1
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Baig S, Nadaf J, Allache R, Le PU, Luo M, Djedid A, Nkili-Meyong A, Safisamghabadi M, Prat A, Antel J, Guiot MC, Petrecca K. Identity and nature of neural stem cells in the adult human subventricular zone. iScience 2024; 27:109342. [PMID: 38495819 PMCID: PMC10940989 DOI: 10.1016/j.isci.2024.109342] [Citation(s) in RCA: 0] [Impact Index Per Article: 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: 10/03/2023] [Revised: 12/26/2023] [Accepted: 02/22/2024] [Indexed: 03/19/2024] Open
Abstract
The existence of neural stem cells (NSCs) in adult human brain neurogenic regions remains unresolved. To address this, we created a cell atlas of the adult human subventricular zone (SVZ) derived from fresh neurosurgical samples using single-cell transcriptomics. We discovered 2 adult radial glia (RG)-like populations, aRG1 and aRG2. aRG1 shared features with fetal early RG (eRG) and aRG2 were transcriptomically similar to fetal outer RG (oRG). We also captured early neuronal and oligodendrocytic NSC states. We found that the biological programs driven by their transcriptomes support their roles as early lineage NSCs. Finally, we show that these NSCs have the potential to transition between states and along lineage trajectories. These data reveal that multipotent NSCs reside in the adult human SVZ.
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Affiliation(s)
- Salma Baig
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Javad Nadaf
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Redouane Allache
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Phuong U. Le
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Michael Luo
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Annisa Djedid
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Andriniaina Nkili-Meyong
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Maryam Safisamghabadi
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Alex Prat
- Neuroimmunology Research Lab, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montreal, QC H2X0A9, Canada
| | - Jack Antel
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Marie-Christine Guiot
- Department of Neuropathology, Montreal Neurological Institute-Hospital, McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital McGill University, 3801 University Avenue, Montreal QC H3A2B4, Canada
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2
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Dankner M, Maritan SM, Priego N, Kruck G, Nkili-Meyong A, Nadaf J, Zhuang R, Annis MG, Zuo D, Nowakowski A, Biondini M, Kiepas A, Mourcos C, Le P, Charron F, Inglebert Y, Savage P, Théret L, Guiot MC, McKinney RA, Muller WJ, Park M, Valiente M, Petrecca K, Siegel PM. Invasive growth of brain metastases is linked to CHI3L1 release from pSTAT3-positive astrocytes. Neuro Oncol 2024:noae013. [PMID: 38271182 DOI: 10.1093/neuonc/noae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 04/19/2023] [Indexed: 01/27/2024] Open
Abstract
BACKGROUND Compared to minimally invasive brain metastases (MI BrM), highly invasive (HI) lesions form abundant contacts with cells in the peritumoral brain parenchyma and are associated with poor prognosis. Reactive astrocytes (RAs) labeled by phosphorylated STAT3 (pSTAT3) have recently emerged as a promising therapeutic target for BrM. Here, we explore whether BrM invasion pattern is influenced by pSTAT3+ RAs and may serve as a predictive biomarker for STAT3 inhibition. METHODS We used immunohistochemistry to identify pSTAT3+ RAs in HI and MI human and patient-derived xenograft (PDX) BrM. Using PDX, syngeneic, and transgenic mouse models of HI and MI BrM, we assessed how pharmacological STAT3 inhibition or RA-specific STAT3 genetic ablation affected BrM growth in vivo. Cancer cell invasion was modeled in vitro using a brain slice-tumor co-culture assay. We performed single-cell RNA sequencing of human BrM and adjacent brain tissue. RESULTS RAs expressing pSTAT3 are situated at the brain-tumor interface and drive BrM invasive growth. HI BrM invasion pattern was associated with delayed growth in the context of STAT3 inhibition or genetic ablation. We demonstrate that pSTAT3+ RAs secrete Chitinase 3-like-1 (CHI3L1), which is a known STAT3 transcriptional target. Furthermore, single-cell RNA sequencing identified CHI3L1-expressing RAs in human HI BrM. STAT3 activation, or recombinant CHI3L1 alone, induced cancer cell invasion into the brain parenchyma using a brain slice-tumor plug co-culture assay. CONCLUSIONS Together, these data reveal that pSTAT3+ RA-derived CHI3L1 is associated with BrM invasion, implicating STAT3 and CHI3L1 as clinically relevant therapeutic targets for the treatment of HI BrM.
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Affiliation(s)
- Matthew Dankner
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Sarah M Maritan
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Neibla Priego
- Brain Metastasis Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Georgia Kruck
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Andriniaina Nkili-Meyong
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University Health Centre, Montreal, QC, Canada
| | - Javad Nadaf
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University Health Centre, Montreal, QC, Canada
| | - Rebecca Zhuang
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Matthew G Annis
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Dongmei Zuo
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Alexander Nowakowski
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Marco Biondini
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
| | - Alexander Kiepas
- Cell Biology Section, National Institute of Dental and Craniofacial Research, National Institutes of Health, Bethesda, MD, USA
| | - Caitlyn Mourcos
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Phuong Le
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University Health Centre, Montreal, QC, Canada
| | - Francois Charron
- Department of Pharmacology, McGill University, Montreal, QC, Canada
| | - Yanis Inglebert
- Department of Neurosciences, University of Montreal, Montreal, QC, Canada
| | - Paul Savage
- Department of Surgery, University of Toronto, Toronto, ON, Canada
| | - Louis Théret
- Research Institute of the University of Montreal (IRIC), Montreal, QC, Canada
| | - Marie-Christine Guiot
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University Health Centre, Montreal, QC, Canada
- Department of Pathology, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - R Anne McKinney
- Department of Pharmacology, McGill University, Montreal, QC, Canada
| | - William J Muller
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Morag Park
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Department of Pathology, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, QC, Canada
| | - Manuel Valiente
- Brain Metastasis Group, Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Faculty of Medicine, McGill University, Montreal, QC, Canada
- Montreal Neurological Institute-Hospital, McGill University Health Centre, Montreal, QC, Canada
| | - Peter M Siegel
- Rosalind and Morris Goodman Cancer Institute, McGill University, Montreal, QC, Canada
- Department of Medicine, Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Department of Biochemistry, Faculty of Medicine, McGill University, Montreal, QC, Canada
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3
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Hautakangas MR, Widgren P, Korpelainen P, Kangas SM, Komulainen T, Vieira P, Rahikkala E, Pylkäs K, Tuominen H, Kokkonen H, Miinalainen I, Nadaf J, Majewski J, Hinttala R, Uusimaa J. Infantile onset encephalomyopathy, retinopathy, optic atrophy, and mitochondrial DNA depletion associated with a novel pathogenic DHX16 variant. Clin Genet 2023; 104:686-693. [PMID: 37574199 DOI: 10.1111/cge.14416] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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] [Received: 06/06/2023] [Revised: 07/29/2023] [Accepted: 07/30/2023] [Indexed: 08/15/2023]
Abstract
We studied a patient with mitochondrial DNA depletion in skeletal muscle and a multiorgan phenotype, including fatal encephalomyopathy, retinopathy, optic atrophy, and sensorineural hearing loss. Instead of pathogenic variants in the mitochondrial maintenance genes, we identified previously unpublished variant in DHX16 gene, a de novo heterozygous c.1360C>T (p. Arg454Trp). Variants in DHX16 encoding for DEAH-box RNA helicase have previously been reported only in five patients with a phenotype called as neuromuscular oculoauditory syndrome including developmental delay, neuromuscular symptoms, and ocular or auditory defects with or without seizures. We performed functional studies on patient-derived fibroblasts and skeletal muscle revealing, that the DHX16 expression was decreased. Clinical features together with functional data suggest, that our patient's disease is associated with a novel pathogenic DHX16 variant, and mtDNA depletion could be a secondary manifestation of the disease.
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Affiliation(s)
- Milla-Riikka Hautakangas
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Paula Widgren
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Paavo Korpelainen
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Salla M Kangas
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Tuomas Komulainen
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Päivi Vieira
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Elisa Rahikkala
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
| | - Katri Pylkäs
- Biocenter Oulu, University of Oulu, Oulu, Finland
- Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | | | - Hannaleena Kokkonen
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Northern Finland Laboratory Centre Oulu, Oulu, Finland
| | | | - Javad Nadaf
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University, Montreal, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Reetta Hinttala
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Biocenter Oulu, University of Oulu, Oulu, Finland
| | - Johanna Uusimaa
- Research Unit of Clinical Medicine, Medical Research Center, University of Oulu, Oulu, Finland
- Oulu University Hospital, Oulu, Finland
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4
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Chen OJ, Castellsagué E, Moustafa-Kamal M, Nadaf J, Rivera B, Fahiminiya S, Wang Y, Gamache I, Pacifico C, Jiang L, Carrot-Zhang J, Witkowski L, Berghuis AM, Schönberger S, Schneider D, Hillmer M, Bens S, Siebert R, Stewart CJR, Zhang Z, Chao WCH, Greenwood CMT, Barford D, Tischkowitz M, Majewski J, Foulkes WD, Teodoro JG. Germline Missense Variants in CDC20 Result in Aberrant Mitotic Progression and Familial Cancer. Cancer Res 2022; 82:3499-3515. [PMID: 35913887 DOI: 10.1158/0008-5472.can-21-3956] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [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: 11/17/2021] [Revised: 04/12/2022] [Accepted: 07/26/2022] [Indexed: 11/16/2022]
Abstract
CDC20 is a coactivator of the anaphase promoting complex/cyclosome (APC/C) and is essential for mitotic progression. APC/CCDC20 is inhibited by the spindle assembly checkpoint (SAC), which prevents premature separation of sister chromatids and aneuploidy in daughter cells. Although overexpression of CDC20 is common in many cancers, oncogenic mutations have never been identified in humans. Using whole-exome sequencing, we identified heterozygous missense CDC20 variants (L151R and N331K) that segregate with ovarian germ cell tumors in two families. Functional characterization showed these mutants retain APC/C activation activity but have impaired binding to BUBR1, a component of the SAC. Expression of L151R and N331K variants promoted mitotic slippage in HeLa cells and primary skin fibroblasts derived from carriers. Generation of mice carrying the N331K variant using CRISPR-Cas9 showed that, although homozygous N331K mice were nonviable, heterozygotes displayed accelerated oncogenicity of Myc-driven cancers. These findings highlight an unappreciated role for CDC20 variants as tumor-promoting genes. SIGNIFICANCE Two germline CDC20 missense variants that segregate with cancer in two families compromise the spindle assembly checkpoint and lead to aberrant mitotic progression, which could predispose cells to transformation. See related commentary by Villarroya-Beltri and Malumbres, p. 3432.
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Affiliation(s)
- Owen J Chen
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Ester Castellsagué
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Division of Medical Genetics and Cancer Axis, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montréal, Québec, Canada
- Translational Research Laboratory, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, L'Hospitalet de Llobregat, Barcelona, Spain
| | - Mohamed Moustafa-Kamal
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Javad Nadaf
- McGill University and Génome Québec Innovation Centre, Montréal, Québec, Canada
| | - Barbara Rivera
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Hereditary Cancer Programme, Catalan Institute of Oncology, Bellvitge Institute for Biomedical Research, L'Hospitalet de Llobregat, Barcelona, Spain
- Gerald Bronfman Department of Oncology, McGill University, Montréal, Québec, Canada
| | - Somayyeh Fahiminiya
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Yilin Wang
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
| | - Isabelle Gamache
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
| | - Caterina Pacifico
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- Department of Biology, McGill University, Montréal, Québec, Canada
| | - Lai Jiang
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montréal, Québec, Canada
| | - Jian Carrot-Zhang
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Leora Witkowski
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Division of Medical Genetics and Cancer Axis, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montréal, Québec, Canada
| | - Albert M Berghuis
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Centre de Recherche en Biologie Structurale, McGill University, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Montréal, Québec, Canada
| | - Stefan Schönberger
- Department of Pediatric Hematology and Oncology, Pediatrics III, University Hospital of Essen, University of Duisburg-Essen, Essen, Germany
| | - Dominik Schneider
- Clinic of Pediatrics, Dortmund Municipal Hospital, Dortmund, Germany
| | - Morten Hillmer
- Institute of Human Genetics, University of Ulm & Ulm University Medical Center, Ulm, Germany
| | - Susanne Bens
- Institute of Human Genetics, University of Ulm & Ulm University Medical Center, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University of Ulm & Ulm University Medical Center, Ulm, Germany
| | - Colin J R Stewart
- Department of Histopathology, King Edward Memorial Hospital, and School for Women's and Infants' Health, University of Western Australia, Perth, Australia
| | - Ziguo Zhang
- Institute of Cancer Research, London, United Kingdom
| | - William C H Chao
- Faculty of Health Sciences, University of Macau, Macau SAR, China
| | - Celia M T Greenwood
- Cancer Axis, Lady Davis Institute, Jewish General Hospital, Montréal, Québec, Canada
- Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montréal, Québec, Canada
- Departments of Oncology and Human Genetics, McGill University, Montréal, Québec, Canada
| | - David Barford
- Institute of Cancer Research, London, United Kingdom
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, United Kingdom
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montréal, Québec, Canada
- Division of Medical Genetics and Cancer Axis, Lady Davis Institute, Segal Cancer Centre, Jewish General Hospital, Montréal, Québec, Canada
- Program in Cancer Genetics, Department of Oncology and Human Genetics, McGill University, Montréal, Québec, Canada
- Division of Medical Genetics and Cancer Research Program, Research Institute of the McGill University Health Centre, Montréal, Québec, Canada
| | - Jose G Teodoro
- Goodman Cancer Institute, McGill University, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- Department of Microbiology and Immunology, Montréal, Québec, Canada
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5
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Thorner PS, Chong A, Nadaf J, Benlimame N, Marrano P, Chami R, Fu L, Foulkes WD. PRAME
protein expression in
DICER1
‐related tumours. J Pathol Clin Res 2022; 8:579-581. [PMID: 35986592 PMCID: PMC9535095 DOI: 10.1002/cjp2.293] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/04/2022] [Indexed: 11/05/2022]
Affiliation(s)
- Paul S Thorner
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
| | - Anne‐Sophie Chong
- Department of Human Genetics McGill University Montreal, QC Canada
- Cancer Axis, Lady Davis Institute for Medical Research Jewish General Hospital Montreal, QC Canada
- Cancer Research Program Research Institute of the McGill University Health Centre Montreal, QC Canada
| | - Javad Nadaf
- Department of Human Genetics McGill University Montreal, QC Canada
- Cancer Axis, Lady Davis Institute for Medical Research Jewish General Hospital Montreal, QC Canada
| | - Naciba Benlimame
- Research Pathology Facility Lady Davis Institute, Jewish General Hospital Montreal, QC Canada
| | - Paula Marrano
- Division of Pathology Hospital for Sick Children Toronto Ontario Canada
| | - Rose Chami
- Department of Laboratory Medicine and Pathobiology University of Toronto Toronto Ontario Canada
- Division of Pathology Hospital for Sick Children Toronto Ontario Canada
| | - Lili Fu
- Department of Pathology McGill University Health Centre, McGill University Montreal, QC Canada
| | - William D Foulkes
- Department of Human Genetics McGill University Montreal, QC Canada
- Cancer Axis, Lady Davis Institute for Medical Research Jewish General Hospital Montreal, QC Canada
- Cancer Research Program Research Institute of the McGill University Health Centre Montreal, QC Canada
- Gerald Bronfman Department of Oncology McGill University Montreal, QC Canada
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6
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Dankner M, Maritan SM, Priego N, Nadaf J, Nkili A, Zhuang R, Kruck G, Zuo D, Nowakowski A, Inglebert Y, Savage P, Park M, Guiot MC, McKinney A, Muller WJ, Valiente M, Petrecca K, Siegel PM. Abstract 1569: pSTAT3+ stromal cells drive the invasive growth of brain metastases. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-1569] [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
Background: Brain metastases (BrM) with highly invasive (HI) growth patterns are associated with shortened local recurrence free- and overall survival compared to minimally invasive (MI) lesions (Dankner et al. 2021). Compared to MI lesions, HI BrM form abundant contacts with cells in the peritumoral brain, particularly GFAP+ reactive astrocytes (RAs). RAs expressing phosphorylated STAT3 (pSTAT3+ GFAP+ cells) have been shown to be required for BrM colonization and outgrowth (Priego et al. 2018). Here, we investigate the role of pSTAT3+ cells in the brain microenvironment in promoting invasive growth.
