mutation; (ii) delete a nonsense codon; and (iii) knockout a gene. Endonucleases could thus be used to treat Duchenne muscular dystrophy and other hereditary diseases that are the result of a nonsense codon or a frame shift mutation.
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Affiliation(s)
- Joel Rousseau
- Unité de Recherche de Recherche en Génétique Humaine, Centre de Recherche de CHUL, CHUQ, Faculté de Médecine, Université Laval, Québec, Canada
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Ramagopalan SV, Dyment DA, Cader MZ, Morrison KM, Disanto G, Morahan JM, Berlanga-Taylor AJ, Handel A, De Luca GC, Sadovnick AD, Lepage P, Montpetit A, Ebers GC. Rare variants in the CYP27B1 gene are associated with multiple sclerosis. Ann Neurol 2012; 70:881-6. [PMID: 22190362 DOI: 10.1002/ana.22678] [Citation(s) in RCA: 177] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
OBJECTIVE Multiple sclerosis (MS) is a complex neurological disease. Genetic linkage analysis and genotyping of candidate genes in families with 4 or more affected individuals more heavily loaded for susceptibility genes has not fully explained familial disease clustering. METHODS We performed whole exome sequencing to further understand the heightened prevalence of MS in these families. RESULTS Forty-three individuals with MS (1 from each family) were sequenced to find rare variants in candidate MS susceptibility genes. On average, >58,000 variants were identified in each individual. A rare variant in the CYP27B1 gene causing complete loss of gene function was identified in 1 individual. Homozygosity for this mutation results in vitamin D-dependent rickets I (VDDR1), whereas heterozygosity results in lower calcitriol levels. This variant showed significant heterozygous association in 3,046 parent-affected child trios (p = 1 × 10(-5)). Further genotyping in >12,500 individuals showed that other rare loss of function CYP27B1 variants also conferred significant risk of MS, Peto odds ratio = 4.7 (95% confidence interval, 2.3-9.4; p = 5 × 10(-7)). Four known VDDR1 mutations were identified, all overtransmitted. Heterozygous parents transmitted these alleles to MS offspring 35 of 35× (p = 3 × 10(-9)). INTERPRETATION A causative role for CYP27B1 in MS is supported; the mutations identified are known to alter function having been shown in vivo to result in rickets when 2 copies are present. CYP27B1 encodes the vitamin D-activating 1-alpha hydroxylase enzyme, and thus a role for vitamin D in MS pathogenesis is strongly implicated.
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Affiliation(s)
- Sreeram V Ramagopalan
- Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, United Kingdom
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Schwartzentruber J, Korshunov A, Liu XY, Jones DTW, Pfaff E, Jacob K, Sturm D, Fontebasso AM, Quang DAK, Tönjes M, Hovestadt V, Albrecht S, Kool M, Nantel A, Konermann C, Lindroth A, Jäger N, Rausch T, Ryzhova M, Korbel JO, Hielscher T, Hauser P, Garami M, Klekner A, Bognar L, Ebinger M, Schuhmann MU, Scheurlen W, Pekrun A, Frühwald MC, Roggendorf W, Kramm C, Dürken M, Atkinson J, Lepage P, Montpetit A, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel P, Kulozik AE, Zapatka M, Guha A, Malkin D, Felsberg J, Reifenberger G, von Deimling A, Ichimura K, Collins VP, Witt H, Milde T, Witt O, Zhang C, Castelo-Branco P, Lichter P, Faury D, Tabori U, Plass C, Majewski J, Pfister SM, Jabado N. Driver mutations in histone H3.3 and chromatin remodelling genes in paediatric glioblastoma. Nature 2012. [PMID: 22286061 DOI: 10.1038/nature11026] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Glioblastoma multiforme (GBM) is a lethal brain tumour in adults and children. However, DNA copy number and gene expression signatures indicate differences between adult and paediatric cases. To explore the genetic events underlying this distinction, we sequenced the exomes of 48 paediatric GBM samples. Somatic mutations in the H3.3-ATRX-DAXX chromatin remodelling pathway were identified in 44% of tumours (21/48). Recurrent mutations in H3F3A, which encodes the replication-independent histone 3 variant H3.3, were observed in 31% of tumours, and led to amino acid substitutions at two critical positions within the histone tail (K27M, G34R/G34V) involved in key regulatory post-translational modifications. Mutations in ATRX (α-thalassaemia/mental retardation syndrome X-linked) and DAXX (death-domain associated protein), encoding two subunits of a chromatin remodelling complex required for H3.3 incorporation at pericentric heterochromatin and telomeres, were identified in 31% of samples overall, and in 100% of tumours harbouring a G34R or G34V H3.3 mutation. Somatic TP53 mutations were identified in 54% of all cases, and in 86% of samples with H3F3A and/or ATRX mutations. Screening of a large cohort of gliomas of various grades and histologies (n = 784) showed H3F3A mutations to be specific to GBM and highly prevalent in children and young adults. Furthermore, the presence of H3F3A/ATRX-DAXX/TP53 mutations was strongly associated with alternative lengthening of telomeres and specific gene expression profiles. This is, to our knowledge, the first report to highlight recurrent mutations in a regulatory histone in humans, and our data suggest that defects of the chromatin architecture underlie paediatric and young adult GBM pathogenesis.
