1
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Moison C, Gracias D, Schmitt J, Girard S, Spinella JF, Fortier S, Boivin I, Mendoza-Sanchez R, Thavonekham B, MacRae T, Mayotte N, Bonneil E, Wittman M, Carmichael J, Ruel R, Thibault P, Hébert J, Marinier A, Sauvageau G. SF3B1 mutations provide genetic vulnerability to copper ionophores in human acute myeloid leukemia. Sci Adv 2024; 10:eadl4018. [PMID: 38517966 PMCID: PMC10959413 DOI: 10.1126/sciadv.adl4018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2023] [Accepted: 02/20/2024] [Indexed: 03/24/2024]
Abstract
In a phenotypical screen of 56 acute myeloid leukemia (AML) patient samples and using a library of 10,000 compounds, we identified a hit with increased sensitivity toward SF3B1-mutated and adverse risk AMLs. Through structure-activity relationship studies, this hit was optimized into a potent, specific, and nongenotoxic molecule called UM4118. We demonstrated that UM4118 acts as a copper ionophore that initiates a mitochondrial-based noncanonical form of cell death known as cuproptosis. CRISPR-Cas9 loss-of-function screen further revealed that iron-sulfur cluster (ISC) deficiency enhances copper-mediated cell death. Specifically, we found that loss of the mitochondrial ISC transporter ABCB7 is synthetic lethal to UM4118. ABCB7 is misspliced and down-regulated in SF3B1-mutated leukemia, creating a vulnerability to copper ionophores. Accordingly, ABCB7 overexpression partially rescued SF3B1-mutated cells to copper overload. Together, our work provides mechanistic insights that link ISC deficiency to cuproptosis, as exemplified by the high sensitivity of SF3B1-mutated AMLs. We thus propose SF3B1 mutations as a biomarker for future copper ionophore-based therapies.
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Affiliation(s)
- Céline Moison
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Deanne Gracias
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Julie Schmitt
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Simon Girard
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Jean-François Spinella
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Simon Fortier
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Isabel Boivin
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | | | - Bounkham Thavonekham
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Tara MacRae
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Nadine Mayotte
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Eric Bonneil
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Mark Wittman
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA, USA
| | - James Carmichael
- Research and Development, Bristol Myers Squibb Company, Cambridge, MA, USA
| | - Réjean Ruel
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
| | - Pierre Thibault
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Chemistry, Université de Montréal, Montréal, Canada
| | - Josée Hébert
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Division of Hematology-Oncology and Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
| | - Anne Marinier
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Department of Chemistry, Université de Montréal, Montréal, Canada
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, Canada
- Division of Hematology-Oncology and Quebec Leukemia Cell Bank, Maisonneuve-Rosemont Hospital, Montréal, Canada
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, Canada
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2
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Spinella JF, Chagraoui J, Moison C, Lavallée VP, Boivin I, Gracias D, Lavallée S, Carpentier GR, Beliveau F, Hébert J, Sauvageau G. DELE1 haploinsufficiency causes resistance to mitochondrial stress-induced apoptosis in monosomy 5/del(5q) AML. Leukemia 2024; 38:530-537. [PMID: 38102204 PMCID: PMC10912023 DOI: 10.1038/s41375-023-02107-4] [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] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 12/17/2023]
Abstract
Monosomy 5 and deletions of the chromosome 5q (-5/del(5q)) are recurrent events in de novo adult acute myeloid leukemia (AML), reaching up to 40% of cases in secondary AML. These chromosome anomalies are associated with TP53 mutations and with very poor prognosis. Using the large Leucegene genomic and transcriptomic dataset composed of 48 -5/del(5q) patient specimens and 367 control AML, we identified DELE1 - located in the common deleted region - as the most consistently downregulated gene in these leukemias. DELE1 encodes a mitochondrial protein recently characterized as the relay of mitochondrial stress to the cytosol through a newly defined OMA1-DELE1-HRI pathway which ultimately leads to the activation of ATF4, the master transcription factor of the integrated stress response. Here, we showed that the partial loss of DELE1 expression observed in -5/del(5q) patients was sufficient to significantly reduce the sensitivity to mitochondrial stress in AML cells. Overall, our results suggest that DELE1 haploinsufficiency could represent a new driver mechanism in -5/del(5q) AML.