Methods: We performed immunohistochemistry to identify pSTAT3+ GFAP+ cells in HI and MI human and patient-derived xenograft BrM. We assessed how pharmacological inhibition or genetic ablation of STAT3 affected HI and MI BrM growth in vivo with patient-derived xenograft and syngeneic models of BrM. The secretome of STAT3+ RAs was interrogated to identify STAT3 target genes that could drive invasive cancer growth. scRNA-Seq from patients with highly invasive brain metastases was used to examine the expression of candidate invasion factors in distinct cell types within the brain. Finally, cancer cell invasion was modeled in vitro using a brain slice-tumor co-culture assay.
Results: HI BrM displayed increased pSTAT3+GFAP+ cells compared to MI lesions. Pharmacological STAT3i with Legasil (Silibinin) or genetic ablation of STAT3 specifically in RAs decreased in vivo growth of HI, but not MI, BrM. Brain slice cultures treated with STAT3-activating cytokines induced cancer cell invasion, a response that was ablated with STAT3i. Chi3L1 was identified as a STAT3 target gene expressed abundantly by stromal cells in the BrM microenvironment. Cancer cells treated with recombinant Chi3L1 showed enhanced invasion into brain slice cultures compared to control-treated cells.
Conclusions: pSTAT3+GFAP+ cells are over-represented in HI BrM, rendering HI BrM preferentially sensitive to STAT3i. pSTAT3+ stromal cells functionally contribute to BrM invasion within the brain, in part through Chi3L1. This work nominates HI histopathological growth pattern as a predictive biomarker of response to STAT3i, and highlights Chi3L1 as a novel therapeutic target for the management of HI BrM.
Citation Format: Matthew Dankner, Sarah M. Maritan, Neibla Priego, Javad Nadaf, Andy Nkili, Rebecca Zhuang, Georgia Kruck, Dongmei Zuo, Alexander Nowakowski, Yanis Inglebert, Paul Savage, Morag Park, Marie-Christine Guiot, Anne McKinney, William J. Muller, Manuel Valiente, Kevin Petrecca, Peter M. Siegel. pSTAT3+ stromal cells drive the invasive growth of brain metastases [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 1569.
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Affiliation(s)
- Matthew Dankner
- 1Rosalind and Morris Goodman Cancer Institute, Montreal, Quebec, Canada
| | - Sarah M. Maritan
- 1Rosalind and Morris Goodman Cancer Institute, Montreal, Quebec, Canada
| | - Neibla Priego
- 2Spanish National Cancer Research Center, Madrid, Spain
| | - Javad Nadaf
- 3Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Andy Nkili
- 3Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Rebecca Zhuang
- 1Rosalind and Morris Goodman Cancer Institute, Montreal, Quebec, Canada
| | - Georgia Kruck
- 1Rosalind and Morris Goodman Cancer Institute, Montreal, Quebec, Canada
| | - Dongmei Zuo
- 1Rosalind and Morris Goodman Cancer Institute, Montreal, Quebec, Canada
| | | | - Yanis Inglebert
- 4Bellini McGill Life Sciences Complex, Montreal, Quebec, Canada
| | - Paul Savage
- 1Rosalind and Morris Goodman Cancer Institute, Montreal, Quebec, Canada
| | - Morag Park
- 1Rosalind and Morris Goodman Cancer Institute, Montreal, Quebec, Canada
| | | | - Anne McKinney
- 4Bellini McGill Life Sciences Complex, Montreal, Quebec, Canada
| | - William J. Muller
- 1Rosalind and Morris Goodman Cancer Institute, Montreal, Quebec, Canada
| | | | - Kevin Petrecca
- 3Montreal Neurological Institute-Hospital, Montreal, Quebec, Canada
| | - Peter M. Siegel
- 1Rosalind and Morris Goodman Cancer Institute, Montreal, Quebec, Canada
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7
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Thorner PS, Chong AS, Nadaf J, Benlimame N, Marrano P, Chami R, Fu L, Foulkes WD. PRAME protein expression in DICER1-related tumours. J Pathol Clin Res 2022; 8:294-304. [PMID: 35297207 PMCID: PMC8977278 DOI: 10.1002/cjp2.264] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Revised: 01/28/2022] [Accepted: 01/30/2022] [Indexed: 11/09/2022]
Abstract
DICER1 syndrome is an autosomal dominant tumour predisposition syndrome usually affecting persons under 30 years of age. Many of the associated benign and malignant lesions occur almost exclusively in DICER1 syndrome. One such tumour, pituitary blastoma (pitB), overexpresses PRAME 500x above control levels. PRAME (PReferentially expressed Antigen in MElanoma) is expressed in malignancies that are not DICER1-related (e.g. melanoma). To address whether PRAME expression is part of the DICER1 phenotype, or simply a feature of pitB, a series of 75 DICER1-mutated specimens and 33 non-mutated specimens was surveyed using immunohistochemistry for PRAME, together with EZH2, which complexes with PRAME. In DICER1-mutated specimens, positive staining for PRAME was only seen in malignant tumours; 7 of 11 histological types and 34/62 individual tumours were positive, while non-tumourous lesions were always negative. Pleuropulmonary blastoma (PPB) showed a continuum in staining, with type I lesions being PRAME negative (n = 7) but all type II and type III lesions PRAME positive (n = 7). Similarly, cystic nephroma (CN) was negative (n = 8), with anaplastic sarcoma of the kidney being positive (n = 2). However, one atypical CN with mesenchymal cell proliferation was PRAME-positive. Embryonal rhabdomyosarcoma (RMS) with DICER1 pathogenic variants (PVs) was positive for PRAME (5/6), but the same tumour type without DICER1 PVs was also positive (9/15). Staining for EZH2 corresponded to that seen with PRAME, validating the latter. This study leads us to conclude that (1) PRAME expression occurs in two-thirds of DICER1-related malignancies; (2) PRAME may be a marker for the progression that certain DICER1-related lesions are thought to undergo, such as PPB and CN; and (3) PRAME expression in some tumours, such as RMS, appears to be an intrinsic feature of the tumour, rather than specifically related to DICER1 PVs. Therapy directed against PRAME may offer novel treatment options in patients with the DICER1 syndrome.
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Affiliation(s)
- Paul S Thorner
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada
| | - Anne-Sophie Chong
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,Cancer Axis, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,Cancer Axis, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada
| | - Naciba Benlimame
- Research Pathology Facility, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Paula Marrano
- Division of Pathology, Hospital for Sick Children, Toronto, ON, Canada
| | - Rose Chami
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, ON, Canada.,Division of Pathology, Hospital for Sick Children, Toronto, ON, Canada
| | - Lili Fu
- Department of Pathology, McGill University Health Centre, McGill University, Montreal, QC, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,Cancer Axis, Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, QC, Canada.,Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
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8
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Couturier CP, Nadaf J, Li Z, Baig S, Riva G, Le P, Kloosterman DJ, Monlong J, Nkili Meyong A, Allache R, Degenhard T, Al-Rashid M, Guiot MC, Bourque G, Ragoussis J, Akkari L, Quintana FJ, Petrecca K. Glioblastoma scRNAseq Shows Treatment-induced, Immune-dependent Rise In Mesenchymal Cancer Cells, and Structural Variants in Distal Neural Stem Cells. Neuro Oncol 2022; 24:1494-1508. [PMID: 35416251 PMCID: PMC9435507 DOI: 10.1093/neuonc/noac085] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND Glioblastoma is a treatment-resistant brain cancer. Its hierarchical cellular nature and its tumour microenvironment (TME) before, during, and after treatments remain unresolved. METHODS Here, we used single-cell RNA-sequencing to analyze new and recurrent glioblastoma, and the nearby subventricular zone (SVZ). RESULTS We found four glioblastoma neural lineages are present in new and recurrent glioblastoma with an enrichment of the cancer mesenchymal lineage, immune cells, and reactive astrocytes in early recurrences. Cancer lineages were hierarchically organized around cycling oligodendrocytic and astrocytic progenitors that are transcriptomically similar but distinct to SVZ neural stem cells (NSCs). Furthermore, NSCs from the SVZ of glioblastoma patients harbored glioblastoma chromosomal anomalies. Lastly, mesenchymal cancer cells and TME reactive astrocytes shared similar gene signatures which were induced by radiotherapy in a myeloid-dependent fashion in vivo. CONCLUSION These data reveal the dynamic, immune-dependent nature of glioblastoma's response to treatments and identify distant NSCs as likely cells of origin.
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Affiliation(s)
- Charles P Couturier
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University
| | - Javad Nadaf
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University.,McGill University and Genome Québec Innovation Centre, Montreal, Quebec, Canada, Department of Human Genetics, Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
| | - Zhaorong Li
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA
| | - Salma Baig
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University
| | - Gabriele Riva
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University
| | - Phuong Le
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University
| | - Daan J Kloosterman
- Tumour Biology and Immunology Division, The Netherlands Cancer Institute, Oncode Institute, Amsterdam, The Netherlands
| | - Jean Monlong
- McGill University and Genome Québec Innovation Centre, Montreal, Quebec, Canada, Department of Human Genetics, Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada.,UC Santa Cruz Genomics Institute, Santa Cruz, CA, USA
| | - Andriniaina Nkili Meyong
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University
| | - Redouane Allache
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University
| | - Theresa Degenhard
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University
| | - Mariam Al-Rashid
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University
| | - Marie-Christine Guiot
- Department of Neuropathology, Montreal Neurological Institute-Hospital, McGill University
| | - Guillaume Bourque
- McGill University and Genome Québec Innovation Centre, Montreal, Quebec, Canada, Department of Human Genetics, Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
| | - Jiannis Ragoussis
- McGill University and Genome Québec Innovation Centre, Montreal, Quebec, Canada, Department of Human Genetics, Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
| | - Leila Akkari
- Tumour Biology and Immunology Division, The Netherlands Cancer Institute, Oncode Institute, Amsterdam, The Netherlands
| | - Francisco J Quintana
- Ann Romney Center for Neurologic Diseases, Brigham and Women's Hospital, Harvard Medical School, Boston, MA, USA.,The Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, McGill University
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9
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Fierheller CT, Guitton-Sert L, Alenezi WM, Revil T, Oros KK, Gao Y, Bedard K, Arcand SL, Serruya C, Behl S, Meunier L, Fleury H, Fewings E, Subramanian DN, Nadaf J, Bruce JP, Bell R, Provencher D, Foulkes WD, El Haffaf Z, Mes-Masson AM, Majewski J, Pugh TJ, Tischkowitz M, James PA, Campbell IG, Greenwood CMT, Ragoussis J, Masson JY, Tonin PN. A functionally impaired missense variant identified in French Canadian families implicates FANCI as a candidate ovarian cancer-predisposing gene. Genome Med 2021; 13:186. [PMID: 34861889 PMCID: PMC8642877 DOI: 10.1186/s13073-021-00998-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [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: 09/02/2020] [Accepted: 10/27/2021] [Indexed: 12/14/2022] Open
Abstract
Background Familial ovarian cancer (OC) cases not harbouring pathogenic variants in either of the BRCA1 and BRCA2 OC-predisposing genes, which function in homologous recombination (HR) of DNA, could involve pathogenic variants in other DNA repair pathway genes. Methods Whole exome sequencing was used to identify rare variants in HR genes in a BRCA1 and BRCA2 pathogenic variant negative OC family of French Canadian (FC) ancestry, a population exhibiting genetic drift. OC cases and cancer-free individuals from FC and non-FC populations were investigated for carrier frequency of FANCI c.1813C>T; p.L605F, the top-ranking candidate. Gene and protein expression were investigated in cancer cell lines and tissue microarrays, respectively. Results In FC subjects, c.1813C>T was more common in familial (7.1%, 3/42) than sporadic (1.6%, 7/439) OC cases (P = 0.048). Carriers were detected in 2.5% (74/2950) of cancer-free females though female/male carriers were more likely to have a first-degree relative with OC (121/5249, 2.3%; Spearman correlation = 0.037; P = 0.011), suggesting a role in risk. Many of the cancer-free females had host factors known to reduce risk to OC which could influence cancer risk in this population. There was an increased carrier frequency of FANCI c.1813C>T in BRCA1 and BRCA2 pathogenic variant negative OC families, when including the discovery family, compared to cancer-free females (3/23, 13%; OR = 5.8; 95%CI = 1.7–19; P = 0.005). In non-FC subjects, 10 candidate FANCI variants were identified in 4.1% (21/516) of Australian OC cases negative for pathogenic variants in BRCA1 and BRCA2, including 10 carriers of FANCI c.1813C>T. Candidate variants were significantly more common in familial OC than in sporadic OC (P = 0.04). Localization of FANCD2, part of the FANCI-FANCD2 (ID2) binding complex in the Fanconi anaemia (FA) pathway, to sites of induced DNA damage was severely impeded in cells expressing the p.L605F isoform. This isoform was expressed at a reduced level, destabilized by DNA damaging agent treatment in both HeLa and OC cell lines, and exhibited sensitivity to cisplatin but not to a poly (ADP-ribose) polymerase inhibitor. By tissue microarray analyses, FANCI protein was consistently expressed in fallopian tube epithelial cells and only expressed at low-to-moderate levels in 88% (83/94) of OC samples. Conclusions This is the first study to describe candidate OC variants in FANCI, a member of the ID2 complex of the FA DNA repair pathway. Our data suggest that pathogenic FANCI variants may modify OC risk in cancer families. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00998-5.
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Affiliation(s)
- Caitlin T Fierheller
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Laure Guitton-Sert
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Wejdan M Alenezi
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Department of Medical Laboratory Technology, Taibah University, Medina, Saudi Arabia
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Kathleen K Oros
- Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada
| | - Yuandi Gao
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Karine Bedard
- Laboratoire de Diagnostic Moléculaire, Centre Hospitalier de l'Université de Montréal (CHUM), Montreal, Quebec, Canada.,Département de pathologie et biologie cellulaire, Université de Montréal, Montreal, Quebec, Canada
| | - Suzanna L Arcand
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Corinne Serruya
- Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada
| | - Supriya Behl
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Liliane Meunier
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Hubert Fleury
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada
| | - Eleanor Fewings
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Deepak N Subramanian
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jeffrey P Bruce
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Rachel Bell
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada
| | - Diane Provencher
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Division of Gynecologic Oncology, Université de Montréal, Montreal, Quebec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Medicine, McGill University, Montreal, Quebec, Canada
| | - Zaki El Haffaf
- Centre de recherche du Centre Hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
| | - Anne-Marie Mes-Masson
- Centre de recherche du Centre hospitalier de l'Université de Montréal and Institut du cancer de Montréal, Montreal, Quebec, Canada.,Department of Medicine, Université de Montréal, Montreal, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Trevor J Pugh
- Princess Margaret Cancer Centre, University Health Network, Toronto, Ontario, Canada.,Department of Medical Biophysics, University of Toronto, Toronto, Ontario, Canada.,Ontario Institute for Cancer Research, Toronto, Ontario, Canada
| | - Marc Tischkowitz
- Department of Medical Genetics, National Institute for Health Research Cambridge Biomedical Research Centre, University of Cambridge, Cambridge, UK
| | - Paul A James
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia.,The Parkville Familial Cancer Centre, Peter MacCallum Cancer Centre and The Royal Melbourne Hospital, Melbourne, Victoria, Australia
| | - Ian G Campbell
- Cancer Genetics Laboratory, Peter MacCallum Cancer Centre, Melbourne, Victoria, Australia.,Sir Peter MacCallum Department of Oncology, University of Melbourne, Melbourne, Victoria, Australia
| | - Celia M T Greenwood
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research, Jewish General Hospital, Montreal, Quebec, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Department of Epidemiology, Biostatistics & Occupational Health, McGill University, Montreal, Quebec, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill Genome Centre, McGill University, Montreal, Quebec, Canada
| | - Jean-Yves Masson
- Genome Stability Laboratory, CHU de Québec-Université Laval Research Center, Oncology Division, Quebec City, Quebec, Canada.,Department of Molecular Biology, Medical Biochemistry and Pathology, Laval University Cancer Research Center, Quebec City, Quebec, Canada
| | - Patricia N Tonin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada. .,Cancer Research Program, Centre for Translational Biology, The Research Institute of the McGill University Health Centre, 1001 Decarie Boulevard, Montreal, Quebec, H4A 3 J1, Canada. .,Department of Medicine, McGill University, Montreal, Quebec, Canada.