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Prithviraj GK, Sommers SR, Jump RL, Halmos B, Chambless LB, Parker SL, Hassam-Malani L, McGirt MJ, Thompson RC, Chambless LB, Parker SL, Hassam-Malani L, McGirt MJ, Thompson RC, Hunter K, Chamberlain MC, Le EM, Lee ELT, Chamberlain MC, Sadighi ZS, Pearlman ML, Slopis JM, Vats TS, Khatua S, DeVito NC, Yu M, Chen R, Pan E, Cloughesy T, Raizer J, Drappatz J, Gerena-Lewis M, Rogerio J, Yacoub S, Desjardin A, Groves MD, DeGroot J, Loghin M, Conrad CA, Hess K, Ni J, Ictech S, Hunter K, Yung WA, Porter AB, Dueck AC, Karlin NJ, Chamberlain MC, Olson J, Silber J, Reiner AS, Panageas KS, Iwamoto FM, Cloughesy TF, Aldape KD, Rivera AL, Eichler AF, Louis DN, Paleologos NA, Fisher BJ, Ashby LS, Cairncross JG, Roldan GB, Wen PY, Ligon KL, Shiff D, Robins HI, Rocque BG, Chamberlain MC, Mason WP, Weaver SA, Green RM, Kamar FG, Abrey LE, DeAngelis LM, Jhanwar SC, Rosenblum MK, Lassman AB, Cachia D, Alderson L, Moser R, Smith T, Yunus S, Saito K, Mukasa A, Narita Y, Tabei Y, Shinoura N, Shibui S, Saito N, Flechl B, Ackerl M, Sax C, Dieckmann K, Crevenna R, Widhalm G, Preusser M, Marosi C, Marosi C, Ay C, Preusser M, Dunkler D, Widhalm G, Pabinger I, Dieckmann K, Zielinski C, Belongia M, Jogal S, Schlingensiepen KH, Bogdahn U, Stockhammer G, Mahapatra AK, Venkataramana NK, Oliushine V, Parfenov V, Poverennova I, Hau P, Jachimczak P, Heinrichs H, Mammoser AG, Shonka NA, de Groot JF, Shibahara I, Sonoda Y, Kumabe T, Saito R, Kanamori M, Yamashita Y, Watanabe M, Ishioka C, Tominaga T, Silvani A, Gaviani P, Lamperti E, Botturi A, DiMeco F, Broggi G, Fariselli L, Solero CL, Salmaggi A, Green RM, Woyshner EA, Cloughesy TF, Shu F, Oh YS, Iganej S, Singh G, Vemuri SL, Theeler BJ, Ellezam B, Gilbert MR, Aoki T, Kobayashi H, Takano S, Nishikawa R, Shinoura N, Nagane M, Narita Y, Muragaki Y, Sugiyama K, Kuratsu J, Matsutani M, Sadighi ZS, Khatua S, Langford LA, Puduvalli VK, Shen D, Chen ZP, Zhang JP, Chen ZP, Bedekar D, Rand S, Connelly J, Malkin M, Paulson E, Mueller W, Schmainda K, Gallego O, Benavides M, Segura PP, Balana C, Gil M, Berrocal A, Reynes G, Garcia JL, Murata P, Bague S, Quintana MJ, Vasishta VG, Nagane M, Kobayashi K, Tanaka M, Tsuchiya K, Shiokawa Y, Bavle AA, Ayyanar K, Puduvalli VK, Prado MP, Hess KR, Hunter K, Ictech S, Groves MD, Gilbert MR, Liu V, Conrad CA, de Groot J, Loghin ME, Colman H, Levin VA, Alfred Yung WK, Hackney JR, Palmer CA, Markert JM, Cure J, Riley KO, Fathallah-Shaykh H, Nabors LB, Saria MG, Corle C, Hu J, Rudnick J, Phuphanich S, Mrugala MM, Lee LK, Fu BD, Bota DA, Kim RY, Brown T, Feely H, Hu A, Drappatz J, Wen PY, Lee JW, Carter B, Kesari S, Fu BD, Kong XT, Bota DA, Fu BD, Bota DA, Sparagana S, Belousova E, Jozwiak S, Korf B, Frost M, Kuperman R, Kohrman M, Witt O, Wu J, Flamini R, Jansen A, Curtalolo P, Thiele E, Whittemore V, De Vries P, Ford J, Shah G, Cauwel H, Edrich P, Sahmoud T, Franz D, Khasraw M, Brown C, Ashley DM, Rosenthal MA, Jiang X, Mou YG, Chen ZP, Oh M, kim E, Chang J, Juratli TA, Kirsch M, Schackert G, Krex D, Gilbert MR, Wang M, Aldape KD, Stupp R, Hegi M, Jaeckle KA, Armstrong TS, Wefel JS, Won M, Blumenthal DT, Mahajan A, Schultz CJ, Erridge SC, Brown PD, Chakravarti A, Curran WJ, Mehta MP, Hofland KF, Hansen S, Sorensen M, Schultz H, Muhic A, Engelholm S, Ask A, Kristiansen C, Thomsen C, Poulsen HS, Lassen UN, Zalatimo O, Weston C, Zoccoli C, Glantz M, Rahmanuddin S, Shiroishi MS, Cen SY, Jones J, Chen T, Pagnini P, Go J, Lerner A, Gomez J, Law M, Ram Z, Wong ET, Gutin PH, Bobola MS, Alnoor M, Silbergeld DL, Rostomily RC, Chamberlain MC, Silber JR, Martha N, Jacqueline S, Thaddaus G, Daniel P, Hans M, Armin M, Eugen T, Gunther S, Hutterer M, Tseng HM, Zoccoli CM, Glantz M, Zalatimo O, Patel A, Rizzo K, Sheehan JM, Sumrall AL, Vredenburgh JJ, Desjardins A, Reardon DA, Friiedman HS, Peters KB, Taylor LP, Stewart M, Blondin NA, Baehring JM, Foote T, Laack N, Call J, Hamilton MG, Walling S, Eliasziw M, Easaw J, Shirsat NV, Kundar R, Gokhale A, Goel A, Moiyadi AA, Wang J, Mutlu E, Oyan A, Yan T, Tsinkalovsky O, Jacobsen HK, Talasila KM, Sleire L, Pettersen K, Miletic H, Andersen S, Mitra S, Weissman I, Li X, Kalland KH, Enger PO, Sepulveda J, Belda C, Balana C, Segura PP, Reynes G, Gil M, Gallego O, Berrocal A, Blumenthal DT, Sitt R, Phishniak L, Bokstein F, Philippe M, Carole C, Andre MDP, Marylin B, Olivier C, L'Houcine O, Dominique FB, Philippe M, Isabelle NM, Olivier C, Frederic F, Stephane F, Henry D, Marylin B, L'Houcine O, Dominique FB, Errico MA, Kunschner LJ, Errico MA, Kunschner LJ, Soffietti R, Trevisan E, Ruda R, Bertero L, Bosa C, Fabrini MG, Lolli I, Jalali R, Julka PK, Anand AK, Bhavsar D, Singhal N, Naik R, John S, Mathew BS, Thaipisuttikul I, Graber J, DeAngelis LM, Shirinian M, Fontebasso AM, Jacob K, Gerges N, Montpetit A, Nantel A, Albrecht S, Jabado N, Mammoser AG, Shah K, Conrad CA, Di K, Linskey M, Bota DA, Thon N, Eigenbrod S, Kreth S, Lutz J, Tonn JC, Kretzschmar H, Peraud A, Kreth FW, Muggeri AD, Alderuccio JP, Diez BD, Jiang P, Chao Y, Gallagher M, Kim R, Pastorino S, Fogal V, Kesari S, Rudnick JD, Bresee