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Affiliation(s)
- Jean-François Spinella
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- The Leucegene Project, Université de Montréal, Montréal, QC, Canada
| | - Jalila Chagraoui
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- The Leucegene Project, Université de Montréal, Montréal, QC, Canada
| | - Céline Moison
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- The Leucegene Project, Université de Montréal, Montréal, QC, Canada
| | - Vincent P Lavallée
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- The Leucegene Project, Université de Montréal, Montréal, QC, Canada
- Sainte-Justine Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montréal, QC, Canada
- Department of Pediatrics, Université de Montréal, Montréal, QC, Canada
| | - Isabel Boivin
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- The Leucegene Project, Université de Montréal, Montréal, QC, Canada
| | - Deanne Gracias
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada
- The Leucegene Project, Université de Montréal, Montréal, QC, Canada
| | - Sylvie Lavallée
- The Leucegene Project, Université de Montréal, Montréal, QC, Canada
- Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada
| | - Guillaume Richard Carpentier
- The Leucegene Project, Université de Montréal, Montréal, QC, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medicine, Division of Medical Oncology and Hematology, Temerty Faculty of Medicine, University of Toronto, Toronto, ON, Canada
| | - François Beliveau
- The Leucegene Project, Université de Montréal, Montréal, QC, Canada
- Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada
| | - Josée Hébert
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada.
- The Leucegene Project, Université de Montréal, Montréal, QC, Canada.
- Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada.
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada.
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
| | - Guy Sauvageau
- Institute for Research in Immunology and Cancer, Université de Montréal, Montréal, QC, Canada.
- The Leucegene Project, Université de Montréal, Montréal, QC, Canada.
- Leukemia Cell Bank of Quebec, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada.
- Division of Hematology, Maisonneuve-Rosemont Hospital, Montréal, QC, Canada.
- Department of Medicine, Faculty of Medicine, Université de Montréal, Montréal, QC, Canada.
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3
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Supper E, Rudat S, Iyer V, Droop A, Wong K, Spinella JF, Thomas P, Sauvageau G, Adams DJ, Wong CC. Cut-like homeobox 1 (CUX1) tumor suppressor gene haploinsufficiency induces apoptosis evasion to sustain myeloid leukemia. Nat Commun 2021; 12:2482. [PMID: 33931647 PMCID: PMC8087769 DOI: 10.1038/s41467-021-22750-8] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 03/24/2021] [Indexed: 01/19/2023] Open
Abstract
While oncogenes promote tumorigenesis, they also induce deleterious cellular stresses, such as apoptosis, that cancer cells must combat by coopting adaptive responses. Whether tumor suppressor gene haploinsufficiency leads to such phenomena and their mechanistic basis is unclear. Here, we demonstrate that elevated levels of the anti-apoptotic factor, CASP8 and FADD-like apoptosis regulator (CFLAR), promotes apoptosis evasion in acute myeloid leukemia (AML) cells haploinsufficient for the cut-like homeobox 1 (CUX1) transcription factor, whose loss is associated with dismal clinical prognosis. Genome-wide CRISPR/Cas9 screening identifies CFLAR as a selective, acquired vulnerability in CUX1-deficient AML, which can be mimicked therapeutically using inhibitor of apoptosis (IAP) antagonists in murine and human AML cells. Mechanistically, CUX1 deficiency directly alleviates CUX1 repression of the CFLAR promoter to drive CFLAR expression and leukemia survival. These data establish how haploinsufficiency of a tumor suppressor is sufficient to induce advantageous anti-apoptosis cell survival pathways and concurrently nominate CFLAR as potential therapeutic target in these poor-prognosis leukemias.