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10
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Fierheller C, Alenezi WM, Serruya C, Revil T, Nadaf J, Mes-Masson AM, Provencher D, Foulkes WD, Haffaf ZE, Greenwood CMT, Masson JY, Ragoussis J, Tonin PN. Abstract 2056: The genomic landscape of carriers of rare variants in FANCI, a new candidate ovarian cancer predisposing gene. Cancer Res 2021. [DOI: 10.1158/1538-7445.am2021-2056] [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
The potentially pathogenic variant (PPV), FANCI c.1813C>T; p.L605F, in a new candidate ovarian cancer (OC) predisposing gene was discovered by whole exome sequencing (WES) of familial OC cases from the founder French Canadian (FC) population for discovering new OC predisposing genes. Modeling this variant in cellulo suggested this variant encodes an unstable protein. FANCI is an essential member upstream of the homologous recombination DNA repair pathway and intersects BRCA1 and BRCA2 function, proteins encoded by genes involved in hereditary OC. Investigating the FC founder population facilitates the discovery of PPVs as they are more likely to harbor recurrent variants due to common ancestors, increasing the likelihood of identifying candidate genes in cancer families.
To further support the candidacy of FANCI as a new OC predisposing gene, we investigated the germline landscape of c.1813C>T carrier FC OC cases for co-occurring PPVs in known or proposed new (emerging) OC predisposing genes or other genes involved in similar pathways (DNA repair).
Using WES of peripheral blood lymphocyte DNA, the genomic landscape of 10 FANCI carriers were investigated for heterozygous PPVs in 276 DNA repair pathways genes, which included known (BRCA1, BRCA2, MSH2, MLH1, MSH6, PMS2) and emerging (BRIP1, RAD51C, RAD51D) OC predisposing genes. Top ranking candidate variants (minor allele frequency <1%) were identified using 11 different in silico tools that assessed amino acid conversation or potential pathogenicity. Pathogenicity of known and emerging OC predisposing genes was assessed using BRCAExchange (www.brcaexchange.org) and ClinVar (www.ncbi.nlm.nih.gov/clinvar/). A similar analysis was done with WES data from 13 FC OC cases harboring pathogenic BRCA1/BRCA2 variants.
We identified 31 variants in 27 genes in FANCI c.1813C>T carriers. A previously known carrier of a pathogenic BRCA1 variant (c.2836_2837del; p.Ile946GlnfsTer5) was also identified in a familial case. No carriers of other pathogenic variants in known or emerging OC predisposing genes were found. However, FANCI carriers were found to carry at least one other PPV in a DNA repair pathway gene (range 2-9; average=4.1). There were no other carriers of variants in common among all OC cases, though at least 2 cases carried a variant in the same gene. FC OC cases harboring BRCA1/BRCA2 variants carried at least one other PPV in a DNA repair pathway gene (range 2-7; average 4).
It is possible that the identified variants influence or modify risk in conjunction with FANCI, though no PPV was identified in all carriers. As new cancer predisposing genes are identified it will become increasingly important to characterize the genetic context in which variants are identified. This will allow for further insight to clinical translatability once penetrance has been established.
Citation Format: Caitlin Fierheller, Wejdan M Alenezi, Corinne Serruya, Timothée Revil, Javad Nadaf, Anne-Marie Mes-Masson, Diane Provencher, William D Foulkes, Zaki El Haffaf, Celia M T Greenwood, Jean-Yves Masson, Jiannis Ragoussis, Patricia N Tonin. The genomic landscape of carriers of rare variants in FANCI, a new candidate ovarian cancer predisposing gene [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2021; 2021 Apr 10-15 and May 17-21. Philadelphia (PA): AACR; Cancer Res 2021;81(13_Suppl):Abstract nr 2056.
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Affiliation(s)
| | | | - Corinne Serruya
- 2The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | | | - Javad Nadaf
- 1McGill University, Montreal, Quebec, Canada
| | | | | | | | - Zaki El Haffaf
- 5Centre de recherche du Centre hospitalier de l'Université de Montréal, Montreal, Quebec, Canada
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11
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Nadaf J, de Kock L, Chong AS, Korbonits M, Thorner P, Benlimame N, Fu L, Peet A, Warner J, Ploner O, Shuangshoti S, Albrecht S, Hamel N, Priest JR, Rivera B, Ragoussis J, Foulkes WD. Molecular characterization of DICER1-mutated pituitary blastoma. Acta Neuropathol 2021; 141:929-944. [PMID: 33644822 DOI: 10.1007/s00401-021-02283-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 12/13/2022]
Abstract
Pituitary blastoma (PitB) has recently been identified as a rare and potentially lethal pediatric intracranial tumor. All cases that have been studied molecularly possess at least one DICER1 pathogenic variant. Here, we characterized nine pituitary samples, including three fresh frozen PitBs, three normal fetal pituitary glands and three normal postnatal pituitary glands using small-RNA-Seq, RNA-Seq, methylation profiling, whole genome sequencing and Nanostring® miRNA analyses; an extended series of 21 pituitary samples was used for validation purposes. These analyses demonstrated that DICER1 RNase IIIb hotspot mutations in PitBs induced improper processing of miRNA precursors, resulting in aberrant 5p-derived miRNA products and a skewed distribution of miRNAs favoring mature 3p over 5p miRNAs. This led to dysregulation of hundreds of 5p and 3p miRNAs and concomitant dysregulation of numerous mRNA targets. Gene expression analysis revealed PRAME as the most significantly upregulated gene (500-fold increase). PRAME is a member of the Retinoic Acid Receptor (RAR) signaling pathway and in PitBs, the RAR, WNT and NOTCH pathways are dysregulated. Cancer Hallmarks analysis showed that PI3K pathway is activated in the tumors. Whole genome sequencing demonstrated a quiet genome with very few somatic alterations. The comparison of methylation profiles to publicly available data from ~ 3000 other central nervous system tumors revealed that PitBs have a distinct methylation profile compared to all other tumors, including pituitary adenomas. In conclusion, this comprehensive characterization of DICER1-related PitB revealed key molecular underpinnings of PitB and identified pathways that could potentially be exploited in the treatment of this tumor.
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Affiliation(s)
- Javad Nadaf
- Department of Medical Genetics, The Lady Davis Institute, Jewish General Hospital, 3755 Cote St. Catherine Road, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - Leanne de Kock
- Department of Medical Genetics, The Lady Davis Institute, Jewish General Hospital, 3755 Cote St. Catherine Road, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- Children's Hospital of Eastern Ontario Research Institute, Ottawa, ON, Canada
| | - Anne-Sophie Chong
- Department of Medical Genetics, The Lady Davis Institute, Jewish General Hospital, 3755 Cote St. Catherine Road, Montreal, QC, H3T 1E2, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Márta Korbonits
- Centre for Endocrinology, William Harvey Research Institute, Barts and the London School of Medicine, Queen Mary University of London, London, UK
| | - Paul Thorner
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Canada
| | - Naciba Benlimame
- Research Pathology Facility, Lady Davis Institute, Jewish General Hospital, Montreal, QC, Canada
| | - Lili Fu
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Andrew Peet
- Birmingham Children's NHS Foundation Trust, Birmingham, UK
- Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Justin Warner
- Department of Child Health, University Hospital of Wales, Heath Park, Cardiff, UK
| | | | - Shanop Shuangshoti
- Department of Pathology and Chulalongkorn GenePRO Center, Faculty of Medicine, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Steffen Albrecht
- Department of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Nancy Hamel
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada
| | | | - Barbara Rivera
- Program in Molecular Mechanisms and Experimental Therapy in Oncology (Oncobell), IDIBELL, Hospitalet de Llobregat, Barcelona, Spain
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University Genome Centre, Montreal, QC, Canada
| | - William D Foulkes
- Department of Medical Genetics, The Lady Davis Institute, Jewish General Hospital, 3755 Cote St. Catherine Road, Montreal, QC, H3T 1E2, Canada.
- Department of Human Genetics, McGill University, Montreal, QC, Canada.
- Cancer Research Program, Research Institute of the McGill University Health Centre, Montreal, QC, Canada.
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Canada.
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12
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Dankner M, Caron M, Al-Saadi T, Yu W, Ouellet V, Ezzeddine R, Maritan SM, Annis MG, Le PU, Nadaf J, Neubarth NS, Savage P, Zuo D, Couturier CP, Monlong J, Djambazian H, Altoukhi H, Bourque G, Ragoussis J, Diaz RJ, Park M, Guiot MC, Lam S, Petrecca K, Siegel PM. Invasive growth associated with Cold-Inducible RNA-Binding Protein expression drives recurrence of surgically resected brain metastases. Neuro Oncol 2021; 23:1470-1480. [PMID: 33433612 DOI: 10.1093/neuonc/noab002] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [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: 12/16/2022] Open
Abstract
BACKGROUND Sixty percent of surgically resected brain metastases (BrM) recur within 1 year. These recurrences have long been thought to result from the dispersion of cancer cells during surgery. We tested the alternative hypothesis that invasion of cancer cells into the adjacent brain plays a significant role in local recurrence and shortened overall survival. METHODS We determined the invasion pattern of 164 surgically resected BrM and correlated with local recurrence and overall survival. We performed single-cell RNA sequencing (scRNAseq) of >15,000 cells from BrM and adjacent brain tissue. Validation of targets was performed with a novel cohort of BrM patient-derived xenografts (PDX) and patient tissues. RESULTS We demonstrate that invasion of metastatic cancer cells into the adjacent brain is associated with local recurrence and shortened overall survival. scRNAseq of paired tumor and adjacent brain samples confirmed the existence of invasive cancer cells in the tumor-adjacent brain. Analysis of these cells identified Cold-Inducible RNA-Binding Protein (CIRBP) overexpression in invasive cancer cells compared to cancer cells located within the metastases. Applying PDX models that recapitulate the invasion pattern observed in patients, we show that CIRBP is overexpressed in highly invasive BrM and is required for efficient invasive growth in the brain. CONCLUSIONS These data demonstrate peritumoral invasion as a driver of treatment failure in BrM that is functionally mediated by CIRBP. These findings improve our understanding of the biology underlying post-operative treatment failure and lay the groundwork for rational clinical trial development based upon invasion pattern in surgically resected brain metastases.
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Affiliation(s)
- Matthew Dankner
- Division of Experimental Medicine, Montréal, Québec, Canada.,Goodman Cancer Research Centre, Montréal, Québec, Canada.,McGill Faculty of Medicine, Montréal, Québec, Canada
| | - Maxime Caron
- McGill University Genome Centre, Department of Human Genetics, Montréal, Québec, Canada
| | - Tariq Al-Saadi
- McGill Faculty of Medicine, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, Montréal, Québec, Canada
| | - WenQing Yu
- McGill Faculty of Medicine, Montréal, Québec, Canada
| | - Veronique Ouellet
- Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Rima Ezzeddine
- Goodman Cancer Research Centre, Montréal, Québec, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada
| | - Sarah M Maritan
- Division of Experimental Medicine, Montréal, Québec, Canada.,Goodman Cancer Research Centre, Montréal, Québec, Canada.,McGill Faculty of Medicine, Montréal, Québec, Canada
| | | | - Phuong Uyen Le
- McGill Faculty of Medicine, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, Montréal, Québec, Canada
| | - Javad Nadaf
- McGill University Genome Centre, Department of Human Genetics, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, Montréal, Québec, Canada
| | - Noah S Neubarth
- Goodman Cancer Research Centre, Montréal, Québec, Canada.,Department of Anatomy & Cell Biology, University of Toronto, Toronto, Ontario, Canada
| | - Paul Savage
- Department of Surgery, University of Toronto, Toronto, Ontario, Canada
| | - Dongmei Zuo
- Goodman Cancer Research Centre, Montréal, Québec, Canada
| | - Charles P Couturier
- McGill Faculty of Medicine, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, Montréal, Québec, Canada
| | - Jean Monlong
- McGill University Genome Centre, Department of Human Genetics, Montréal, Québec, Canada
| | - Haig Djambazian
- McGill University Genome Centre, Department of Human Genetics, Montréal, Québec, Canada
| | - Huda Altoukhi
- McGill Faculty of Medicine, Montréal, Québec, Canada.,Department of Radiation Oncology, McGill University, Montreal Quebec Canada
| | - Guillaume Bourque
- McGill University Genome Centre, Department of Human Genetics, Montréal, Québec, Canada
| | - Jiannis Ragoussis
- McGill University Genome Centre, Department of Human Genetics, Montréal, Québec, Canada
| | - Roberto J Diaz
- McGill Faculty of Medicine, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, Montréal, Québec, Canada
| | - Morag Park
- Division of Experimental Medicine, Montréal, Québec, Canada.,Goodman Cancer Research Centre, Montréal, Québec, Canada.,McGill Faculty of Medicine, Montréal, Québec, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology, McGill University, Montreal Quebec Canada
| | - Marie-Christine Guiot
- Goodman Cancer Research Centre, Montréal, Québec, Canada.,McGill Faculty of Medicine, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, Montréal, Québec, Canada.,Department of Pathology, McGill University, Montreal Quebec Canada
| | - Stephanie Lam
- McGill Faculty of Medicine, Montréal, Québec, Canada.,Department of Diagnostic Radiology, McGill University, Montreal Quebec Canada
| | - Kevin Petrecca
- McGill Faculty of Medicine, Montréal, Québec, Canada.,Department of Neurology and Neurosurgery, Montreal Neurological Institute-Hospital, Montréal, Québec, Canada
| | - Peter M Siegel
- Division of Experimental Medicine, Montréal, Québec, Canada.,Goodman Cancer Research Centre, Montréal, Québec, Canada.,McGill Faculty of Medicine, Montréal, Québec, Canada.,Department of Biochemistry, University of Toronto, Toronto, Ontario, Canada.,Department of Anatomy & Cell Biology, University of Toronto, Toronto, Ontario, Canada.,Department of Radiation Oncology, McGill University, Montreal Quebec Canada
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13
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Chong AS, Nadaf J, Grau E, Apellaniz-Ruiz M, Fahiminiya S, Saskin A, Han H, Turcotte R, Muchantef K, Thomas C, Wagener R, Bassenden A, Mete O, Pusztaszeri M, Paulus W, Berghuis A, Siebert R, Albrecht S, Hasselblatt M, Lazaro C, Teule A, Fabian M, Brunet J, Foulkes W, Rivera B. RARE-22. GERMLINE PATHOGENIC VARIANT c.1552G>A;p.E518K IN DGCR8 CONFERS SUSCEPTIBILITY FOR SCHWANNOMATOSIS AND THYROID TUMORS. Neuro Oncol 2020. [PMCID: PMC7715759 DOI: 10.1093/neuonc/noaa222.733] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Abstract
Germline mutations in DICER1 cause a pleiotropic susceptibility syndrome characterized by the development of pediatric or early-onset tumors including pleuropulmonary blastoma, Wilms tumors, pineoblastomas, multinodular goiter (MNG) and thyroid cancers. Somatic mutations in the other two microprocessors DROSHA and DGCR8 have been found in Wilms Tumors and pineoblastomas. We present here two families with peripheral schwannomatosis and thyroid tumors carrying a germline variant c.1552G>A;p.E518K in DGCR8. Family one had six affected members with early-onset MNG and five of them developed schwannomatosis. All five members were heterozygous for the variant. One of the carriers had also been diagnosed with a choroid plexus papilloma at 7 years old. The common second event in all tumors tested was the loss of chromosome 22 at the somatic level. In family two, a 35-year-old male was diagnosed with a peripheral schwannoma at the age of 12. Since then, he has developed seven extra peripheral schwannomas (one of which was an ancient schwannoma) and papillary thyroid cancer. DGCR8 lies on chromosome 22q, adjacent to the three schwannoma genes: LZTR1, SMARCB1 and NF2. The variant, c.1552G>A;p.E518K localizes to the first RNA-binding domain of DGCR8 and structural modelling predicts that it abolishes proper binding of RNA. It is also a hotspot somatic mutation in Wilms tumors. Using miRNA profiling, we show that this variant disrupts global microRNA production and DGCR8 mutated tumors show a specific miRNA profile different from DGCR8 wild type tumors. These findings reinforce DGCR8 as a novel susceptibility gene for schwannomatosis and thyroid tumors.