C, Rogatko A, Sakowsky S, Franco M, Hu J, Lim S, Lopez A, Yu L, Ryback K, Tsang V, Lill M, Steinberg A, Sheth R, Grimm S, Helenowski I, Rademaker A, Raizer J, Nunes FP, Merker V, Jennings D, Caruso P, Muzikansky A, Stemmer-Rachamimov A, Plotkin S, Spalding AC, Vitaz TW, Sun DA, Parsons S, Welch MR, Omuro A, DeAngelis LM, Omuro A, Beal K, Correa D, Chan T, DeAngelis L, Gavrilovic I, Nolan C, Hormigo A, Lassman AB, Kaley T, Mellinghoff I, Grommes C, Panageas K, Reiner A, Barradas R, Abrey L, Gutin P, Lee SY, Slagle-Webb B, Glantz MJ, Sheehan JM, Connor JR, Schlimper CA, Schlag H, Stoffels G, Weber F, Krueger DA, Care MM, Holland K, Agricola K, Tudor C, Byars A, Sahmoud T, Franz DN, Raizer J, Rice L, Rademaker A, Chandler J, Levy R, Muro K, Grimm S, Nayak L, Iwamoto FM, Rudnick JD, Norden AD, Omuro A, Kaley TJ, Thomas AA, Fadul CE, Meyer LP, Lallana EC, Colman H, Gilbert M, Alfred Yung WK, Aldape K, De Groot J, Conrad C, Levin V, Groves M, Loghin M, Chris P, Puduvalli V, Nagpal S, Feroze A, Recht L, Rangarajan HG, Kieran MW, Scott RM, Lew SM, Firat SY, Segura AD, Jogal SA, Kumthekar PU, Grimm SA, Avram M, Patel J, Kaklamani V, McCarthy K, Cianfrocca M, Gradishar W, Mulcahy M, Von Roenn J, Helenowski I, Rademaker A, Raizer J, Galanis E, Anderson SK, Lafky JM, Kaufmann TJ, Uhm JH, Giannini C, Kumar SK, Northfelt DW, Flynn PJ, Jaeckle KA, Buckner JC, Omar AI, Panageas KS, Iwamoto FM, Cloughesy TF, Aldape KD, Rivera AL, Eichler AF, Louis DN, Paleologos NA, Fisher BJ, Ashby LS, Cairncross JG, Roldan GB, Wen PY, Ligon KL, Schiff D, Robins HI, Rocque BG, Chamberlain MC, Mason WP, Weaver SA, Green RM, Kamar FG, Abrey LE, DeAngelis LM, Jhanwar SC, Rosenblum MK, Lassman AB, Delios A, Jakubowski A, DeAngelis L, Grommes C, Lassman AB, Theeler BJ, Melguizo-Gavilanes I, Shonka NA, Qiao W, Wang X, Mahajan A, Puduvalli V, Hashemi-Sadraei N, Bawa H, Rahmathulla G, Patel M, Elson P, Stevens G, Peereboom D, Vogelbaum M, Weil R, Barnett G, Ahluwalia MS, Alvord EC, Rockne RC, Rockhill JK, Mrugala MM, Rostomily R, Lai A, Cloughesy T, Wardlaw J, Spence AM, Swanson KR, Zadeh G, Alahmadi H, Wilson J, Gentili F, Lassman AB, Wang M, Gilbert MR, Aldape KD, Beumer JJ, Wright J, Takebe N, Puduvalli VK, Hormigo A, Gaur R, Werner-Wasik M, Mehta MP, Gupta AJ, Campos-Gines A, Le K, Arango C, Richards M, Landeros M, Juan H, Chang JH, Kim JS, Cho JH, Seo CO, Baldock AL, Rockne R, Canoll P, Born D, Yagle K, Swanson KR, Alexandru D, Bota D, Linskey ME, Nabeel S, Raval SN, Raizer J, Grimm S, Rice L, Rosenow J, Levy R, Bredel M, Chandler J, New PZ, Plotkin SR, Supko JG, Curry WT, Chi AS, Gerstner ER, Stemmer-Rachamimov A, Batchelor TT, Ahluwalia MS, Hashemi N, Rahmathulla G, Patel M, Chao ST, Peereboom D, Weil RJ, Suh JH, Vogelbaum MA, Stevens GH, Barnett GH, Corwin D, Holdsworth C, Stewart R, Rockne R, Swanson K, Graber JJ, Kaley T, Rockne RC, Anderson AR, Swanson KR, Jeyapalan S, Goldman M, Boxerman J, Donahue J, Elinzano H, Evans D, O'Connor B, Puthawala MY, Oyelese A, Cielo D, Blitstein M, Dargush M, Santaniello A, Constantinou M, DiPetrillo T, Safran H, Plotkin SR, Halpin C, Merker V, Barker FG, Maher EA, Ganji S, DeBerardinis R, Hatanpaa K, Rakheja D, Yang XL, Mashimo T, Raisanen J, Madden C, Mickey B, Malloy C, Bachoo R, Choi C, Ranjan T, Yono N, Zalatimo O, Zoccoli C, Glantz M, Han SJ, Sun M, Berger MS, Aghi M, Gupta N, Parsa AT. MEDICAL AND NEURO-ONCOLOGY. Neuro Oncol 2011. [DOI: 10.1093/neuonc/nor152] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
Recent advances in next-generation sequencing technologies have brought a paradigm shift in how medical researchers investigate both rare and common human disorders. The ability cost-effectively to generate genome-wide sequencing data with deep coverage in a short time frame is replacing approaches that focus on specific regions for gene discovery and clinical testing. While whole genome sequencing remains prohibitively expensive for most applications, exome sequencing--a technique which focuses on only the protein-coding portion of the genome--places many advantages of the emerging technologies into researchers' hands. Recent successes using this technology have uncovered genetic defects with a limited number of probands regardless of shared genetic heritage, and are changing our approach to Mendelian disorders where soon all causative variants, genes and their relation to phenotype will be uncovered. The expectation is that, in the very near future, this technology will enable us to identify all the variants in an individual's personal genome and, in particular, clinically relevant alleles. Beyond this, whole genome sequencing is also expected to bring a major shift in clinical practice in terms of diagnosis and understanding of diseases, ultimately enabling personalised medicine based on one's genome. This paper provides an overview of the current and future use of next generation sequencing as it relates to whole exome sequencing in human disease by focusing on the technical capabilities, limitations and ethical issues associated with this technology in the field of genetics and human disease.