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MESH Headings
- Animals
- Apoptosis/drug effects
- Apoptosis/genetics
- CASP8 and FADD-Like Apoptosis Regulating Protein/genetics
- CASP8 and FADD-Like Apoptosis Regulating Protein/metabolism
- Cell Cycle/drug effects
- Cell Cycle/genetics
- Cell Line, Tumor
- Cell Proliferation/drug effects
- Cell Proliferation/genetics
- Cell Survival/genetics
- Chromatin Immunoprecipitation
- Dipeptides/pharmacology
- Gene Expression Regulation, Neoplastic/drug effects
- Gene Expression Regulation, Neoplastic/genetics
- Gene Ontology
- Genes, Tumor Suppressor
- Haploinsufficiency
- Hematopoietic Stem Cells/metabolism
- Homeodomain Proteins/genetics
- Homeodomain Proteins/metabolism
- Humans
- Indoles/pharmacology
- Kaplan-Meier Estimate
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Leukemia, Myeloid, Acute/pathology
- Leukemia, Myelomonocytic, Chronic/genetics
- Leukemia, Myelomonocytic, Chronic/metabolism
- Mice
- Mice, Inbred C57BL
- Mice, Knockout
- Mutation
- Nuclear Proteins/deficiency
- Nuclear Proteins/genetics
- Nuclear Proteins/metabolism
- Promoter Regions, Genetic
- Protein Array Analysis
- Repressor Proteins/deficiency
- Repressor Proteins/genetics
- Repressor Proteins/metabolism
- fms-Like Tyrosine Kinase 3/genetics
- fms-Like Tyrosine Kinase 3/metabolism
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Affiliation(s)
- Emmanuelle Supper
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Saskia Rudat
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Vivek Iyer
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Alastair Droop
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Kim Wong
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Jean-François Spinella
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC, Canada
| | - Patrick Thomas
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Guy Sauvageau
- The Leucegene Project at Institute for Research in Immunology and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC, Canada
| | - David J Adams
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK
| | - Chi C Wong
- Experimental Cancer Genetics, Wellcome Sanger Institute, Hinxton, UK.
- Department of Haematology, Addenbrooke's Hospital, Cambridge, UK.
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4
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Hajmirza A, Simon L, Spinella JF, MacRae T, Lehnertz B, Chagraoui J, Mayotte N, Bertomeu T, Coulombe-Huntington J, Boucher G, Feghaly A, Bordeleau ME, Lemieux S, Tyers M, Hébert J, Sauvageau G. 3082 – EXPLORING GLUCOCORTICOID SENSITIVITY MODULATORS IN HUMAN ACUTE MYELOID LEUKEMIA. Exp Hematol 2020. [DOI: 10.1016/j.exphem.2020.09.097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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5
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Bordeleau ME, Thérêt L, Audemard É, Spinella JF, Aubert L, Boivin I, Bonneil É, Thibault P, Lemieux S, Lavallée VP, Hébert J, Roux P, Sauvageau G. 3058 – SURFACE PROTEOMICS REVEALS NOVEL POTENTIAL AML ANTIGENS FOR IMMUNOTHERAPEUTIC TARGETING. Exp Hematol 2020. [DOI: 10.1016/j.exphem.2020.09.075] [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: 11/24/2022]
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6
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Bisaillon R, Moison C, Thiollier C, Krosl J, Bordeleau ME, Lehnertz B, Lavallée VP, MacRae T, Mayotte N, Labelle C, Boucher G, Spinella JF, Boivin I, D’Angelo G, Lavallée S, Marinier A, Lemieux S, Hébert J, Sauvageau G. Genetic characterization of ABT-199 sensitivity in human AML. Leukemia 2019; 34:63-74. [DOI: 10.1038/s41375-019-0485-x] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2019] [Revised: 03/06/2019] [Accepted: 04/05/2019] [Indexed: 02/04/2023]
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7
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Baccelli I, Gareau Y, Lehnertz B, Gingras S, Spinella JF, Corneau S, Mayotte N, Girard S, Frechette M, Blouin-Chagnon V, Leveillé K, Boivin I, MacRae T, Krosl J, Thiollier C, Lavallée VP, Kanshin E, Bertomeu T, Coulombe-Huntington J, St-Denis C, Bordeleau ME, Boucher G, Roux PP, Lemieux S, Tyers M, Thibault P, Hébert J, Marinier A, Sauvageau G. Mubritinib Targets the Electron Transport Chain Complex I and Reveals the Landscape of OXPHOS Dependency in Acute Myeloid Leukemia. Cancer Cell 2019; 36:84-99.e8. [PMID: 31287994 DOI: 10.1016/j.ccell.2019.06.003] [Citation(s) in RCA: 134] [Impact Index Per Article: 26.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/30/2018] [Revised: 04/06/2019] [Accepted: 06/04/2019] [Indexed: 12/12/2022]
Abstract