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Affiliation(s)
| | - Javad Nadaf
- Jewish General Hospital, Montreal, QC, Canada
| | - Elia Grau
- Catalan Institute of Oncology, Barcelona, Spain
| | - Maria Apellaniz-Ruiz
- McGill University, Montreal, QC, Canada
- Jewish General Hospital, Montreal, QC, Canada
| | | | - Avi Saskin
- McGill University, Montreal, QC, Canada
- McGill University Health Centre, Montreal, QC, Canada
| | - HyeRim Han
- Bellvitge Biomedical Research Institute, IDIBELL, Barcelona, Spain
- University of Barcelona, Barcelona, Spain
| | - Robert Turcotte
- McGill University, Montreal, QC, Canada
- McGill University Health Centre, Montreal, QC, Canada
| | - Karl Muchantef
- McGill University, Montreal, QC, Canada
- McGill University Health Centre, Montreal, QC, Canada
| | | | - Rabea Wagener
- University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | | | - Ozgur Mete
- University of Toronto, Toronto, ON, Canada
- University Health Network, Toronto, ON, Canada
| | | | | | | | - Reiner Siebert
- University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | | | | | | | | | - Marc Fabian
- Jewish General Hospital, Montreal, QC, Canada
- McGill University, Montreal, QC, Canada
| | - Joan Brunet
- Catalan Institute of Oncology, Barcelona, Spain
| | - William Foulkes
- McGill University, Montreal, QC, Canada
- Jewish General Hospital, Montreal, QC, Canada
| | - Barbara Rivera
- Bellvitge Biomedical Research Institute, IDIBELL, Barcelona, Spain
- McGill University, Montreal, QC, Canada
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14
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Dankner M, Caron M, Al-Saadi T, Yu W, Ouellet V, Ezzeddine R, Annis MG, Le PU, Nadaf J, Neubarth NS, Savage P, Zuo D, Couturier CP, Monlong J, Djambazian H, Altoukhi H, Bourque G, Ragoussis J, Diaz RJ, Park M, Guiot MC, Lam S, Petrecca K, Siegel PM. BIOM-03. INVASIVE HISTOPATHOLOGY DRIVES POOR OUTCOMES IN SURGICALLY RESECTED BRAIN METASTASES. Neuro Oncol 2020. [DOI: 10.1093/neuonc/noaa215.003] [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: 11/14/2022] Open
Abstract
Abstract
BACKGROUND
Surgery as a single modality for the treatment of brain metastases (BrM) results in local recurrence (LR) in 60% of patients. These failure rates are reduced by half with post-operative radiotherapy. The non-invasive nature of BrM has led to the assumption that local recurrence is caused by spillage of cancer cells into the surgical cavity at the time of surgery. We present evidence suggesting that invasion of metastatic cancer cells into the adjacent brain is present in the majority of BrM and is associated with LR, leptomeningeal metastasis (LM), and overall survival (OS).
METHODS
We assessed the histopathological growth pattern (HGP) of 164 surgically resected BrM. HGP was correlated with LR, LM and OS. Single-cell transcriptomics (scRNAseq) was performed on 15,615 cells from metastasis center (MC) and surrounding brain (SB) adjacent to the tumor. N=30 orthotopic patient-derived xenograft models (OPDX) were established from BrM.
RESULTS
56/164 (34%) BrM specimens showed a minimally invasive (MI) HGP between the tumor and adjacent brain while 108/164 (66%) showed significant invasion of tumor lobules or single-cells into the brain (HI-HGP). HI-HGP was associated with LR, LM and shortened OS in BrM patients. scRNAseq identified abundant cancer cells in SB that overexpressed pathways and genes involved in cell survival and stress adaptation compared to matched cancer cells in MC. Validation of these targets with immunohistochemistry in patient and OPDX tissues revealed cold-inducible RNA binding protein (CIRBP) overexpression in HI-HGP patient and OPDX BrM. Modulation of CIRBP expression in OPDX and cell line models of HI-HGP BrM delayed BrM progression and extended OS.
CONCLUSION
HI-HGP is a poor prognostic indicator in patients with surgically resected BrM, establishing HGP as an important prognostic factor that should be considered by clinicians treating BrM patients. We identify CIRBP as a functional mediator of this process.
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15
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Rivera B, Nadaf J, Fahiminiya S, Apellaniz-Ruiz M, Saskin A, Chong AS, Sharma S, Wagener R, Revil T, Condello V, Harra Z, Hamel N, Sabbaghian N, Muchantef K, Thomas C, de Kock L, Hébert-Blouin MN, Bassenden AV, Rabenstein H, Mete O, Paschke R, Pusztaszeri MP, Paulus W, Berghuis A, Ragoussis J, Nikiforov YE, Siebert R, Albrecht S, Turcotte R, Hasselblatt M, Fabian MR, Foulkes WD. DGCR8 microprocessor defect characterizes familial multinodular goiter with schwannomatosis. J Clin Invest 2020; 130:1479-1490. [PMID: 31805011 DOI: 10.1172/jci130206] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [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: 05/10/2019] [Accepted: 11/26/2019] [Indexed: 12/25/2022] Open
Abstract
BACKGROUNDDICER1 is the only miRNA biogenesis component associated with an inherited tumor syndrome, featuring multinodular goiter (MNG) and rare pediatric-onset lesions. Other susceptibility genes for familial forms of MNG likely exist.METHODSWhole-exome sequencing of a kindred with early-onset MNG and schwannomatosis was followed by investigation of germline pathogenic variants that fully segregated with the disease. Genome-wide analyses were performed on 13 tissue samples from familial and nonfamilial DGCR8-E518K-positive tumors, including MNG, schwannomas, papillary thyroid cancers (PTCs), and Wilms tumors. miRNA profiles of 4 tissue types were compared, and sequencing of miRNA, pre-miRNA, and mRNA was performed in a subset of 9 schwannomas, 4 of which harbor DGCR8-E518K.RESULTSWe identified c.1552G>A;p.E518K in DGCR8, a microprocessor component located in 22q, in the kindred. The variant identified is a somatic hotspot in Wilms tumors and has been identified in 2 PTCs. Copy number loss of chromosome 22q, leading to loss of heterozygosity at the DGCR8 locus, was found in all 13 samples harboring c.1552G>A;p.E518K. miRNA profiling of PTCs, MNG, schwannomas, and Wilms tumors revealed a common profile among E518K hemizygous tumors. In vitro cleavage demonstrated improper processing of pre-miRNA by DGCR8-E518K. MicroRNA and RNA profiling show that this variant disrupts precursor microRNA production, impacting populations of canonical microRNAs and mirtrons.CONCLUSIONWe identified DGCR8 as the cause of an unreported autosomal dominant mendelian tumor susceptibility syndrome: familial multinodular goiter with schwannomatosis.FUNDINGCanadian Institutes of Health Research, Compute Canada, Alex's Lemonade Stand Foundation, the Mia Neri Foundation for Childhood Cancer, Cassa di Sovvenzioni e Risparmio fra il Personale della Banca d'Italia, and the KinderKrebsInitiative Buchholz/Holm-Seppensen.
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Affiliation(s)
- Barbara Rivera
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Javad Nadaf
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Somayyeh Fahiminiya
- Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada
| | - Maria Apellaniz-Ruiz
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Avi Saskin
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Division of Medical Genetics, Department of Medicine, McGill University Health Centre and Jewish General Hospital, Montreal, Quebec, Canada
| | - Anne-Sophie Chong
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Sahil Sharma
- Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Rabea Wagener
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Timothée Revil
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Génome Québec Innovation Centre, McGill University, Montreal, Quebec, Canada
| | - Vincenzo Condello
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Zineb Harra
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Nancy Hamel
- Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada
| | - Nelly Sabbaghian
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada
| | - Karl Muchantef
- Department of Diagnostic Radiology, McGill University, Montreal, Quebec, Canada.,Pediatric Radiology, Montreal Children's Hospital, Montreal, Quebec, Canada
| | - Christian Thomas
- Institute of Neuropathology, University Hospital Muenster, Muenster, Germany
| | - Leanne de Kock
- Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | | | | | - Hannah Rabenstein
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Ozgur Mete
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada.,Department of Pathology, University Health Network, Toronto, Ontario, Canada
| | - Ralf Paschke
- Department of Medicine.,Department of Oncology.,Department of Pathology.,Biochemistry and Molecular Biology Institute, and.,Arnie Charbonneau Cancer Institute, Cumming School of Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Marc P Pusztaszeri
- Department of Pathology, Jewish General Hospital, Montreal, Quebec, Canada
| | - Werner Paulus
- Institute of Neuropathology, University Hospital Muenster, Muenster, Germany
| | - Albert Berghuis
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Jiannis Ragoussis
- Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada.,Génome Québec Innovation Centre, McGill University, Montreal, Quebec, Canada
| | - Yuri E Nikiforov
- Department of Pathology, University of Pittsburgh Medical Center, Pittsburgh, Pennsylvania, USA
| | - Reiner Siebert
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Steffen Albrecht
- Department of Pathology, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Robert Turcotte
- Division of Orthopedic Surgery (Experimental Surgery), McGill University, Montreal, Quebec, Canada.,Department of Surgical Oncology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Muenster, Muenster, Germany
| | - Marc R Fabian
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Department of Experimental Medicine, McGill University, Montreal, Quebec, Canada.,Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - William D Foulkes
- Gerald Bronfman Department of Oncology, McGill University, Montreal, Quebec, Canada.,Lady Davis Institute for Medical Research and.,Segal Cancer Centre, Jewish General Hospital, Montreal, Quebec, Canada.,Cancer Research Program, McGill University Health Centre, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Division of Medical Genetics, Department of Medicine, McGill University Health Centre and Jewish General Hospital, Montreal, Quebec, Canada
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16
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Couturier CP, Ayyadhury S, Le PU, Nadaf J, Monlong J, Riva G, Allache R, Baig S, Yan X, Bourgey M, Lee C, Wang YCD, Yong VW, Guiot MC, Najafabadi H, Misic B, Antel J, Bourque G, Ragoussis J, Petrecca K. Author Correction: Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy. Nat Commun 2020; 11:4041. [PMID: 32769982 PMCID: PMC7415133 DOI: 10.1038/s41467-020-17979-8] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
Affiliation(s)
- Charles P Couturier
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Shamini Ayyadhury
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Phuong U Le
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Javad Nadaf
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada.,Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada
| | - Jean Monlong
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Gabriele Riva
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Redouane Allache
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Salma Baig
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Xiaohua Yan
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Mathieu Bourgey
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada.,Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
| | - Changseok Lee
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Yu Chang David Wang
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada
| | - V Wee Yong
- Department of Clinical Neurosciences, University of Calgary, Calgary, AB, Canada
| | - Marie-Christine Guiot
- Department of Neuropathology, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Hamed Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada
| | - Bratislav Misic
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Jack Antel
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada.,Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada.,McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada.,Department of Bioengineering, McGill University, Montreal, QC, Canada
| | - Kevin Petrecca
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada.
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17
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Couturier CP, Ayyadhury S, Le PU, Nadaf J, Monlong J, Riva G, Allache R, Baig S, Yan X, Bourgey M, Lee C, Wang YCD, Wee Yong V, Guiot MC, Najafabadi H, Misic B, Antel J, Bourque G, Ragoussis J, Petrecca K. Single-cell RNA-seq reveals that glioblastoma recapitulates a normal neurodevelopmental hierarchy. Nat Commun 2020; 11:3406. [PMID: 32641768 PMCID: PMC7343844 DOI: 10.1038/s41467-020-17186-5] [Citation(s) in RCA: 221] [Impact Index Per Article: 55.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 06/17/2020] [Indexed: 02/07/2023] Open
Abstract
Cancer stem cells are critical for cancer initiation, development, and treatment resistance. Our understanding of these processes, and how they relate to glioblastoma heterogeneity, is limited. To overcome these limitations, we performed single-cell RNA sequencing on 53586 adult glioblastoma cells and 22637 normal human fetal brain cells, and compared the lineage hierarchy of the developing human brain to the transcriptome of cancer cells. We find a conserved neural tri-lineage cancer hierarchy centered around glial progenitor-like cells. We also find that this progenitor population contains the majority of the cancer's cycling cells, and, using RNA velocity, is often the originator of the other cell types. Finally, we show that this hierarchal map can be used to identify therapeutic targets specific to progenitor cancer stem cells. Our analyses show that normal brain development reconciles glioblastoma development, suggests a possible origin for glioblastoma hierarchy, and helps to identify cancer stem cell-specific targets.
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Affiliation(s)
- Charles P Couturier
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Shamini Ayyadhury
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Phuong U Le
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Javad Nadaf
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada
| | - Jean Monlong
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Gabriele Riva
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Redouane Allache
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Salma Baig
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Xiaohua Yan
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Mathieu Bourgey
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
| | - Changseok Lee
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Yu Chang David Wang
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada
| | - V Wee Yong
- Department of Clinical Neurosciences, University of Calgary, Calgary, AB, Canada
| | - Marie-Christine Guiot
- Department of Neuropathology, Montreal Neurological Institute and Hospital, McGill University, Montreal, QC, Canada
| | - Hamed Najafabadi
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada
| | - Bratislav Misic
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Jack Antel
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada
- Canadian Centre for Computational Genomics, McGill University, Montreal, QC, Canada
| | - Jiannis Ragoussis
- Department of Human Genetics, McGill University, Montreal, QC, Canada
- McGill University and Genome Québec Innovation Centre, Montreal, QC, Canada
- Department of Bioengineering, McGill University, Montreal, QC, Canada
| | - Kevin Petrecca
- Department of Neurosciences, Montreal Neurological Institute-Hospital, McGill University, Montreal, QC, Canada.
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18
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Amrom D, Poduri A, Goldman JS, Dan B, Deconinck N, Pichon B, Nadaf J, Andermann F, Andermann E, Walsh CA, Dobyns WB. Duplication 2p16 is associated with perisylvian polymicrogyria. Am J Med Genet A 2019; 179:2343-2356. [PMID: 31660690 DOI: 10.1002/ajmg.a.61342] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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: 12/19/2018] [Revised: 07/01/2019] [Accepted: 08/12/2019] [Indexed: 11/07/2022]
Abstract
Polymicrogyria (PMG) is a heterogeneous brain malformation that may result from prenatal vascular disruption or infection, or from numerous genetic causes that still remain difficult to identify. We identified three unrelated patients with polymicrogyria and duplications of chromosome 2p, defined the smallest region of overlap, and performed gene pathway analysis using Cytoscape. The smallest region of overlap in all three children involved 2p16.1-p16.3. All three children have bilateral perisylvian polymicrogyria (BPP), intrauterine and postnatal growth deficiency, similar dysmorphic features, and poor feeding. Two of the three children had documented intellectual disability. Gene pathway analysis suggested a number of developmentally relevant genes and gene clusters that were over-represented in the critical region. We narrowed a rare locus for polymicrogyria to a region of 2p16.1-p16.3 that contains 33-34 genes, 23 of which are expressed in cerebral cortex during human fetal development. Using pathway analysis, we showed that several of the duplicated genes contribute to neurodevelopmental pathways including morphogen, cytokine, hormonal and growth factor signaling, regulation of cell cycle progression, cell morphogenesis, axonal guidance, and neuronal migration. These findings strengthen the evidence for a novel locus associated with polymicrogyria on 2p16.1-p16.3, and comprise the first step in defining the underlying genetic etiology.