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Affiliation(s)
- Jacek Majewski
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
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Abstract
Recent advances in next-generation sequencing technologies have brought a paradigm shift in how medical researchers investigate both rare and common human disorders. The ability cost-effectively to generate genome-wide sequencing data with deep coverage in a short time frame is replacing approaches that focus on specific regions for gene discovery and clinical testing. While whole genome sequencing remains prohibitively expensive for most applications, exome sequencing--a technique which focuses on only the protein-coding portion of the genome--places many advantages of the emerging technologies into researchers' hands. Recent successes using this technology have uncovered genetic defects with a limited number of probands regardless of shared genetic heritage, and are changing our approach to Mendelian disorders where soon all causative variants, genes and their relation to phenotype will be uncovered. The expectation is that, in the very near future, this technology will enable us to identify all the variants in an individual's personal genome and, in particular, clinically relevant alleles. Beyond this, whole genome sequencing is also expected to bring a major shift in clinical practice in terms of diagnosis and understanding of diseases, ultimately enabling personalised medicine based on one's genome. This paper provides an overview of the current and future use of next generation sequencing as it relates to whole exome sequencing in human disease by focusing on the technical capabilities, limitations and ethical issues associated with this technology in the field of genetics and human disease.
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Affiliation(s)
- Jacek Majewski
- McGill University and Genome Quebec Innovation Centre, Montreal, Canada
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Tucker T, Montpetit A, Chai D, Chan S, Chénier S, Coe BP, Delaney A, Eydoux P, Lam WL, Langlois S, Lemyre E, Marra M, Qian H, Rouleau GA, Vincent D, Michaud JL, Friedman JM. Comparison of genome-wide array genomic hybridization platforms for the detection of copy number variants in idiopathic mental retardation. BMC Med Genomics 2011; 4:25. [PMID: 21439053 PMCID: PMC3076225 DOI: 10.1186/1755-8794-4-25] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2010] [Accepted: 03/25/2011] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Clinical laboratories are adopting array genomic hybridization as a standard clinical test. A number of whole genome array genomic hybridization platforms are available, but little is known about their comparative performance in a clinical context. METHODS We studied 30 children with idiopathic MR and both unaffected parents of each child using Affymetrix 500 K GeneChip SNP arrays, Agilent Human Genome 244 K oligonucleotide arrays and NimbleGen 385 K Whole-Genome oligonucleotide arrays. We also determined whether CNVs called on these platforms were detected by Illumina Hap550 beadchips or SMRT 32 K BAC whole genome tiling arrays and tested 15 of the 30 trios on Affymetrix 6.0 SNP arrays. RESULTS The Affymetrix 500 K, Agilent and NimbleGen platforms identified 3061 autosomal and 117 X chromosomal CNVs in the 30 trios. 147 of these CNVs appeared to be de novo, but only 34 (22%) were found on more than one platform. Performing genotype-phenotype correlations, we identified 7 most likely pathogenic and 2 possibly pathogenic CNVs for MR. All 9 of these putatively pathogenic CNVs were detected by the Affymetrix 500 K, Agilent, NimbleGen and the Illumina arrays, and 5 were found by the SMRT BAC array. Both putatively pathogenic CNVs identified in the 15 trios tested with the Affymetrix 6.0 were identified by this platform. CONCLUSIONS Our findings demonstrate that different results are obtained with different platforms and illustrate the trade-off that exists between sensitivity and specificity. The large number of apparently false positive CNV calls on each of the platforms supports the need for validating clinically important findings with a different technology.
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Affiliation(s)
- Tracy Tucker
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada.
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Morcos L, Ge B, Koka V, Lam KCL, Pokholok DK, Gunderson KL, Montpetit A, Verlaan DJ, Pastinen T. Genome-wide assessment of imprinted expression in human cells. Genome Biol 2011; 12:R25. [PMID: 21418647 PMCID: PMC3129675 DOI: 10.1186/gb-2011-12-3-r25] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2010] [Revised: 01/21/2011] [Accepted: 03/21/2011] [Indexed: 01/19/2023] Open
Abstract
Background Parent-of-origin-dependent expression of alleles, imprinting, has been suggested to impact a substantial proportion of mammalian genes. Its discovery requires allele-specific detection of expressed transcripts, but in some cases detected allelic expression bias has been interpreted as imprinting without demonstrating compatible transmission patterns and excluding heritable variation. Therefore, we utilized a genome-wide tool exploiting high density genotyping arrays in parallel measurements of genotypes in RNA and DNA to determine allelic expression across the transcriptome in lymphoblastoid cell lines (LCLs) and skin fibroblasts derived from families. Results We were able to validate 43% of imprinted genes with previous demonstration of compatible transmission patterns in LCLs and fibroblasts. In contrast, we only validated 8% of genes suggested to be imprinted in the literature, but without clear evidence of parent-of-origin-determined expression. We also detected five novel imprinted genes and delineated regions of imprinted expression surrounding annotated imprinted genes. More subtle parent-of-origin-dependent expression, or partial imprinting, could be verified in four genes. Despite higher prevalence of monoallelic expression, immortalized LCLs showed consistent imprinting in fewer loci than primary cells. Random monoallelic expression has previously been observed in LCLs and we show that random monoallelic expression in LCLs can be partly explained by aberrant methylation in the genome. Conclusions Our results indicate that widespread parent-of-origin-dependent expression observed recently in rodents is unlikely to be captured by assessment of human cells derived from adult tissues where genome-wide assessment of both primary and immortalized cells yields few new imprinted loci.