To identify therapeutic targets in acute myeloid leukemia (AML), we chemically interrogated 200 sequenced primary specimens. Mubritinib, a known ERBB2 inhibitor, elicited strong anti-leukemic effects in vitro and in vivo. In the context of AML, mubritinib functions through ubiquinone-dependent inhibition of electron transport chain (ETC) complex I activity. Resistance to mubritinib characterized normal CD34+ hematopoietic cells and chemotherapy-sensitive AMLs, which displayed transcriptomic hallmarks of hypoxia. Conversely, sensitivity correlated with mitochondrial function-related gene expression levels and characterized a large subset of chemotherapy-resistant AMLs with oxidative phosphorylation (OXPHOS) hyperactivity. Altogether, our work thus identifies an ETC complex I inhibitor and reveals the genetic landscape of OXPHOS dependency in AML.
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MESH Headings
- Animals
- Antineoplastic Agents/pharmacology
- Biomarkers
- Cell Line, Tumor
- Cell Survival/drug effects
- Disease Models, Animal
- Dose-Response Relationship, Drug
- Electron Transport Complex I/antagonists & inhibitors
- Female
- Hematopoiesis/drug effects
- Humans
- Leukemia, Myeloid, Acute/drug therapy
- Leukemia, Myeloid, Acute/genetics
- Leukemia, Myeloid, Acute/metabolism
- Leukemia, Myeloid, Acute/mortality
- Mice
- Models, Biological
- Oxazoles/pharmacology
- Oxidative Phosphorylation/drug effects
- Protein Kinase Inhibitors/pharmacology
- Receptor, ErbB-2/antagonists & inhibitors
- Triazoles/pharmacology
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Affiliation(s)
- Irène Baccelli
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada.
| | - Yves Gareau
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada; Department of Chemistry, Université de Montréal Pavillon Roger-Gaudry, 2900 Boulevard Édouard-Montpetit, Montréal, QC H3C 3J7, Canada
| | - Bernhard Lehnertz
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Stéphane Gingras
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada; Department of Chemistry, Université de Montréal Pavillon Roger-Gaudry, 2900 Boulevard Édouard-Montpetit, Montréal, QC H3C 3J7, Canada
| | - Jean-François Spinella
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Sophie Corneau
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Nadine Mayotte
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Simon Girard
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Mélanie Frechette
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Valérie Blouin-Chagnon
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Koryne Leveillé
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Isabel Boivin
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Tara MacRae
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Jana Krosl
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Clarisse Thiollier
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Vincent-Philippe Lavallée
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Evgeny Kanshin
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Thierry Bertomeu
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Jasmin Coulombe-Huntington
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Corinne St-Denis
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Marie-Eve Bordeleau
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Geneviève Boucher
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Philippe P Roux
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada; Department of Pathology & Cell Biology, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal QC H3T 1J4, Canada
| | - Sébastien Lemieux
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada; Department of Computer Science & Operations Research, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada; Department of Biochemistry & Molecular Medicine, Université de Montréal Pavillon Roger-Gaudry, 2900 Boulevard Édouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - Mike Tyers
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Pierre Thibault
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada
| | - Josée Hébert
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada; Leukemia Cell Bank of Quebec, 5415 Assumption Boulevard, Montréal, QC H1T 2M4, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, 5415 Assumption Boulevard, Montréal, QC H1T 2M4, Canada; Department of Medicine, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal, QC H3T 1J4, Canada
| | - Anne Marinier
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada; Department of Chemistry, Université de Montréal Pavillon Roger-Gaudry, 2900 Boulevard Édouard-Montpetit, Montréal, QC H3C 3J7, Canada.
| | - Guy Sauvageau
- The Leucegene Project at Institute for Research in Immunology (IRIC) and Cancer, Université de Montréal, 2950 Chemin de Polytechnique Pavillon, Marcelle-Coutu, Montréal, QC H3T 1J4, Canada; Leukemia Cell Bank of Quebec, 5415 Assumption Boulevard, Montréal, QC H1T 2M4, Canada; Division of Hematology, Maisonneuve-Rosemont Hospital, 5415 Assumption Boulevard, Montréal, QC H1T 2M4, Canada; Department of Medicine, Université de Montréal, 2900 Boulevard Édouard-Montpetit, Montréal, QC H3T 1J4, Canada.