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Affiliation(s)
- Dina Amrom
- Neurogenetics Unit, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada.,Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada.,Department of Neurology, Hôpital Universitaire des Enfants Reine Fabiola (HUDERF), Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Annapurna Poduri
- Division of Epilepsy & Clinical Neurophysiology, Children's Hospital, Boston, Massachusetts.,Department of Neurology, Children's Hospital, Boston, Massachusetts
| | - Jennifer S Goldman
- Ludmer Centre for Neuroinformatics and Mental Health and the Department of Biomedical Engineering, McGill Centre for Integrative Neuroscience, McGill University, Montreal, Quebec, Canada
| | | | | | - Bruno Pichon
- Department of Medical Genetics, Hôpital Erasme, Université Libre de Bruxelles (ULB), Brussels, Belgium
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Genome Quebec Innovation Center, McGill University, Montreal, Quebec, Canada
| | - Frederick Andermann
- Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada.,Epilepsy Research Group, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada.,Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Eva Andermann
- Neurogenetics Unit, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada.,Department of Neurology & Neurosurgery, McGill University, Montreal, Quebec, Canada.,Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Epilepsy Research Group, Montreal Neurological Institute and Hospital, Montreal, Quebec, Canada
| | - Christopher A Walsh
- Department of Neurology, Children's Hospital, Boston, Massachusetts.,Division of Genetics and Manton Center for Orphan Disease Research, Children's Hospital, Boston, Massachusetts.,Howard Hughes Medical Institute, Harvard Medical School, Boston, Massachusetts
| | - William B Dobyns
- Department of Pediatrics (Genetics) and Neurology, University of Washington, and Seattle Children's Research Institute, Seattle, Washington
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19
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Meloche J, Brunet V, Gagnon PA, Lavoie MÈ, Bouchard JB, Nadaf J, Majewski J, Morin C, Laprise C. Exome sequencing study of partial agenesis of the corpus callosum in men with developmental delay, epilepsy, and microcephaly. Mol Genet Genomic Med 2019; 8:e992. [PMID: 31578829 PMCID: PMC6978259 DOI: 10.1002/mgg3.992] [Citation(s) in RCA: 7] [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: 08/24/2018] [Revised: 08/28/2019] [Accepted: 09/03/2019] [Indexed: 12/24/2022] Open
Abstract
Background This study reports the genetic features of four Caucasian males from the Saguenay‒Lac‐St‐Jean region affected by partial agenesis of the corpus callosum (ACC) with hypotonia, epilepsy, developmental delay, microcephaly, hypoplasia, and autistic behavior. Methods We performed whole exome sequencing (WES) to identify new genes involved in this pathological phenotype. The regions of interest were subsequently sequenced for family members. Results Single‐nucleotide variations (SNVs) and insertions or deletions were detected in genes potentially implicated in brain defects observed in these patients. One patient did not have mutations in genes related to ACC, but carried a de novo pathogenic mutation in Mucolipin‐1 (MCOLN1) and was diagnosed with mucolipidosis type IV. Among the other probands, missense SNVs were observed in DCLK2 (Doublecortin Like Kinase 2), HERC2 (HECT And RLD Domain Containing E3 Ubiquitin Protein Ligase 2), and KCNH3 (Potassium channel, voltage‐gated, subfamily H, member 3). One patient also carried a non‐frameshift insertion in CACNA1A (Cav2.1(P/Q‐type) calcium channels). Conclusion Although no common genetic defect was observed in this study, we provide evidence for new avenues of investigation for ACC, such as molecular pathways involving HERC2, CACNA1A, KCNH3, and more importantly DCLK2. We also allowed to diagnose an individual with mucolipidosis type IV.
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Affiliation(s)
- Jolyane Meloche
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, QC, Canada.,Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Vanessa Brunet
- Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Pierre-Alexandre Gagnon
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, QC, Canada.,Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | - Marie-Ève Lavoie
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, QC, Canada.,Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
| | | | - Javad Nadaf
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Charles Morin
- Centre de Santé et de Services Sociaux de Chicoutimi, Saguenay, QC, Canada
| | - Catherine Laprise
- Centre intersectoriel en santé durable, Université du Québec à Chicoutimi, Saguenay, QC, Canada.,Département des Sciences Fondamentales, Université du Québec à Chicoutimi, Saguenay, QC, Canada
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20
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Gayden T, Dickson BC, Nikbakht H, Fiset PO, Jay ND, Nadaf J, Burk DL, Berghuis A, Gladdy R, Wunder J, Turcotte R, Majewski J, Jabado N. Abstract 756: Whole exome sequencing identifies frequent mutations of PTPRB and KDR in secondary angiosarcoma. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-756] [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
Angiosarcoma is an uncommon malignant vascular tumor that can occur anywhere on the body, with a predilection for the skin or soft tissues of the scalp and face.
By whole exome sequencing, we identified recurrent somatic mutations in PTPRB, which encodes an endothelial-specific phosphatase that negatively regulates angiogenesis, in three secondary angiosarcoma tumors (3/10). In addition, four tumors harbored missense variants in the KDR gene, including three germline substitutions. Neither the PTPRB nor the KDR alterations were found in the 5 primary tumors studied. Copy number analysis derived from the exome and methylation data revealed frequent MYC amplification in the majority of secondary angiosarcoma tumors (9/10).
Altogether, our data provide a comprehensive overview of genetic and epigenetic landscapes of angiosarcoma, and demonstrate that aberrant angiogenesis associated with PTPRB and KDR mutations may contribute to the pathogenesis of angiosarcoma.
Citation Format: Tenzin Gayden, Brendan C. Dickson, Hamid Nikbakht, Pierre-Olivier Fiset, Nicolas De Jay, Javad Nadaf, David L. Burk, Albert Berghuis, Rebecca Gladdy, Jay Wunder, Robert Turcotte, Jacek Majewski, Nada Jabado. Whole exome sequencing identifies frequent mutations of PTPRB and KDR in secondary angiosarcoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 756.
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Affiliation(s)
| | | | | | | | | | - Javad Nadaf
- 1McGill University, Montreal, Quebec, Canada
| | | | | | | | - Jay Wunder
- 2Mount Sinai Hospital, Toronto, Ontario, Canada
| | | | | | - Nada Jabado
- 1McGill University, Montreal, Quebec, Canada
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21
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Uusimaa J, Kaarteenaho R, Paakkola T, Tuominen H, Karjalainen MK, Nadaf J, Varilo T, Uusi-Mäkelä M, Suo-Palosaari M, Pietilä I, Hiltunen AE, Ruddock L, Alanen H, Biterova E, Miinalainen I, Salminen A, Soininen R, Manninen A, Sormunen R, Kaakinen M, Vuolteenaho R, Herva R, Vieira P, Dunder T, Kokkonen H, Moilanen JS, Rantala H, Nogee LM, Majewski J, Rämet M, Hallman M, Hinttala R. NHLRC2 variants identified in patients with fibrosis, neurodegeneration, and cerebral angiomatosis (FINCA): characterisation of a novel cerebropulmonary disease. Acta Neuropathol 2018; 135:727-742. [PMID: 29423877 DOI: 10.1007/s00401-018-1817-z] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2017] [Revised: 01/30/2018] [Accepted: 01/31/2018] [Indexed: 11/26/2022]
Abstract
A novel multi-organ disease that is fatal in early childhood was identified in three patients from two non-consanguineous families. These children were born asymptomatic but at the age of 2 months they manifested progressive multi-organ symptoms resembling no previously known disease. The main clinical features included progressive cerebropulmonary symptoms, malabsorption, progressive growth failure, recurrent infections, chronic haemolytic anaemia and transient liver dysfunction. In the affected children, neuropathology revealed increased angiomatosis-like leptomeningeal, cortical and superficial white matter vascularisation and congestion, vacuolar degeneration and myelin loss in white matter, as well as neuronal degeneration. Interstitial fibrosis and previously undescribed granuloma-like lesions were observed in the lungs. Hepatomegaly, steatosis and collagen accumulation were detected in the liver. A whole-exome sequencing of the two unrelated families with the affected children revealed the transmission of two heterozygous variants in the NHL repeat-containing protein 2 (NHLRC2); an amino acid substitution p.Asp148Tyr and a frameshift 2-bp deletion p.Arg201GlyfsTer6. NHLRC2 is highly conserved and expressed in multiple organs and its function is unknown. It contains a thioredoxin-like domain; however, an insulin turbidity assay on human recombinant NHLRC2 showed no thioredoxin activity. In patient-derived fibroblasts, NHLRC2 levels were low, and only p.Asp148Tyr was expressed. Therefore, the allele with the frameshift deletion is likely non-functional. Development of the Nhlrc2 null mouse strain stalled before the morula stage. Morpholino knockdown of nhlrc2 in zebrafish embryos affected the integrity of cells in the midbrain region. This is the first description of a fatal, early-onset disease; we have named it FINCA disease based on the combination of pathological features that include fibrosis, neurodegeneration, and cerebral angiomatosis.
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Affiliation(s)
- Johanna Uusimaa
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland.
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland.
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland.
| | - Riitta Kaarteenaho
- Research Unit of Internal Medicine, Respiratory Research, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Medical Research Center Oulu and Unit of Internal Medicine and Respiratory Medicine, Oulu University Hospital, PO Box 20, 90029, Oulu, Finland
| | - Teija Paakkola
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Hannu Tuominen
- Department of Pathology, Cancer and Translational Medicine Research Unit, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Department of Pathology, Oulu University Hospital, PO Box 50, 90029, Oulu, Finland
| | - Minna K Karjalainen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
| | - Javad Nadaf
- McGill University and Génome Québec Innovation Centre, Montreal, QC, H3A 0G1, Canada
- St. Jude Children's Research Hospital (SJCRH), 262 Danny Thomas Place, Memphis, TN, 38105, USA
| | - Teppo Varilo
- Department of Medical Genetics, University of Helsinki, Haartmaninkatu 8, 00251, Helsinki, Finland
| | - Meri Uusi-Mäkelä
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Maria Suo-Palosaari
- Department of Diagnostic Radiology and Medical Research Center Oulu, Oulu University Hospital and University of Oulu, PO Box 50, 90029, Oulu, Finland
| | - Ilkka Pietilä
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Anniina E Hiltunen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Lloyd Ruddock
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Heli Alanen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Ekaterina Biterova
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Ilkka Miinalainen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Annamari Salminen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
| | - Raija Soininen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Aki Manninen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Faculty of Biochemistry and Molecular Medicine, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Raija Sormunen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
- Department of Pathology, Cancer and Translational Medicine Research Unit, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Mika Kaakinen
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | | | - Riitta Herva
- Department of Pathology, Cancer and Translational Medicine Research Unit, University of Oulu, PO Box 5000, 90014, Oulu, Finland
| | - Päivi Vieira
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
| | - Teija Dunder
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
| | - Hannaleena Kokkonen
- Northern Finland Laboratory Centre NordLab, Oulu University Hospital, PO Box 500, 90029, Oulu, Finland
- Department of Clinical Chemistry and Medical Research Center Oulu, University Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
| | - Jukka S Moilanen
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Clinical Genetics, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
| | - Heikki Rantala
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
| | - Lawrence M Nogee
- Division of Neonatology, Johns Hopkins University School of Medicine, CMSC 6-104A, 600 N. Wolfe St., Baltimore, MD, 21287, USA
| | - Jacek Majewski
- McGill University and Génome Québec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Mika Rämet
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
- BioMediTech Institute and Faculty of Medicine and Life Sciences, University of Tampere, Tampere, Finland
| | - Mikko Hallman
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Department of Children and Adolescents, Oulu University Hospital, PO Box 23, 90029, Oulu, Finland
| | - Reetta Hinttala
- PEDEGO Research Unit and Medical Research Center Oulu, University of Oulu and Oulu University Hospital, PO Box 5000, 90014, Oulu, Finland
- Biocenter Oulu, University of Oulu, PO Box 5000, 90014, Oulu, Finland
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22
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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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23
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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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Rivera B, Di Iorio M, Frankum J, Nadaf J, Fahiminiya S, Arcand SL, Burk DL, Grapton D, Tomiak E, Hastings V, Hamel N, Wagener R, Aleynikova O, Giroux S, Hamdan FF, Dionne-Laporte A, Zogopoulos G, Rousseau F, Berghuis AM, Provencher D, Rouleau GA, Michaud JL, Mes-Masson AM, Majewski J, Bens S, Siebert R, Narod SA, Akbari MR, Lord CJ, Tonin PN, Orthwein A, Foulkes WD. Functionally Null RAD51D Missense Mutation Associates Strongly with Ovarian Carcinoma. Cancer Res 2017; 77:4517-4529. [PMID: 28646019 DOI: 10.1158/0008-5472.can-17-0190] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [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: 01/24/2017] [Revised: 03/23/2017] [Accepted: 06/06/2017] [Indexed: 11/16/2022]
Abstract
RAD51D is a key player in DNA repair by homologous recombination (HR), and RAD51D truncating variant carriers have an increased risk for ovarian cancer. However, the contribution of nontruncating RAD51D variants to cancer predisposition remains uncertain. Using deep sequencing and case-control genotyping studies, we show that in French Canadians, the missense RAD51D variant c.620C>T;p.S207L is highly prevalent and is associated with a significantly increased risk for ovarian high-grade serous carcinoma (HGSC; 3.8% cases vs. 0.2% controls). The frequency of the p.S207L variant did not significantly differ from that of controls in breast, endometrial, pancreas, or colorectal adenocarcinomas. Functionally, we show that this mutation impairs HR by disrupting the RAD51D-XRCC2 interaction and confers PARP inhibitor sensitivity. These results highlight the importance of a functional RAD51D-XRCC2 interaction to promote HR and prevent the development of HGSC. This study identifies c.620C>T;p.S207L as the first bona fide pathogenic RAD51D missense cancer susceptibility allele and supports the use of targeted PARP-inhibitor therapies in ovarian cancer patients carrying deleterious missense RAD51D variants. Cancer Res; 77(16); 4517-29. ©2017 AACR.
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Affiliation(s)
- Barbara Rivera
- Department of Human Genetics, McGill University, Montreal, Canada
- Lady Davis Institute, Montreal, Canada
| | - Massimo Di Iorio
- Department of Human Genetics, McGill University, Montreal, Canada
| | - Jessica Frankum
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Canada
- Genome Quebec Innovation Centre, Montreal, Canada
| | - Somayyeh Fahiminiya
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Suzanna L Arcand
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - David L Burk
- Department of Biochemistry, McGill University, Montreal, Canada
| | | | - Eva Tomiak
- Department of Genetics, University of Ottawa, Children's Hospital of Eastern Ontario, Canada
| | - Valerie Hastings
- Department of Genetics, University of Ottawa, Children's Hospital of Eastern Ontario, Canada
| | - Nancy Hamel
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
| | - Rabea Wagener
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Olga Aleynikova
- Department of pathology, Jewish General Hospital, Montreal, Canada
| | - Sylvie Giroux
- University of Laval and CHU Research Centre, Quebec; Canada
| | - Fadi F Hamdan
- CHU Sainte-Justine Research Center, Montreal, Canada
| | | | - George Zogopoulos
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
- The Goodman Cancer Research Centre, McGill University, Montreal, Canada
| | | | | | - Diane Provencher
- Centre de recherche du CHUM and Institut du cancer de Montréal, University of Montreal, Montreal, Canada
| | - Guy A Rouleau
- Montreal Neurological Institute, McGill University, Montreal, Canada
| | | | - Anne-Marie Mes-Masson
- Centre de recherche du CHUM and Institut du cancer de Montréal, University of Montreal, Montreal, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Canada
- Genome Quebec Innovation Centre, Montreal, Canada
| | - Susanne Bens
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Reiner Siebert
- Institute of Human Genetics, University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Steven A Narod
- Dalla Lana School of Public Health, Toronto, Canada
- Women's College Hospital, Toronto, Canada
| | - Mohammad R Akbari
- Dalla Lana School of Public Health, Toronto, Canada
- Women's College Hospital, Toronto, Canada
| | - Christopher J Lord
- The CRUK Gene Function Laboratory and Breast Cancer Now Toby Robins Research Centre, The Institute of Cancer Research, London, United Kingdom
| | - Patricia N Tonin
- Department of Human Genetics, McGill University, Montreal, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
- Department of Medicine, McGill University, Montreal, Canada
| | - Alexandre Orthwein
- Lady Davis Institute, Montreal, Canada
- Department of Oncology, McGill University, Montreal, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Canada.
- Lady Davis Institute, Montreal, Canada
- Cancer Research Program, The Research Institute of the McGill University Health Centre, Montreal, Canada
- Department of Medical Genetics, Research Institute, McGill University Health Centre, Montreal, Canada
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25
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Rivera B, Iorio MRD, Frankum J, Nadaf J, Fahiminiya S, Arcand SL, Burk D, Grapton D, Tomiak E, Hastings V, Hamel N, Wagener R, Aleynikova O, Giroux S, Hamdan FF, Orthwein A, Zogopoulos G, Rousseau F, Berghuis A, Provencher DM, Rouleau GA, Michaud JL, Mes-Masson AM, Majewski J, Bens S, Siebert R, Narod S, Akbari M, Lord CJ, Tonin PN, Dionne-Laporte A, Foulkes WD. Abstract 2479: A functionally null RAD51D missense mutation is strongly associated with ovarian carcinoma. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-2479] [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
Background and goal: RAD51D is a key player in DNA repair by homologous recombination (HR) and carriers of truncating RAD51D mutations have an increased risk for ovarian cancer (OC). However, the contribution of non-truncating RAD51D variants to cancer predisposition remains uncertain. We sought to fully characterize the previously described missense RAD51D variant c.620C>T;p.S207L in order to elucidate its role in OC.