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Affiliation(s)
- Lisanne Morcos
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, Quebec, H3A 1A4, Canada
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Witola WH, Mui E, Hargrave A, Liu S, Hypolite M, Montpetit A, Cavailles P, Bisanz C, Cesbron-Delauw MF, Fournié GJ, McLeod R. NALP1 influences susceptibility to human congenital toxoplasmosis, proinflammatory cytokine response, and fate of Toxoplasma gondii-infected monocytic cells. Infect Immun 2011; 79:756-66. [PMID: 21098108 PMCID: PMC3028851 DOI: 10.1128/iai.00898-10] [Citation(s) in RCA: 137] [Impact Index Per Article: 10.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2010] [Revised: 09/20/2010] [Accepted: 11/11/2010] [Indexed: 11/20/2022] Open
Abstract
NALP1 is a member of the NOD-like receptor (NLR) family of proteins that form inflammasomes. Upon cellular infection or stress, inflammasomes are activated, triggering maturation of proinflammatory cytokines and downstream cellular signaling mediated through the MyD88 adaptor. Toxoplasma gondii is an obligate intracellular parasite that stimulates production of high levels of proinflammatory cytokines that are important in innate immunity. In this study, susceptibility alleles for human congenital toxoplasmosis were identified in the NALP1 gene. To investigate the role of the NALP1 inflammasome during infection with T. gondii, we genetically engineered a human monocytic cell line for NALP1 gene knockdown by RNA interference. NALP1 silencing attenuated progression of T. gondii infection, with accelerated host cell death and eventual cell disintegration. In line with this observation, upregulation of the proinflammatory cytokines interleukin-1β (IL-1β), IL-18, and IL-12 upon T. gondii infection was not observed in monocytic cells with NALP1 knockdown. These findings suggest that the NALP1 inflammasome is critical for mediating innate immune responses to T. gondii infection and pathogenesis. Although there have been recent advances in understanding the potent activity of inflammasomes in directing innate immune responses to disease, this is the first report, to our knowledge, on the crucial role of the NALP1 inflammasome in the pathogenesis of T. gondii infections in humans.
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Affiliation(s)
- William H. Witola
- Departments of Surgery (Ophthalmology) and Pediatrics (Infectious Disease), The University of Chicago, Chicago, Illinois 60637, Laboratoire Adaptation et Pathogénie des Micro-Organismes, CNRS UMR 5163, Université Joseph Fourier Grenoble 1, Institut Jean Roget, BP 170, 38042 Grenoble Cedex 9, France, Centre d'Innovation, Génome Québec, Montréal, Québec H3A 1A4, Canada, INSERM, U563, F-31000 Toulouse, France, University Toulouse III Paul Sabatier, F-31000 Toulouse, France
| | - Ernest Mui
- Departments of Surgery (Ophthalmology) and Pediatrics (Infectious Disease), The University of Chicago, Chicago, Illinois 60637, Laboratoire Adaptation et Pathogénie des Micro-Organismes, CNRS UMR 5163, Université Joseph Fourier Grenoble 1, Institut Jean Roget, BP 170, 38042 Grenoble Cedex 9, France, Centre d'Innovation, Génome Québec, Montréal, Québec H3A 1A4, Canada, INSERM, U563, F-31000 Toulouse, France, University Toulouse III Paul Sabatier, F-31000 Toulouse, France
| | - Aubrey Hargrave
- Departments of Surgery (Ophthalmology) and Pediatrics (Infectious Disease), The University of Chicago, Chicago, Illinois 60637, Laboratoire Adaptation et Pathogénie des Micro-Organismes, CNRS UMR 5163, Université Joseph Fourier Grenoble 1, Institut Jean Roget, BP 170, 38042 Grenoble Cedex 9, France, Centre d'Innovation, Génome Québec, Montréal, Québec H3A 1A4, Canada, INSERM, U563, F-31000 Toulouse, France, University Toulouse III Paul Sabatier, F-31000 Toulouse, France
| | - Susan Liu
- Departments of Surgery (Ophthalmology) and Pediatrics (Infectious Disease), The University of Chicago, Chicago, Illinois 60637, Laboratoire Adaptation et Pathogénie des Micro-Organismes, CNRS UMR 5163, Université Joseph Fourier Grenoble 1, Institut Jean Roget, BP 170, 38042 Grenoble Cedex 9, France, Centre d'Innovation, Génome Québec, Montréal, Québec H3A 1A4, Canada, INSERM, U563, F-31000 Toulouse, France, University Toulouse III Paul Sabatier, F-31000 Toulouse, France
| | - Magali Hypolite
- Departments of Surgery (Ophthalmology) and Pediatrics (Infectious Disease), The University of Chicago, Chicago, Illinois 60637, Laboratoire Adaptation et Pathogénie des Micro-Organismes, CNRS UMR 5163, Université Joseph Fourier Grenoble 1, Institut Jean Roget, BP 170, 38042 Grenoble Cedex 9, France, Centre d'Innovation, Génome Québec, Montréal, Québec H3A 1A4, Canada, INSERM, U563, F-31000 Toulouse, France, University Toulouse III Paul Sabatier, F-31000 Toulouse, France
| | - Alexandre Montpetit
- Departments of Surgery (Ophthalmology) and Pediatrics (Infectious Disease), The University of Chicago, Chicago, Illinois 60637, Laboratoire Adaptation et Pathogénie des Micro-Organismes, CNRS UMR 5163, Université Joseph Fourier Grenoble 1, Institut Jean Roget, BP 170, 38042 Grenoble Cedex 9, France, Centre d'Innovation, Génome Québec, Montréal, Québec H3A 1A4, Canada, INSERM, U563, F-31000 Toulouse, France, University Toulouse III Paul Sabatier, F-31000 Toulouse, France