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8
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Abaji R, Ceppi F, Patel S, Gagné V, Xu CJ, Spinella JF, Colombini A, Parasole R, Buldini B, Basso G, Conter V, Cazzaniga G, Leclerc JM, Laverdière C, Sinnett D, Krajinovic M. Genetic risk factors for VIPN in childhood acute lymphoblastic leukemia patients identified using whole-exome sequencing. Pharmacogenomics 2018; 19:1181-1193. [PMID: 30191766 DOI: 10.2217/pgs-2018-0093] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [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: 12/12/2022] Open
Abstract
AIM To identify genetic markers associated with vincristine-induced peripheral neuropathy (VIPN) in childhood acute lymphoblastic leukemia. PATIENTS & METHODS Whole-exome sequencing data were combined with exome-wide association study to identify predicted-functional germline variants associated with high-grade VIPN. Genotyping was then performed for top-ranked signals (n = 237), followed by validation in independent replication group (n = 405). RESULTS Minor alleles of rs2781377/SYNE2 (p = 0.01) and rs10513762/MRPL47 (p = 0.01) showed increased risk, whereas that of rs3803357/BAHD1 had a protective effect (p = 0.007). Using a genetic model based on weighted genetic risk scores, an additive effect of combining these loci was observed (p = 0.003). The addition of rs1135989/ACTG1 further enhanced model performance (p = 0.0001). CONCLUSION Variants in SYNE2, MRPL47 and BAHD1 genes are putative new risk factors for VIPN in childhood acute lymphoblastic leukemia.
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Affiliation(s)
- Rachid Abaji
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pharmacology & Physiology, Faculty of Medicine, University of Montreal, Montreal, QC, H3C 3J7, Canada
| | - Francesco Ceppi
- Pediatric Hematology-Oncology Unit & Pediatric Hematology-Oncology Research Laboratory, Division of Pediatrics, Department of Woman-Mother-Child, University Hospital of Lausanne, 1004 Lausanne, Switzerland
| | - Swati Patel
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Vincent Gagné
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Chang J Xu
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Jean-François Spinella
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada
| | - Antonella Colombini
- Department of Pediatrics, University of Milano-Bicocca, Ospedale S Gerardo, 20835 Monza, Italy
| | - Rosanna Parasole
- Department of Pediatric Hemato-Oncology, Santobono-Pausilipon Hospital, 80129 Naples, Italy
| | - Barbara Buldini
- Department of Woman & Child Health, Laboratory of Haematology-Oncology, University of Padova, 35128 Padova, Italy
| | - Giuseppe Basso
- Department of Woman & Child Health, Laboratory of Haematology-Oncology, University of Padova, 35128 Padova, Italy
| | - Valentino Conter
- Department of Pediatrics, University of Milano-Bicocca, Ospedale S Gerardo, 20835 Monza, Italy
| | - Giovanni Cazzaniga
- Centro Ricerca Tettamanti, Department of Pediatrics, University Milano Bicocca, 20835 Monza, Italy
| | - Jean-Marie Leclerc
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, H4A 3J1, Canada
| | - Caroline Laverdière
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, H4A 3J1, Canada
| | - Daniel Sinnett
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, H4A 3J1, Canada
| | - Maja Krajinovic
- Charles-Bruneau Cancer Center, CHU Sainte-Justine Research Center, Montreal, QC, H3T1C5, Canada.,Department of Pharmacology & Physiology, Faculty of Medicine, University of Montreal, Montreal, QC, H3C 3J7, Canada.,Centro Ricerca Tettamanti, Department of Pediatrics, University Milano Bicocca, 20835 Monza, Italy
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9
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Abaji R, Gagné V, Xu CJ, Spinella JF, Ceppi F, Laverdière C, Leclerc JM, Sallan SE, Neuberg D, Kutok JL, Silverman LB, Sinnett D, Krajinovic M. Whole-exome sequencing identified genetic risk factors for asparaginase-related complications in childhood ALL patients. Oncotarget 2018; 8:43752-43767. [PMID: 28574850 PMCID: PMC5546438 DOI: 10.18632/oncotarget.17959] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 04/21/2017] [Accepted: 04/27/2017] [Indexed: 01/19/2023] Open