Methods: A clinical panel screening was used to identify the RAD51D variant c.620C>T;p.S207L in two French Canadian (FC) kindred affected with familial High Grade Serous Cancer (HGSC) of the ovary or endometrium. High resolution melting, TaqMan genotyping and Sanger sequencing were used to genotype the p.S207L variant in a series of unselected cases of HGSC of the ovary and endometrium, breast, pancreas and colorectal cancer and healthy controls, all of a FC origin. Whole exome sequencing (WES) was performed to study the genetic signature characterizing RAD51D associated tumors. RAD51 foci formation and CRISPR-Cas9-stimulated and HR-mediated gene targeting assays were used to assess HR activity of RAD51D-S207L mutated CHO cells. HR activity in RAD51D-S207L mutated human cells was tested by a DR-GFP assay. The effect of RAD51D p.S207L on RAD51D-XRCC2 interactions was analyzed by co-immunoprecipitation and quantified in-vivo in a single cell colocalization assay. Sensitivity to PARP inhibitors (PARPi) was evaluated in a cell survival assay.
Results: Using deep sequencing and case-control genotyping studies, we showed that the missense RAD51D variant c.620C>T;p.S207L is over-represented in the French Canadian population affected by HGSC of the ovary (3.8% cases vs 0.002% controls; p < 0.0001).The frequency of the p.S207L variant did not differ from that of controls in breast, endometrial, pancreas and colorectal adenocarcinomas. A common haplotype shared by all the carriers suggested a founder origin for c.620C>T;p.S207L mutation. WES analysis of RAD51D tumor profiles revealed the presence of signature 3 which is known to be associated with HR defects. Functionally, we show that this mutation impairs HR by disrupting the RAD51D-XRCC2 interaction and confers PARP-inhibitor sensitivity to CHO cells.
Conclusions: This work identifies RAD51D p.S207L as the first bona fide pathogenic missense susceptibility allele for HGSC of the ovary and supports the use of targeted PARPi therapies in OC patients carrying missense RAD51D mutations.
Citation Format: Barbara Rivera, Massimo R. Di Iorio, Jessica Frankum, Javad Nadaf, Somayyeh Fahiminiya, Suzanna L. Arcand, David Burk, Damien Grapton, Eva Tomiak, Valerie Hastings, Nancy Hamel, Rabea Wagener, Olga Aleynikova, Sylvie Giroux, Fadi F. Hamdan, Alexandre Orthwein, George Zogopoulos, Francois Rousseau, Albert Berghuis, Diane M. Provencher, Guy A. Rouleau, Jacques L. Michaud, Anne-Marie Mes-Masson, Jacek Majewski, Susanne Bens, Reiner Siebert, Steven Narod, Mohammad Akbari, Chris J. Lord, Patricia N. Tonin, Alexandre Dionne-Laporte, William D. Foulkes. A functionally null RAD51D missense mutation is strongly associated with ovarian carcinoma [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 2479. doi:10.1158/1538-7445.AM2017-2479
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Affiliation(s)
| | | | | | - Javad Nadaf
- 1McGill University, Montreal, Quebec, Canada
| | - Somayyeh Fahiminiya
- 3The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Suzanna L. Arcand
- 3The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - David Burk
- 1McGill University, Montreal, Quebec, Canada
| | | | - Eva Tomiak
- 5University of Ottawa, Children's Hospital of Eastern Ontario, Ontario, Ontario, Canada
| | - Valerie Hastings
- 5University of Ottawa, Children's Hospital of Eastern Ontario, Ontario, Ontario, Canada
| | - Nancy Hamel
- 3The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Rabea Wagener
- 6University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | | | - Sylvie Giroux
- 8University of Laval and CHU Research Centre, Montreal, Quebec, Canada
| | - Fadi F. Hamdan
- 9CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | | | - George Zogopoulos
- 3The Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - Francois Rousseau
- 8University of Laval and CHU Research Centre, Montreal, Quebec, Canada
| | | | - Diane M. Provencher
- 10Centre de recherche du CHUM and Institut du cancer de Montréal, University of Montreal, Montreal, Quebec, Canada
| | - Guy A. Rouleau
- 11Montreal Neurological Institute, McGill University, Montreal, Quebec, Canada
| | | | - Anne-Marie Mes-Masson
- 10Centre de recherche du CHUM and Institut du cancer de Montréal, University of Montreal, Montreal, Quebec, Canada
| | | | - Susanne Bens
- 6University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Reiner Siebert
- 6University of Ulm and University of Ulm Medical Center, Ulm, Germany
| | - Steven Narod
- 12Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - Mohammad Akbari
- 12Dalla Lana School of Public Health, Toronto, Ontario, Canada
| | - Chris J. Lord
- 2The Institute of Cancer Research, London, United Kingdom
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26
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Keser V, Khan A, Siddiqui S, Lopez I, Ren H, Qamar R, Nadaf J, Majewski J, Chen R, Koenekoop RK. The Genetic Causes of Nonsyndromic Congenital Retinal Detachment: A Genetic and Phenotypic Study of Pakistani Families. Invest Ophthalmol Vis Sci 2017; 58:1028-1036. [PMID: 28192794 PMCID: PMC5308768 DOI: 10.1167/iovs.16-20281] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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] [Indexed: 11/24/2022] Open
Abstract
Purpose To evaluate consanguineous pedigrees from Pakistan with a clinical diagnosis of nonsyndromic congenital retinal nonattachment (NCRNA) and identify genes responsible for the disease as currently only one NCRNA gene is known (atonal basic helix-loop-helix transcription factor 7: ATOH7). Methods We implemented a three-step genotyping platform: single nucleotide polymorphism genotyping to identify loss of heterozygosity regions in patients, Retinal Information Network panel screening for mutations in currently known retinal genes. Negative patients were then subjected to whole exome sequencing. Results We evaluated 21 consanguineous NCRNA pedigrees and identified the causal mutations in known retinal genes in 13 out of our 21 families. We found mutations in ATOH7 in three families. Surprisingly, we then found mutations in familial exudative vitreoretinopathy (FEVR) genes; low-density lipoprotein receptor-related protein 5 mutations (six families), tetraspanin 12 mutations (two families), and NDP mutations (two families). Thus, 62% of the patients were successfully genotyped in our study with seven novel and six previously reported mutations in known retinal genes. Conclusions Although the clinical diagnosis of all children was NCRNA with severe congenital fibrotic retinal detachments, the molecular diagnosis determined that the disease process was in fact a very severe form of FEVR in 10 families. Because severe congenital retinal detachment has not been previously associated with all the FEVR genes, we have thus expanded the phenotypic spectrum of FEVR, a highly variable retinal detachment phenotype that has clinical overlap with NCRNA. We identified seven novel mutations. We also established for the first time genetic overlap between the Iranian and Pakistani populations. We identified eight NCRNA families that do not harbor mutations in any known retinal genes, suggesting novel causal genes in these families.
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Affiliation(s)
- Vafa Keser
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec, Canada
| | - Ayesha Khan
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec, Canada
| | - Sorath Siddiqui
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec, Canada
| | - Irma Lopez
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec, Canada
| | - Huanan Ren
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec, Canada
| | - Raheel Qamar
- Department of Pediatric Ophthalmology, Al Shifa Trust Eye Hospital, Rawalpindi, Pakistan
| | - Javad Nadaf
- Quebec Genome Centre, Montreal, Quebec, Canada
| | - Jacek Majewski
- Quebec Genome Centre, Montreal, Quebec, Canada 4Faculty of Medicine, Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Rui Chen
- Department of Molecular and Human Genetics, Human Genome Sequencing Center, Baylor College of Medicine, Houston, Texas, United States
| | - Robert K Koenekoop
- McGill Ocular Genetics Laboratory, McGill University Health Centre, Montreal, Quebec, Canada
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27
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Fahiminiya S, Witkowski L, Nadaf J, Carrot-Zhang J, Goudie C, Hasselblatt M, Johann P, Kool M, Lee RS, Gayden T, Roberts CWM, Biegel JA, Jabado N, Majewski J, Foulkes WD. Molecular analyses reveal close similarities between small cell carcinoma of the ovary, hypercalcemic type and atypical teratoid/rhabdoid tumor. Oncotarget 2016; 7:1732-40. [PMID: 26646792 PMCID: PMC4811493 DOI: 10.18632/oncotarget.6459] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [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: 09/09/2015] [Accepted: 11/16/2015] [Indexed: 01/04/2023] Open
Abstract
Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is the most common undifferentiated ovarian malignancy diagnosed in women under age 40. We and others recently determined that germline and/or somatic deleterious mutations in SMARCA4 characterize SCCOHT. Alterations in this gene, or the related SWI/SNF chromatin remodeling gene SMARCB1, have been previously reported in atypical teratoid/rhabdoid tumors (ATRTs) and malignant rhabdoid tumors (MRTs). To further describe the somatic landscape of SCCOHT, we performed whole exome sequencing on 14 tumors and their matched normal tissues and compared their genomic alterations with those in ATRT and ovarian high grade serous carcinoma (HGSC). We confirmed that SMARCA4 is the only recurrently mutated gene in SCCOHT, and show that recurrent allelic imbalance is observed exclusively on chromosome 19p, where SMARCA4 resides. By comparing genomic alterations between SCCOHT, ATRT and HGSC, we demonstrate that SCCOHTs, like ATRTs, have a remarkably simple genome and harbor significantly fewer somatic protein-coding mutations and chromosomal alterations than HGSC. Furthermore, a comparison of global DNA methylation profiles of 45 SCCOHTs, 65 ATRTs, and 92 HGSCs demonstrates a strong epigenetic correlation between SCCOHT and ATRT. Our results further confirm that the genomic and epigenomic signatures of SCCOHT are more similar to those of ATRT than HGSC, supporting our previous hypothesis that SCCOHT is a rhabdoid tumor and should be renamed MRT of the ovary. Furthermore, we conclude that SMARCA4 inactivation is the main cause of SCCOHT, and that new distinct therapeutic approaches should be developed to specifically target this devastating tumor.
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Affiliation(s)
- Somayyeh Fahiminiya
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Leora Witkowski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Jian Carrot-Zhang
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Catherine Goudie
- Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Martin Hasselblatt
- Institute of Neuropathology, University Hospital Münster, Münster, Germany
| | - Pascal Johann
- Pediatric Hematology and Oncology, University Hospital Heidelberg, Heidelberg, Germany
| | - Marcel Kool
- Division of Pediatric Neuro-Oncology, German Cancer Research Center DKFZ, Heidelberg, Germany.,German Cancer Consortium (DKTK), Core Center Heidelberg, Heidelberg, Germany
| | - Ryan S Lee
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA
| | - Tenzin Gayden
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Charles W M Roberts
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, Massachusetts, USA.,Current affiliation: Comprehensive Cancer Center and Department of Oncology, St. Jude Children's Research Hospital, Memphis, Tennessee, USA
| | - Jaclyn A Biegel
- Department of Pediatrics, Keck School of Medicine of USC, Los Angeles, California, USA
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Pediatrics, McGill University, Montreal, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - William D Foulkes
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada.,Department of Medical Genetics, Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, Montreal, Quebec, Canada.,Department of Medical Genetics, Research Institute, McGill University Health Centre, Montreal, Quebec, Canada
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28
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Rivera B, Gayden T, Zhang J, Nadaf J, Boshari T, Faury D, Zeinieh M, Blanc R, Burk D, Fahiminiya S, Bareke E, Schueller U, Monoranu CM, Sträter R, Kerl K, Niederstadt T, Kurlemann G, Ellezam B, Michalak Z, Thom M, Lockhart P, Leventer R, Ohm M, McGregor D, Jones D, Karamchandani J, Greenwood C, Berghuis A, Bens S, Siebert R, Zakrzewska M, Liberski P, Zakrzewski K, Sisodiya S, Paulus W, Albrecht S, Hasselblatt M, Jabado N, Foulkes WD, Majewski J. Abstract LB-019: FGFR1 abnormalities in seizure-associated familial and sporadic dysembryoplastic neuroepithelial tumors. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-lb-019] [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
Background: Dysembryoplastic neuroepithelial tumors (DNETs) are benign developmental brain tumors associated with intractable, drug-resistant epilepsy. Distinguishing this entity from other low-grade ganglioneuronal tumors is challenging for neuro-pathologists. We set out to identify the genetic causes of DNETs and to clarify the molecular mechanisms underlying this condition.
Experimental procedures: We collected a family with three individuals with seizures and multinodular DNETs together with 100 sporadic tumors from 96 persons referred to us as DNETs. Whole-exome sequencing was performed on 46 tumours and targeted sequencing for hotspot FGFR1 mutations and BRAFp.V600E was used on the remaining samples. Blind neuropathology review and molecular characterization were performed. FISH, Copy Number Variation assays and Sanger sequencing were used to validate the findings. Supporting evidence for functional defects was obtained by in silico modelling of novel FGFR1p.R661P variant. Functional impact of this and other FGFR1 mutations were assessed using Flow Cytometry and β-galactosidase staining in HEK293 cells.
Results: We identified a novel germline FGFR1 mutation, p.R661P, in a father and his two children with DNETs. Somatic activating FGFR1 mutations (p.N546K or p.K656E) were observed in cis in the tumors with the germline mutation. Pathology review distinguished DNETs (WHO grade I) (45%) from DNET-like tumors (55%). FGFR1 alterations, mainly intragenic tyrosine kinase FGFR1 duplication and multiple mutants in cis, characterized DNETs (25/43;58.1%) whereas FGFR1 mutations (10/53;19%) (p < 0.0001) and hotspot BRAFp.V600E (12/53;22.6%) (p < 0.001) were identified in DNET-like tumors. Phospho-ERK overexpression in FGFR1p.R661P and p.N546K mutant cells support enhanced MAPK/ERK activation in this condition.
Conclusions: This study identifies constitutional and somatic FGFR1 alterations and hotspot BRAFV600E as key events in DNETs and DNET-like tumors respectively. The final common effect of these alterations appears to be a balanced level of signalling that results in benign rather than malignant tumors. The integrated pathology and molecular characterization performed here reveals the key role of the MAP-Kinase pathway in these epileptogenic low-grade glioneuronal tumors, pointing the way towards existing targeted therapies.
Citation Format: Barbara Rivera, Tenzin Gayden, Jian Zhang, Javad Nadaf, Talia Boshari, Damien Faury, Michele Zeinieh, Romeo Blanc, David Burk, Somayyeh Fahiminiya, Eric Bareke, Ulrich Schueller, Camelia M. Monoranu, Ronald Sträter, Kornelius Kerl, Thomas Niederstadt, Gerhard Kurlemann, Benjamin Ellezam, Zuzanna Michalak, Maria Thom, Paul Lockhart, Richard Leventer, Milou Ohm, Duncan McGregor, David Jones, Jason Karamchandani, Celia Greenwood, Albert Berghuis, Susanne Bens, Reiner Siebert, Magdalena Zakrzewska, Pawel Liberski, Krzysztof Zakrzewski, Sanjay Sisodiya, Werner Paulus, Steffen Albrecht, Martin Hasselblatt, Nada Jabado, William D. Foulkes, Jacek Majewski. FGFR1 abnormalities in seizure-associated familial and sporadic dysembryoplastic neuroepithelial tumors. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr LB-019.