| | - Pierre Cavailles
- Departments of Surgery (Ophthalmology) and Pediatrics (Infectious Disease), The University of Chicago, Chicago, Illinois 60637, Laboratoire Adaptation et Pathogénie des Micro-Organismes, CNRS UMR 5163, Université Joseph Fourier Grenoble 1, Institut Jean Roget, BP 170, 38042 Grenoble Cedex 9, France, Centre d'Innovation, Génome Québec, Montréal, Québec H3A 1A4, Canada, INSERM, U563, F-31000 Toulouse, France, University Toulouse III Paul Sabatier, F-31000 Toulouse, France
| | - Cordelia Bisanz
- Departments of Surgery (Ophthalmology) and Pediatrics (Infectious Disease), The University of Chicago, Chicago, Illinois 60637, Laboratoire Adaptation et Pathogénie des Micro-Organismes, CNRS UMR 5163, Université Joseph Fourier Grenoble 1, Institut Jean Roget, BP 170, 38042 Grenoble Cedex 9, France, Centre d'Innovation, Génome Québec, Montréal, Québec H3A 1A4, Canada, INSERM, U563, F-31000 Toulouse, France, University Toulouse III Paul Sabatier, F-31000 Toulouse, France
| | - Marie-France Cesbron-Delauw
- Departments of Surgery (Ophthalmology) and Pediatrics (Infectious Disease), The University of Chicago, Chicago, Illinois 60637, Laboratoire Adaptation et Pathogénie des Micro-Organismes, CNRS UMR 5163, Université Joseph Fourier Grenoble 1, Institut Jean Roget, BP 170, 38042 Grenoble Cedex 9, France, Centre d'Innovation, Génome Québec, Montréal, Québec H3A 1A4, Canada, INSERM, U563, F-31000 Toulouse, France, University Toulouse III Paul Sabatier, F-31000 Toulouse, France
| | - Gilbert J. Fournié
- Departments of Surgery (Ophthalmology) and Pediatrics (Infectious Disease), The University of Chicago, Chicago, Illinois 60637, Laboratoire Adaptation et Pathogénie des Micro-Organismes, CNRS UMR 5163, Université Joseph Fourier Grenoble 1, Institut Jean Roget, BP 170, 38042 Grenoble Cedex 9, France, Centre d'Innovation, Génome Québec, Montréal, Québec H3A 1A4, Canada, INSERM, U563, F-31000 Toulouse, France, University Toulouse III Paul Sabatier, F-31000 Toulouse, France
| | - Rima McLeod
- Departments of Surgery (Ophthalmology) and Pediatrics (Infectious Disease), The University of Chicago, Chicago, Illinois 60637, Laboratoire Adaptation et Pathogénie des Micro-Organismes, CNRS UMR 5163, Université Joseph Fourier Grenoble 1, Institut Jean Roget, BP 170, 38042 Grenoble Cedex 9, France, Centre d'Innovation, Génome Québec, Montréal, Québec H3A 1A4, Canada, INSERM, U563, F-31000 Toulouse, France, University Toulouse III Paul Sabatier, F-31000 Toulouse, France
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Tremblay N, Yang SW, Hitz MP, Asselin G, Ginns J, Riopel K, Gendron R, Montpetit A, Duhig E, Dubé MP, Radford D, Andelfinger G. Familial ventricular aneurysms and septal defects map to chromosome 10p15. Eur Heart J 2010; 32:568-73. [DOI: 10.1093/eurheartj/ehq447] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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44
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Do R, Bailey SD, Paré G, Montpetit A, Desbiens K, Hudson TJ, Yusuf S, Bouchard C, Gaudet D, Pérusse L, Anand S, Vohl MC, Pastinen T, Engert JC. Fine Mapping of the Insulin-Induced Gene 2 Identifies a Variant Associated With LDL Cholesterol and Total Apolipoprotein B Levels. ACTA ACUST UNITED AC 2010; 3:454-61. [DOI: 10.1161/circgenetics.109.917039] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Background—
In a whole-genome scan, a single nucleotide polymorphism (SNP) (rs7566605) upstream of the insulin-induced gene 2 (
INSIG2
) was shown to influence body mass index and obesity in the Framingham Heart Study, with replication of these results in an additional 4 of 5 studies. However, other studies could not replicate the association. Because
INSIG2
plays an important role in cholesterol biosynthesis, we hypothesized that human
INSIG2
variants might play a role in the regulation of plasma lipid and lipoprotein levels.
Methods and Results—
We selected tagging SNPs spanning >100 kb of
INSIG2
locus and sequenced 18 434 base pairs to discover novel SNPs. Thirty-two SNPs were genotyped in 645 individuals from the Quebec Family Study. Two SNPs (rs10490626 and rs12464355) were associated with plasma low-density lipoprotein cholesterol (LDL-C) (
P
<0.0015) and total apolipoprotein B (apoB) levels (
P
<0.014), whereas no association was found between any SNP and body mass index. We replicated the finding of rs10490626 for both LDL-C and total apoB in additional study samples, including 758 individuals from Saguenay–Lac St. Jean, Quebec (
P
=0.040 for LDL-C,
P
=0.044 for apoB), 3247 Europeans (
P
=0.028 for LDL-C,
P
=0.030 for apoB), and 1695 South Asians (
P
=0.0036 for LDL-C,
P
=0.034 for apoB) from the INTERHEART study (for LDL-C, the combined 2-sided
P
=6.2×10
−5
and for total apoB,
P
=0.0011). Furthermore, we identified a variant in the human sorbin and SH
3
-domain–containing-1 gene that was associated with
INSIG2
mRNA levels, and this SNP was shown to act in combination with rs10490626 to affect LDL-C (
P
=0.022) in the Quebec Family Study and in INTERHEART South Asians (
P
=0.019) and Europeans (
P
=0.052).
Conclusion—
These results suggest that
INSIG2
genetic variants may have a more direct role in lipid and lipoprotein metabolism than in obesity.
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Affiliation(s)
- Ron Do
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Swneke D. Bailey
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Guillaume Paré
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Alexandre Montpetit
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Katia Desbiens
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Thomas J. Hudson
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Salim Yusuf
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Claude Bouchard
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Daniel Gaudet
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Louis Pérusse
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Sonia Anand
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Marie-Claude Vohl
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - Tomi Pastinen
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
| | - James C. Engert
- From the Department of Human Genetics (R.D., S.D.B, G.P., T.P., J.C.E.), McGill University, McGill University and Genome Québec Innovation Centre (G.P., A.M., T.J.H., T.P.); and Research Institute of McGill University Health Centre (K.D., J.C.E.), Montreal, Canada; Pennington Biomedical Research Center (C.B.), Baton Rouge, La; Department of Medicine (D.G.), University of Montreal, and ECOGENE-21 Clinical Research Center, Chicoutimi Hospital; Department of Social and Preventive Medicine (L.P.),
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45
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Bailey SD, Xie C, Do R, Montpetit A, Diaz R, Mohan V, Keavney B, Yusuf S, Gerstein HC, Engert JC, Anand S. Variation at the NFATC2 locus increases the risk of thiazolidinedione-induced edema in the Diabetes REduction Assessment with ramipril and rosiglitazone Medication (DREAM) study. Diabetes Care 2010; 33:2250-3. [PMID: 20628086 PMCID: PMC2945168 DOI: 10.2337/dc10-0452] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
OBJECTIVE Thiazolidinediones are used to treat type 2 diabetes. Their use has been associated with peripheral edema and congestive heart failure-outcomes that may have a genetic etiology. RESEARCH DESIGN AND METHODS We genotyped 4,197 participants of the multiethnic DREAM (Diabetes REduction Assessment with ramipril and rosiglitazone Medication) trial with a 50k single nucleotide polymorphisms (SNP) array, which captures ∼2000 cardiovascular, inflammatory, and metabolic genes. We tested 32,088 SNPs for an association with edema among Europeans who received rosiglitazone (n = 965). RESULTS One SNP, rs6123045, in NFATC2 was significantly associated with edema (odds ratio 1.89 [95% CI 1.47-2.42]; P = 5.32 × 10(-7), corrected P = 0.017). Homozygous individuals had the highest edema rate (hazard ratio 2.89, P = 4.22 × 10(-4)) when compared with individuals homozygous for the protective allele, with heterozygous individuals having an intermediate risk. The interaction between the SNP and rosiglitazone for edema was significant (P = 7.68 × 10(-3)). Six SNPs in NFATC2 were significant in both Europeans and Latin Americans (P < 0.05). CONCLUSIONS Genetic variation at the NFATC2 locus contributes to edema among individuals who receive rosiglitazone.
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Affiliation(s)
- Swneke D Bailey
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
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46
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Manolescu DC, El-Kares R, Lakhal-Chaieb L, Montpetit A, Bhat PV, Goodyer P. Newborn serum retinoic acid level is associated with variants of genes in the retinol metabolism pathway. Pediatr Res 2010; 67:598-602. [PMID: 20308937 DOI: 10.1203/pdr.0b013e3181dcf18a] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Retinoic acid (RA) is a critical regulator of gene expression during embryonic development. In rodents, moderate maternal vitamin A deficiency leads to subtle morphogenetic defects and inactivation of RA pathway genes causes major disturbances of embryogenesis. In this study, we quantified RA in umbilical cord blood of 145 healthy full-term Caucasian infants from Montreal. Sixty seven percent of values were <10 nmol/L (84 were <0.07 nmol/L) and 33% had moderate or high levels. Variation in RA could not be explained by parallel variation in its precursor, retinol (ROL). However, we found that the (A) allele of the rs12591551 single nucleotide polymorphism (SNP) in the ALDH1A2 gene (ALDH1A2rs12591551(A)), occurring in 19% of newborns, was associated with 2.5-fold higher serum RA levels. ALDH1A2 encodes retinaldehyde dehydrogenase (RALDH) 2, which synthesizes RA in fetal tissues. We also found that homozygosity for the (A) allele of the rs12724719 SNP in the CRABP2 gene (CRABP2rs12724719(A/A)) was associated with 4.4-fold increase in umbilical cord serum RA. CRABP2 facilitates RA binding to its cognate receptor complex and transfer to the nucleus. We hypothesize that individual variation in RA pathway genes may account for subtle variations in RA-dependent human embryogenesis.
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Affiliation(s)
- Daniel C Manolescu
- Department of Medicine, University of Montreal, and Department of Pediatrics, Montreal Children's Hospital Research Institute, Montreal, Quebec H3Z 2Z3, Canada
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47
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El Kares R, Manolescu DC, Lakhal-Chaieb L, Montpetit A, Zhang Z, Bhat PV, Goodyer P. A human ALDH1A2 gene variant is associated with increased newborn kidney size and serum retinoic acid. Kidney Int 2010; 78:96-102. [PMID: 20375987 DOI: 10.1038/ki.2010.101] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Nephron number varies widely between 0.3 and 1.3 million per kidney in humans. During fetal life, the rate of nephrogenesis is influenced by local retinoic acid (RA) level such that even moderate maternal vitamin A deficiency limits the final nephron number in rodents. Inactivation of genes in the RA pathway causes renal agenesis in mice; however, the impact of retinoids on human kidney development is unknown. To resolve this, we tested for associations between variants of genes involved in RA metabolism (ALDH1A2, CYP26A1, and CYP26B1) and kidney size among normal newborns. Homozygosity for a common (1 in 5) variant, rs7169289(G), within an Sp1 transcription factor motif of the ALDH1A2 gene, showed a significant 22% increase in newborn kidney volume when adjusted for body surface area. Infants bearing this allele had higher umbilical cord blood RA levels compared to those with homozygous wild-type ALDH1A2 rs7169289(A) alleles. Furthermore, the effect of the rs7169289(G) variant was evident in subgroups with or without a previously reported hypomorphic RET 1476(A) proto-oncogene allele that is critical in determining final nephron number. As maternal vitamin A deficiency is widespread in developing countries and may compromise availability of retinol for fetal RA synthesis, our study suggests that the ALDH1A2 rs7169289(G) variant might be protective for such individuals.