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Affiliation(s)
| | | | - Jian Zhang
- 1McGill University, Montreal, Quebec, Canada
| | - Javad Nadaf
- 1McGill University, Montreal, Quebec, Canada
| | | | | | | | - Romeo Blanc
- 1McGill University, Montreal, Quebec, Canada
| | - David Burk
- 1McGill University, Montreal, Quebec, Canada
| | | | - Eric Bareke
- 1McGill University, Montreal, Quebec, Canada
| | | | | | | | - Kornelius Kerl
- 5University Children's Hospital Münster, Münster, Germany
| | | | | | | | | | - Maria Thom
- 8UCL Institute of Neurology, London, United Kingdom
| | | | | | - Milou Ohm
- 10VUMC School of Medical Sciences, Amsterdam, Netherlands
| | | | - David Jones
- 12German Cancer Research Center, Heidelberg, Germany
| | | | | | | | | | | | | | | | | | | | | | | | | | - Nada Jabado
- 1McGill University, Montreal, Quebec, Canada
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29
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Rivera B, Gayden T, Carrot-Zhang J, Nadaf J, Boshari T, Faury D, Zeinieh M, Blanc R, Burk D, Fahiminiya S, Bareke E, Schüller U, Monoranu CM, Sträter R, Kerl K, Niederstadt T, Kurlemann G, Ellezam B, Michalak Z, Thom M, Lockhart P, Leventer R, Ohm M, MacGregor D, Jones D, Karamchandani J, Greenwood CM, Berghuis A, Bens S, Siebert R, Zakrzewska M, Liberski PP, Zakrzewski K, Sisodiya S, Paulus W, Albrecht S, Hasselblatt M, Jabado N, Foulkes WD, Majewski J. LG-26GERMLINE AND SOMATIC FGFR1 ABNORMALITIES IN DYSEMBRYOPLASTIC NEUROEPITHELIAL TUMORS. Neuro Oncol 2016. [DOI: 10.1093/neuonc/now075.26] [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: 11/12/2022] Open
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30
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Lu C, Jain SU, Hoelper D, Bechet D, Molden RC, Ran L, Murphy D, Venneti S, Hameed M, Pawel BR, Wunder JS, Dickson BC, Lundgren SM, Jani KS, De Jay N, Papillon-Cavanagh S, Andrulis IL, Sawyer SL, Grynspan D, Turcotte RE, Nadaf J, Fahiminiyah S, Muir TW, Majewski J, Thompson CB, Chi P, Garcia BA, Allis CD, Jabado N, Lewis PW. Histone H3K36 mutations promote sarcomagenesis through altered histone methylation landscape. Science 2016; 352:844-9. [PMID: 27174990 DOI: 10.1126/science.aac7272] [Citation(s) in RCA: 279] [Impact Index Per Article: 34.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2015] [Accepted: 03/11/2016] [Indexed: 12/11/2022]
Abstract
Several types of pediatric cancers reportedly contain high-frequency missense mutations in histone H3, yet the underlying oncogenic mechanism remains poorly characterized. Here we report that the H3 lysine 36-to-methionine (H3K36M) mutation impairs the differentiation of mesenchymal progenitor cells and generates undifferentiated sarcoma in vivo. H3K36M mutant nucleosomes inhibit the enzymatic activities of several H3K36 methyltransferases. Depleting H3K36 methyltransferases, or expressing an H3K36I mutant that similarly inhibits H3K36 methylation, is sufficient to phenocopy the H3K36M mutation. After the loss of H3K36 methylation, a genome-wide gain in H3K27 methylation leads to a redistribution of polycomb repressive complex 1 and de-repression of its target genes known to block mesenchymal differentiation. Our findings are mirrored in human undifferentiated sarcomas in which novel K36M/I mutations in H3.1 are identified.
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Affiliation(s)
- Chao Lu
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA
| | - Siddhant U Jain
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA. Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA
| | - Dominik Hoelper
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA. Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA
| | - Denise Bechet
- Department of Human Genetics, McGill University, Montreal, Quebec H3Z 2Z3, Canada
| | - Rosalynn C Molden
- Epigenetics Program and Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA. Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Leili Ran
- Human Oncology and Pathogenesis Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Devan Murphy
- Human Oncology and Pathogenesis Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Sriram Venneti
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109, USA
| | - Meera Hameed
- Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Bruce R Pawel
- Department of Pathology and Laboratory Medicine, The Children's Hospital of Philadelphia and Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - Jay S Wunder
- University Musculoskeletal Oncology Unit, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. Department of Surgical Oncology and Division of Orthopedic Surgery, Princess Margaret Hospital, University of Toronto, Toronto, Ontario M5T 2M9, Canada
| | - Brendan C Dickson
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada
| | - Stefan M Lundgren
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA. Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA
| | - Krupa S Jani
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Nicolas De Jay
- Department of Human Genetics, McGill University, Montreal, Quebec H3Z 2Z3, Canada
| | | | - Irene L Andrulis
- Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario M5S 1A8, Canada. Department of Pathology and Laboratory Medicine, Mount Sinai Hospital, Toronto, Ontario M5G 1X5, Canada. Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada. The Lunenfeld-Tanenbaum Research Institute, Sinai Health System, Toronto, Ontario M5G 1X5, Canada
| | - Sarah L Sawyer
- Department of Medical Genetics and Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
| | - David Grynspan
- Department of Medical Genetics and Children's Hospital of Eastern Ontario Research Institute, University of Ottawa, Ottawa, Ontario K1H 8L1, Canada
| | - Robert E Turcotte
- Division of Orthopaedic Surgery, Montreal General Hospital, McGill University Health Centre, Montreal, Quebec H3G 1A4, Canada
| | - Javad Nadaf
- Department of Human Genetics, McGill University, Montreal, Quebec H3Z 2Z3, Canada
| | - Somayyeh Fahiminiyah
- Department of Human Genetics, McGill University, Montreal, Quebec H3Z 2Z3, Canada
| | - Tom W Muir
- Department of Chemistry, Princeton University, Princeton, NJ 08544, USA
| | - Jacek Majewski
- Department of Human Genetics, McGill University, Montreal, Quebec H3Z 2Z3, Canada
| | - Craig B Thompson
- Cancer Biology and Genetics Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Ping Chi
- Human Oncology and Pathogenesis Program and Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA. Department of Medicine, Weill Cornell Medical College, New York, NY 10065, USA
| | - Benjamin A Garcia
- Epigenetics Program and Department of Biochemistry and Biophysics, Perelman School of Medicine at the University of Pennsylvania, Philadelphia, PA 19104, USA
| | - C David Allis
- Laboratory of Chromatin Biology and Epigenetics, The Rockefeller University, New York, NY 10065, USA.
| | - Nada Jabado
- Department of Human Genetics, McGill University, Montreal, Quebec H3Z 2Z3, Canada. Department of Pediatrics, McGill University, Montreal, Quebec H3Z 2Z3, Canada.
| | - Peter W Lewis
- Epigenetics Theme, Wisconsin Institute for Discovery, University of Wisconsin, Madison, WI 53715, USA. Department of Biomolecular Chemistry, School of Medicine and Public Health, University of Wisconsin, Madison, WI 53715, USA.
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31
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Rivera B, Gayden T, Carrot-Zhang J, Nadaf J, Boshari T, Faury D, Zeinieh M, Blanc R, Burk DL, Fahiminiya S, Bareke E, Schüller U, Monoranu CM, Sträter R, Kerl K, Niederstadt T, Kurlemann G, Ellezam B, Michalak Z, Thom M, Lockhart PJ, Leventer RJ, Ohm M, MacGregor D, Jones D, Karamchandani J, Greenwood CMT, Berghuis AM, Bens S, Siebert R, Zakrzewska M, Liberski PP, Zakrzewski K, Sisodiya SM, Paulus W, Albrecht S, Hasselblatt M, Jabado N, Foulkes WD, Majewski J. Germline and somatic FGFR1 abnormalities in dysembryoplastic neuroepithelial tumors. Acta Neuropathol 2016; 131:847-63. [PMID: 26920151 PMCID: PMC5039033 DOI: 10.1007/s00401-016-1549-x] [Citation(s) in RCA: 124] [Impact Index Per Article: 15.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2016] [Revised: 02/16/2016] [Accepted: 02/16/2016] [Indexed: 12/12/2022]
Abstract
Dysembryoplastic neuroepithelial tumor (DNET) is a benign brain tumor associated with intractable drug-resistant epilepsy. In order to identify underlying genetic alterations and molecular mechanisms, we examined three family members affected by multinodular DNETs as well as 100 sporadic tumors from 96 patients, which had been referred to us as DNETs. We performed whole-exome sequencing on 46 tumors and targeted sequencing for hotspot FGFR1 mutations and BRAF p.V600E was used on the remaining samples. FISH, copy number variation assays and Sanger sequencing were used to validate the findings. By whole-exome sequencing of the familial cases, we identified a novel germline FGFR1 mutation, p.R661P. Somatic activating FGFR1 mutations (p.N546K or p.K656E) were observed in the tumor samples and further evidence for functional relevance was obtained by in silico modeling. The FGFR1 p.K656E mutation was confirmed to be in cis with the germline p.R661P variant. In 43 sporadic cases, in which the diagnosis of DNET could be confirmed on central blinded neuropathology review, FGFR1 alterations were also frequent and mainly comprised intragenic tyrosine kinase FGFR1 duplication and multiple mutants in cis (25/43; 58.1 %) while BRAF p.V600E alterations were absent (0/43). In contrast, in 53 cases, in which the diagnosis of DNET was not confirmed, FGFR1 alterations were less common (10/53; 19 %; p < 0.0001) and hotspot BRAF p.V600E (12/53; 22.6 %) (p < 0.001) prevailed. We observed overexpression of phospho-ERK in FGFR1 p.R661P and p.N546K mutant expressing HEK293 cells as well as FGFR1 mutated tumor samples, supporting enhanced MAP kinase pathway activation under these conditions. In conclusion, constitutional and somatic FGFR1 alterations and MAP kinase pathway activation are key events in the pathogenesis of DNET. These findings point the way towards existing targeted therapies.
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32
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Mendoza-Londono R, Fahiminiya S, Majewski J, Tétreault M, Nadaf J, Kannu P, Sochett E, Howard A, Stimec J, Dupuis L, Roschger P, Klaushofer K, Palomo T, Ouellet J, Al-Jallad H, Mort J, Moffatt P, Boudko S, Bächinger HP, Rauch F, Rauch F. Recessive osteogenesis imperfecta caused by missense mutations in SPARC. Am J Hum Genet 2015; 96:979-85. [PMID: 26027498 DOI: 10.1016/j.ajhg.2015.04.021] [Citation(s) in RCA: 86] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2015] [Accepted: 04/28/2015] [Indexed: 11/26/2022] Open
Abstract
Secreted protein, acidic, cysteine-rich (SPARC) is a glycoprotein that binds to collagen type I and other proteins in the extracellular matrix. Using whole-exome sequencing to identify the molecular defect in two unrelated girls with severe bone fragility and a clinical diagnosis of osteogenesis imperfecta type IV, we identified two homozygous variants in SPARC (GenBank: NM_003118.3; c.497G>A [p.Arg166His] in individual 1; c.787G>A [p.Glu263Lys] in individual 2). Published modeling and site-directed mutagenesis studies had previously shown that the residues substituted by these mutations form an intramolecular salt bridge in SPARC and are essential for the binding of SPARC to collagen type I. The amount of SPARC secreted by skin fibroblasts was reduced in individual 1 but appeared normal in individual 2. The migration of collagen type I alpha chains produced by these fibroblasts was mildly delayed on SDS-PAGE gel, suggesting some overmodification of collagen during triple helical formation. Pulse-chase experiments showed that collagen type I secretion was mildly delayed in skin fibroblasts from both individuals. Analysis of an iliac bone sample from individual 2 showed that trabecular bone was hypermineralized on the material level. In conclusion, these observations show that homozygous mutations in SPARC can give rise to severe bone fragility in humans.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Frank Rauch
- Shriners Hospital for Children, Montréal, QC H3G 1A6, Canada.
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Tetreault M, Bareke E, Nadaf J, Alirezaie N, Majewski J. Whole-exome sequencing as a diagnostic tool: current challenges and future opportunities. Expert Rev Mol Diagn 2015; 15:749-60. [PMID: 25959410 DOI: 10.1586/14737159.2015.1039516] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [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: 12/26/2022]
Abstract
Whole-exome sequencing (WES) represents a significant breakthrough in the field of human genetics. This technology has largely contributed to the identification of new disease-causing genes and is now entering clinical laboratories. WES represents a powerful tool for diagnosis and could reduce the 'diagnostic odyssey' for many patients. In this review, we present a technical overview of WES analysis, variants annotation and interpretation in a clinical setting. We evaluate the usefulness of clinical WES in different clinical indications, such as rare diseases, cancer and complex diseases. Finally, we discuss the efficacy of WES as a diagnostic tool and the impact on patient management.
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Affiliation(s)
- Martine Tetreault
- Department of Human Genetics, McGill University, Montreal, QC H3A 1B1, Canada
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34
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Ben-Omran T, Fahiminiya S, Sorfazlian N, Almuriekhi M, Nawaz Z, Nadaf J, Abu Khadija K, Zaineddin S, Kamel H, Majewski J, Tropepe V. Nonsense mutation in theWDR73gene is associated with Galloway-Mowat syndrome. J Med Genet 2015; 52:381-90. [DOI: 10.1136/jmedgenet-2014-102707] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2014] [Accepted: 03/22/2015] [Indexed: 01/10/2023]
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35
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Almuriekhi M, Shintani T, Fahiminiya S, Fujikawa A, Kuboyama K, Takeuchi Y, Nawaz Z, Nadaf J, Kamel H, Kitam AK, Samiha Z, Mahmoud L, Ben-Omran T, Majewski J, Noda M. Loss-of-Function Mutation in APC2 Causes Sotos Syndrome Features. Cell Rep 2015; 10:1585-1598. [PMID: 25753423 DOI: 10.1016/j.celrep.2015.02.011] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Revised: 01/14/2015] [Accepted: 01/31/2015] [Indexed: 01/24/2023] Open
Abstract
Sotos syndrome, characterized by intellectual disability and characteristic facial features, is caused by haploinsufficiency in the NSD1 gene. We conducted an etiological study on two siblings with Sotos features without mutations in NSD1 and detected a homozygous frameshift mutation in the APC2 gene by whole-exome sequencing, which resulted in the loss of function of cytoskeletal regulation in neurons. Apc2-deficient (Apc2-/-) mice exhibited impaired learning and memory abilities along with an abnormal head shape. Endogenous Apc2 expression was downregulated by the knockdown of Nsd1, indicating that APC2 is a downstream effector of NSD1 in neurons. Nsd1 knockdown in embryonic mouse brains impaired the migration and laminar positioning of cortical neurons, as observed in Apc2-/- mice, and this defect was rescued by the forced expression of Apc2. Thus, APC2 is a crucial target of NSD1, which provides an explanation for the intellectual disability associated with Sotos syndrome.
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Affiliation(s)
- Mariam Almuriekhi
- Section of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Takafumi Shintani
- Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki 444-8787, Japan; School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8787, Japan
| | - Somayyeh Fahiminiya
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Génome Québec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Akihiro Fujikawa
- Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki 444-8787, Japan
| | - Kazuya Kuboyama
- Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki 444-8787, Japan
| | - Yasushi Takeuchi
- Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki 444-8787, Japan
| | - Zafar Nawaz
- Cytogenetic and Molecular Cytogenetic Laboratory, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Javad Nadaf
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Génome Québec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Hussein Kamel
- Department of Radiology, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Abu Khadija Kitam
- Cytogenetic and Molecular Cytogenetic Laboratory, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Zaineddin Samiha
- Cytogenetic and Molecular Cytogenetic Laboratory, Department of Laboratory Medicine and Pathology, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Laila Mahmoud
- Section of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Tawfeg Ben-Omran
- Section of Clinical and Metabolic Genetics, Department of Pediatrics, Hamad Medical Corporation, P.O. Box 3050, Doha, Qatar
| | - Jacek Majewski
- Department of Human Genetics, Faculty of Medicine, McGill University, Montreal, QC H3A 1B1, Canada; McGill University and Génome Québec Innovation Centre, Montreal, QC H3A 0G1, Canada
| | - Masaharu Noda
- Division of Molecular Neurobiology, National Institute for Basic Biology, Okazaki 444-8787, Japan; School of Life Science, The Graduate University for Advanced Studies (SOKENDAI), Okazaki 444-8787, Japan.