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Affiliation(s)
- Reyhan El Kares
- Department of Pediatrics, Montreal Children's Hospital Research Institute, McGill University, and Département de Médecine, Centre Hospitalier de l'Université de Montréal,Montreal, Quebec, Canada
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48
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Tan TG, Mui E, Cong H, Witola WH, Montpetit A, Muench SP, Sidney J, Alexander J, Sette A, Grigg ME, Maewal A, McLeod R. Identification of T. gondii epitopes, adjuvants, and host genetic factors that influence protection of mice and humans. Vaccine 2010; 28:3977-89. [PMID: 20347630 DOI: 10.1016/j.vaccine.2010.03.028] [Citation(s) in RCA: 62] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2009] [Revised: 03/09/2010] [Accepted: 03/15/2010] [Indexed: 11/19/2022]
Abstract
Toxoplasma gondii is an intracellular parasite that causes severe neurologic and ocular disease in immune-compromised and congenitally infected individuals. There is no vaccine protective against human toxoplasmosis. Herein, immunization of L(d) mice with HF10 (HPGSVNEFDF) with palmitic acid moieties or a monophosphoryl lipid A derivative elicited potent IFN-gamma production from L(d)-restricted CD8(+) T cells in vitro and protected mice. CD8(+) T cell peptide epitopes from T. gondii dense granule proteins GRA 3, 6, 7, and Sag 1, immunogenic in humans for HLA-A02(+), HLA-A03(+), and HLA-B07(+) cells were identified. Since peptide repertoire presented by MHC class I molecules to CD8(+) T cells is shaped by endoplasmic reticulum-associated aminopeptidase (ERAAP), polymorphisms in the human ERAAP gene ERAP1 were studied and associate with susceptibility to human congenital toxoplasmosis (p<0.05). These results have important implications for vaccine development.
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MESH Headings
- Adjuvants, Immunologic/pharmacology
- Aminopeptidases/genetics
- Animals
- Antigens, Protozoan/immunology
- CD8-Positive T-Lymphocytes/immunology
- Epitopes, T-Lymphocyte/immunology
- Female
- Genetic Predisposition to Disease
- HLA-A Antigens/immunology
- HLA-B Antigens/immunology
- Humans
- Interferon-gamma/immunology
- Leukocytes, Mononuclear/immunology
- Lipopeptides/immunology
- Mice
- Mice, Inbred BALB C
- Mice, Transgenic
- Minor Histocompatibility Antigens
- Models, Molecular
- Polymorphism, Genetic
- Protozoan Proteins/immunology
- Protozoan Vaccines/immunology
- Toxoplasma/immunology
- Toxoplasmosis/genetics
- Toxoplasmosis/immunology
- Toxoplasmosis, Congenital/genetics
- Toxoplasmosis, Congenital/immunology
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Affiliation(s)
- Tze Guan Tan
- Department of Surgery, Committees on Immunology, Molecular Medicine, and Genetics, Institute of Genomics and Systems Biology, and The College, The University of Chicago, Chicago, IL 60637, USA
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49
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Ge B, Pokholok DK, Kwan T, Grundberg E, Morcos L, Verlaan DJ, Le J, Koka V, Lam KCL, Gagné V, Dias J, Hoberman R, Montpetit A, Joly MM, Harvey EJ, Sinnett D, Beaulieu P, Hamon R, Graziani A, Dewar K, Harmsen E, Majewski J, Göring HHH, Naumova AK, Blanchette M, Gunderson KL, Pastinen T. Global patterns of cis variation in human cells revealed by high-density allelic expression analysis. Nat Genet 2009; 41:1216-22. [PMID: 19838192 DOI: 10.1038/ng.473] [Citation(s) in RCA: 186] [Impact Index Per Article: 12.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2009] [Accepted: 08/24/2009] [Indexed: 12/15/2022]
Abstract
Cis-acting variants altering gene expression are a source of phenotypic differences. The cis-acting components of expression variation can be identified through the mapping of differences in allelic expression (AE), which is the measure of relative expression between two allelic transcripts. We generated a map of AE associated SNPs using quantitative measurements of AE on Illumina Human1M BeadChips. In 53 lymphoblastoid cell lines derived from donors of European descent, we identified common cis variants affecting 30% (2935/9751) of the measured RefSeq transcripts at 0.001 permutation significance. The pervasive influence of cis-regulatory variants, which explain 50% of population variation in AE, extend to full-length transcripts and their isoforms as well as to unannotated transcripts. These strong effects facilitate fine mapping of cis-regulatory SNPs, as demonstrated by dissection of heritable control of transcripts in the systemic lupus erythematosus-associated C8orf13-BLK region in chromosome 8. The dense collection of associations will facilitate large-scale isolation of cis-regulatory SNPs.
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Affiliation(s)
- Bing Ge
- McGill University and Genome Québec Innovation Centre, Montréal, Québec, Canada
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50
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Qu HQ, Jacob K, Fatet S, Ge B, Barnett D, Delattre O, Faury D, Montpetit A, Solomon L, Hauser P, Garami M, Bognar L, Hansely Z, Mio R, Farmer JP, Albrecht S, Polychronakos C, Hawkins C, Jabado N. Genome-wide profiling using single-nucleotide polymorphism arrays identifies novel chromosomal imbalances in pediatric glioblastomas. Neuro Oncol 2009; 12:153-63. [PMID: 20150382 DOI: 10.1093/neuonc/nop001] [Citation(s) in RCA: 65] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Available data on genetic events in pediatric grade IV astrocytomas (glioblastoma [pGBM]) are scarce. This has traditionally been a major impediment in understanding the pathogenesis of this tumor and in developing ways for more effective management. Our aim is to chart DNA copy number aberrations (CNAs) and get insight into genetic pathways involved in pGBM. Using the Illumina Infinium Human-1 bead-chip-array (100K single-nucleotide polymorphisms [SNPs]), we genotyped 18 pediatric and 6 adult GBMs. Results were compared to BAC-array profiles harvested on 16 of the same pGBM, to an independent data set of 9 pediatric high-grade astrocytomas (HGAs) analyzed on Affymetrix 250K-SNP arrays, and to existing data sets on HGAs. CNAs were additionally validated by real-time qPCR in a set of genes in pGBM. Our results identify with nonrandom clustering of CNAs in several novel, previously not reported, genomic regions, suggesting that alterations in tumor suppressors and genes involved in the regulation of RNA processing and the cell cycle are major events in the pathogenesis of pGBM. Most regions were distinct from CNAs in aGBMs and show an unexpectedly low frequency of genetic amplification and homozygous deletions and a high frequency of loss of heterozygosity for a high-grade I rapidly dividing tumor. This first, complete, high-resolution profiling of the tumor cell genome fills an important gap in studies on pGBM. It ultimately guides the mapping of oncogenic networks unique to pGBM, identification of the related therapeutic predictors and targets, and development of more effective therapies. It further shows that, despite commonalities in a few CNAs, pGBM and aGBMs are two different diseases.
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Affiliation(s)
- Hui-Qi Qu
- Montreal Children's Hospital, 2300 Tupper, Montreal, Que., Canada, H3H 1P3.
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