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Abstract
SUMMARY Whole-exome sequencing (WES) has extensively been used in cancer genome studies; however, the use of WES data in the study of loss of heterozygosity or more generally allelic imbalance (AI) has so far been very limited, which highlights the need for user-friendly and flexible software that can handle low-quality datasets. We have developed a statistical approach, ExomeAI, for the detection of recurrent AI events using WES datasets, specifically where matched normal samples are not available. AVAILABILITY ExomeAI is a web-based application, publicly available at: http://genomequebec.mcgill.ca/exomeai. CONTACT JavadNadaf@gmail.com or somayyeh.fahiminiya@mcgill.ca SUPPLEMENTARY INFORMATION Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Javad Nadaf
- Department of Human Genetics, Faculty of Medicine, McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | - Jacek Majewski
- Department of Human Genetics, Faculty of Medicine, McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | - Somayyeh Fahiminiya
- Department of Human Genetics, Faculty of Medicine, McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
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Witkowski L, Carrot-Zhang J, Albrecht S, Hamel N, Tomiak E, Grynspan D, Saloustros E, Gilpin C, Silva-Smith R, Plourde F, Rivera B, Castellsagué E, Wu M, Fahiminiya S, Nadaf J, Saskin A, Arseneault M, Karabakhtsian RG, Reilly EA, Ueland FR, Margiolaki A, Pavlakis K, Castellino SM, Lamovec J, Roth LM, Ulbright TM, Bender T, Longy M, Berchuck A, Tischkowitz M, Siebert R, Nagel I, Georgoulias V, Stewart CJ, McCluggage G, Arseneau J, Clarke BA, Riazalhosseini Y, Hasselblatt M, Majewski J, Foulkes WD. Abstract LB-89: Germ-line and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-lb-89] [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
Small-cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is an aggressive tumor and the most common type of undifferentiated ovarian malignancy presenting at less than 40 years of age. Its cause and histogenesis remain unknown. We sequenced the exomes of individuals from three familial cases of SCCOHT. Subsequently, we used whole exome sequencing, Sanger sequencing and immunohistochemistry to analyze germline and tumor DNA from three additional familial cases, 35 non-familial cases and one SCCOHT cell line (BIN-67). DNA sequencing revealed likely deleterious germ-line mutations in the chromatin remodeling gene SMARCA4 in all four familial cases of SCCOHT where DNA was available. This was accompanied by either a somatic mutation or loss of the wild-type allele in the tumor. BIN-67 contained bi-allelic deleterious mutations in SMARCA4. Sequencing of 24 non-familial pathologically-confirmed SCCOHT cases revealed at least one germ-line or somatic likely deleterious SMARCA4 mutation in 22 cases. Immunohistochemical (IHC) analyses of these and an additional 11 tumors showed loss of BRG1 protein in 38/40 cases. Our findings identify alterations in SMARCA4 as a major cause of SCCOHT, which could pave the way for genetic counseling and new treatment approaches.
Citation Format: Leora Witkowski, Jian Carrot-Zhang, Steffen Albrecht, Nancy Hamel, Eva Tomiak, David Grynspan, Emmanouil Saloustros, Catherine Gilpin, Rachel Silva-Smith, François Plourde, Barbara Rivera, Ester Castellsagué, Mona Wu, Somayyeh Fahiminiya, Javad Nadaf, Avi Saskin, Madeleine Arseneault, Rouzan G. Karabakhtsian, Elizabeth A. Reilly, Frederick R. Ueland, Anna Margiolaki, Kitty Pavlakis, Sharon M. Castellino, Janez Lamovec, Lawrence M. Roth, Thomas M. Ulbright, Tracey Bender, Michel Longy, Andrew Berchuck, Marc Tischkowitz, Reiner Siebert, Inga Nagel, Vassilis Georgoulias, Colin J.r. Stewart, Glenn McCluggage, Jocelyne Arseneau, Blaise A. Clarke, Yasser Riazalhosseini, Martin Hasselblatt, Jacek Majewski, William D. Foulkes. Germ-line and somatic SMARCA4 mutations characterize small cell carcinoma of the ovary, hypercalcemic type. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr LB-89. doi:10.1158/1538-7445.AM2014-LB-89
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Affiliation(s)
- Leora Witkowski
- 1Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill Univ, Montreal, Quebec, Canada
| | - Jian Carrot-Zhang
- 2McGill Univ Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | - Steffen Albrecht
- 3Montreal Children's Hospital, McGill Univ Health Centre, Montreal, Quebec, Canada
| | - Nancy Hamel
- 4Research Institute, McGill Univ Health Centre, Montreal, Quebec, Canada
| | - Eva Tomiak
- 5Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - David Grynspan
- 5Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - Emmanouil Saloustros
- 6Hereditary Cancer Clinic, Department of Medical Oncology, University Hospital of Heraklion, Crete, Greece
| | - Catherine Gilpin
- 5Children's Hospital of Eastern Ontario, University of Ottawa, Ottawa, Ontario, Canada
| | - Rachel Silva-Smith
- 7Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | - François Plourde
- 7Lady Davis Institute and Segal Cancer Centre, Jewish General Hospital, McGill University, Montreal, Quebec, Canada
| | | | | | - Mona Wu
- 8McGill University, Montreal, Quebec, Canada
| | - Somayyeh Fahiminiya
- 9McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | - Javad Nadaf
- 9McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | - Avi Saskin
- 8McGill University, Montreal, Quebec, Canada
| | - Madeleine Arseneault
- 9McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
| | | | | | | | | | - Kitty Pavlakis
- 12National and Kapodistrian University of Athens, Athens, Greece
| | | | | | | | | | - Tracey Bender
- 15Indiana University School of Medicine, Indianapolis, IN
| | - Michel Longy
- 16Institut Bergonié, Université de Bordeaux, Bordeaux, France
| | | | | | - Reiner Siebert
- 19Institute of Human Genetics, University of Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Inga Nagel
- 19Institute of Human Genetics, University of Kiel & University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | | | | | | | - Jocelyne Arseneau
- 22McGill University Health Centre, McGill University, Montreal, Quebec, Canada
| | | | | | | | - Jacek Majewski
- 9McGill University and Genome Quebec Innovation Center, Montreal, Quebec, Canada
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Donadeu FX, Fahiminiya S, Esteves CL, Nadaf J, Miedzinska K, McNeilly AS, Waddington D, Gérard N. Transcriptome profiling of granulosa and theca cells during dominant follicle development in the horse. Biol Reprod 2014; 91:111. [PMID: 25253738 DOI: 10.1095/biolreprod.114.118943] [Citation(s) in RCA: 20] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
Several aspects of equine ovarian physiology are unique among domestic species. Moreover, follicular growth patterns are very similar between horses and humans. This study aimed to characterize, for the first time, global gene expression profiles associated with growth and preovulatory (PO) maturation of equine dominant follicles. Granulosa cells (GCs) and theca interna cells (TCs) were harvested from follicles (n = 5) at different stages of an ovulatory wave in mares corresponding to early dominance (ED; diameter ≥22 mm), late dominance (LD; ≥33 mm) and PO stage (34 h after administration of crude equine gonadotropins at LD stage), and separately analyzed on a horse gene expression microarray, followed by validation using quantitative PCR and immunoblotting/immunohistochemistry. Numbers of differentially expressed transcripts (DETs; ≥2-fold; P < 0.05) during the ED-LD and LD-PO transitions were 546 and 2419 in GCs and 5 and 582 in TCs. The most prominent change in GCs was the down-regulation of transcripts associated with cell division during both ED-LD and LD-PO. In addition, DET sets during LD-PO in GCs were enriched for genes involved in cell communication/adhesion, antioxidation/detoxification, immunity/inflammation, and cholesterol biosynthesis. In contrast, the largest change in TCs during the LD-PO transition was an up-regulation of genes involved in immune activation, with other DET sets mapping to GPCR/cAMP signaling, lipid/amino acid metabolism, and cell proliferation/survival and differentiation. In conclusion, distinct expression profiles were identified between growing and PO follicles and, particularly, between GCs and TCs within each stage. Several DETs were identified that have not been associated with follicle development in other species.
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Affiliation(s)
- F Xavier Donadeu
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Somayyeh Fahiminiya
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom INRA and CNRS, UMR 6175 Physiologie de la Reproduction et des Comportements, Nouzilly, France Université François Rabelais de Tours, UMR 6175 Physiologie de la Reproduction et des Comportements, Tours, France
| | - Cristina L Esteves
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Javad Nadaf
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Katarzyna Miedzinska
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Alan S McNeilly
- The Queen's Medical Research Institute, MRC Centre for Reproductive Health, Edinburgh, United Kingdom
| | - David Waddington
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian, United Kingdom
| | - Nadine Gérard
- INRA and CNRS, UMR 6175 Physiologie de la Reproduction et des Comportements, Nouzilly, France Université François Rabelais de Tours, UMR 6175 Physiologie de la Reproduction et des Comportements, Tours, France Haras Nationaux, UMR 6175 Physiologie de la Reproduction et des Comportements, Nouzilly, France
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39
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Abstract
Background Five main methods, commonly applied in genomic selection, were used to estimate the GEBV on the 15th QTLMAS workshop dataset: GBLUP, LASSO, Bayes A and two Bayes B type of methods (BBn and BBt). GBLUP is a mixed model approach where GEBV are obtained using a relationship matrix calculated from the SNP genotypes. The remaining methods are regression-based approaches where the SNP effects are first estimated and, then GEBV are calculated given the individuals' genotypes. Methods The differences between the regression-based methods are in their prior distributions for the SNP effects. The prior distribution for LASSO is a Laplace distribution, for Bayes A is a scaled Student-t distribution, and the Bayes B type methods have a Spike and Slab prior where only a proportion (π) of SNP has an effect, following a given distribution. In this study, two different distributions were considered for the Bayes B type methods: (i) normal and (ii) scaled Student-t. They are referred here as the BBn and BBt methods, respectively. These prior distributions are defined by one or more parameters controlling their scale/rate (λ), shape (df) or proportion of SNP with effect (π). LASSO requires one (λ); two for Bayes A (λ, df) and Bayes Bn (λ, π); and three for Bayes Bt (λ, df, π). In this study, all parameters were estimated from the data. An extra scenario for Bayes A and BBt was included where df was not estimated but fixed to 4 (suffixed _4df). The implementation of GBLUP was done using ASREML, the heritability was also estimated from the data. All other methods were implemented using a MCMC approach. Results All Bayes A and B methods showed accuracy (correlation between True and Estimated BV) as high as 0.94 except for BA_4df (r = 0.91). Compared to the traditional BLUP using pedigree information, these methods improved the accuracy between 50 and 55%. GBLUP and LASSO were less accurate (0.81 and 0.85 respectively) and the improvements were 34 and 40% compared to BLUP. Conclusions Results of all methods were consistent and the accuracies for GEBV ranged between 0.81 and 0.94. When all parameters were estimated the results were similar for the Bayes A and Bayes B methods. Results showed that Bayes A was more sensitive to the changes in the shape parameter, and the parameter changes led to change in the accuracy of GEBV. However BBt was more robust to the change in this parameter. This may be explained by the fact that BBt estimates one extra parameter and it can buffer against a non-proper shape parameter.
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Affiliation(s)
- Javad Nadaf
- DNA Landmarks Inc, St-Jean-Sur-Richelieu, J3B 6X3 Quebec, Canada.
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40
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Abstract
BACKGROUND We applied a range of genome-wide association (GWA) methods to map quantitative trait loci (QTL) in the simulated dataset provided by the QTLMAS2009 workshop to derive a comprehensive set of results. A Gompertz curve was modelled on the yield data and showed good predictive properties. QTL analyses were done on the raw measurements and on the individual parameters of the Gompertz curve and its predicted growth for each interval. Half-sib and variance component linkage analysis revealed QTL with different modes of inheritance but with low resolution. This was complemented by association studies using single markers or haplotypes, and additive, dominance, parent-of-origin and epistatic QTL effects. All association analyses were done on phenotypes pre-corrected for pedigree effects. These methods detected QTL positions with high concordance to each other and with greater refinement of the linkage signals. Two-locus interaction analysis detected no epistatic pairs of QTL. Overall, using stringent thresholds we identified QTL regions using linkage analyses, corroborated by 6 individual SNPs with significant effects as well as two putatively imprinted SNPs. CONCLUSIONS We obtained consistent results across a combination of intra- and inter- family based methods using flexible linear models to evaluate a variety of models. The Gompertz curve fitted the data really well, and provided complementary information on the detected QTL. Retrospective comparisons of the results with actual data simulated showed that best results were obtained by including both yield and the parameters from the Gompertz curve despite the data being simulated using a logistic function.
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Affiliation(s)
- Georgia Hadjipavlou
- Division of Genetics and Genomics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK
| | - Gib Hemani
- Division of Genetics and Genomics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK
| | - Richard Leach
- Division of Genetics and Genomics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK
| | - Bruno Louro
- Division of Genetics and Genomics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK
| | - Javad Nadaf
- Division of Genetics and Genomics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK
| | - Suzanne Rowe
- Division of Genetics and Genomics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK
| | - Dirk-Jan de Koning
- Division of Genetics and Genomics, Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Roslin, Midlothian, EH25 9PS, UK
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Nadaf J, Pitel F, Gilbert H, Duclos MJ, Vignoles F, Beaumont C, Vignal A, Porter TE, Cogburn LA, Aggrey SE, Simon J, Le Bihan-Duval E. QTL for several metabolic traits map to loci controlling growth and body composition in an F2 intercross between high- and low-growth chicken lines. Physiol Genomics 2009; 38:241-9. [DOI: 10.1152/physiolgenomics.90384.2008] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Quantitative trait loci (QTL) for metabolic and body composition traits were mapped at 7 and 9 wk, respectively, in an F2 intercross between high-growth and low-growth chicken lines. These lines also diverged for abdominal fat percentage (AFP) and plasma insulin-like growth factor-I (IGF-I), insulin, and glucose levels. Genotypings were performed with 129 microsatellite markers covering 21 chromosomes. A total of 21 QTL with genomewide level of significance were detected by single-trait analyses for body weight (BW), breast muscle weight (BMW) and percentage (BMP), AF weight (AFW) and percentage (AFP), shank length (ShL) and diameter (ShD), fasting plasma glucose level (Gluc), and body temperature (Tb). Other suggestive QTL were identified for these parameters and for plasma IGF-I and nonesterified fatty acid levels. QTL controlling adiposity and Gluc were colocalized on GGA3 and GGA5 and QTL for BW, ShL and ShD, adiposity, and Tb on GGA4. Multitrait analyses revealed two QTL controlling Gluc and AFP on GGA5 and Gluc and Tb on GGA26. Significant effects of the reciprocal cross were observed on BW, ShD, BMW, and Gluc, which may result from mtDNA and/or maternal effects. Most QTL regions for Gluc and adiposity harbor genes for which alleles have been associated with increased susceptibility to diabetes and/or obesity in humans. Identification of genes responsible for these metabolic QTL will increase our understanding of the constitutive “hyperglycemia” found in chickens. Furthermore, a comparative approach could provide new information on the genetic causes of diabetes and obesity in humans.
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Affiliation(s)
- Javad Nadaf
- Institut National de la Recherche Agronomique (INRA, UR83) Recherches Avicoles, Nouzilly
| | | | - Hélène Gilbert
- INRA, UMR1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Michel J. Duclos
- Institut National de la Recherche Agronomique (INRA, UR83) Recherches Avicoles, Nouzilly
| | | | - Catherine Beaumont
- Institut National de la Recherche Agronomique (INRA, UR83) Recherches Avicoles, Nouzilly
| | - Alain Vignal
- INRA, ENVT, UMR444 Génétique Cellulaire, Castanet-Tolosan
| | - Tom E. Porter
- Department of Animal and Avian Sciences, University of Maryland, College Park, Maryland
| | - Larry A. Cogburn
- Department of Animal and Food Sciences, University of Delaware, Newark, Delaware
| | - Samuel E. Aggrey
- Department of Poultry Science, University of Georgia, Athens, Georgia
| | - Jean Simon
- Institut National de la Recherche Agronomique (INRA, UR83) Recherches Avicoles, Nouzilly
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Le Bihan-Duval E, Berri C, Pitel F, Nadaf J, Sibut V, Jenkins C, Duclos MJ. A general approach combining QTL research and gene expression profiling to identify genes controlling chicken meat quality. ACTA ACUST UNITED AC 2007. [DOI: 10.3166/sda.27.143-152] [Citation(s) in RCA: 2] [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: 11/20/2022]
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