Abstract
Allergy, pancreatitis and thrombosis are common side-effects of childhood acute lymphoblastic leukemia (ALL) treatment that are associated with the use of asparaginase (ASNase), a key component in most ALL treatment protocols. Starting with predicted functional germline variants obtained through whole-exome sequencing (WES) data of the Quebec childhood ALL cohort we performed exome-wide association studies with ASNase-related toxicities. A subset of top-ranking variants was further confirmed by genotyping (N=302) followed by validation in an independent replication group (N=282); except for thrombosis which was not available for that dataset. SNPs in 12 genes were associated with ASNase complications in discovery cohort including 3 that were associated with allergy, 3 with pancreatitis and 6 with thrombosis. The risk was further increased through combined SNPs effect (p≤0.002), suggesting synergistic interactions between the SNPs identified in each of the studied toxicities. Interestingly, rs3809849 in the MYBBP1A gene was associated with allergy (p= 0.0006), pancreatitis (p=0.002), thrombosis (p=0.02), event-free survival (p=0.02) and overall survival (p=0.003). Furthermore, rs11556218 in IL16 and rs34708521 in SPEF2 were both associated with thrombosis (p=0.01 and p=0.03, respectively) and pancreatitis (p=0.02). The association of SNPs in MYBBP1A, SPEF2 and IL16 geneswith pancreatitis was replicated in the validation cohort (p ≤0.05) as well as in combined cohort (p=0.0003, p=0.008 and p=0.02, respectively). The synergistic effect of combining risk loci had the highest power to predict the development of pancreatitis in both cohorts and was further potentiated in the combined cohort (p=1×10-8). The present work demonstrates that using WES data is a successful “hypothesis-free” strategy for identifying significant genetic markers modulating the effect of the treatment in childhood ALL.
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Affiliation(s)
- Rachid Abaji
- Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC, Canada.,Department of Pharmacology, University of Montreal, Montreal, QC, Canada
| | - Vincent Gagné
- Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC, Canada
| | - Chang Jiang Xu
- Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC, Canada
| | | | - Francesco Ceppi
- Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC, Canada
| | - Caroline Laverdière
- Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC, Canada.,Department of Pediatrics, University of Montreal, Montreal, QC, Canada
| | - Jean-Marie Leclerc
- Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC, Canada.,Department of Pediatrics, University of Montreal, Montreal, QC, Canada
| | - Stephen E Sallan
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Hematology/Oncology, Children's Hospital, Boston, MA, USA
| | - Donna Neuberg
- Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Jeffery L Kutok
- Department of Pathology, Brigham and Women's Hospital, Boston, MA, USA
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, USA.,Division of Hematology/Oncology, Children's Hospital, Boston, MA, USA
| | - Daniel Sinnett
- Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC, Canada.,Department of Pediatrics, University of Montreal, Montreal, QC, Canada
| | - Maja Krajinovic
- Research Center, Centre Hospitalier Universitaire Sainte-Justine, Montreal, QC, Canada.,Department of Pediatrics, University of Montreal, Montreal, QC, Canada.,Department of Pharmacology, University of Montreal, Montreal, QC, Canada
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10
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Mehanna P, Gagné V, Lajoie M, Spinella JF, St-Onge P, Sinnett D, Brukner I, Krajinovic M. Characterization of the microDNA through the response to chemotherapeutics in lymphoblastoid cell lines. PLoS One 2017; 12:e0184365. [PMID: 28877255 PMCID: PMC5587290 DOI: 10.1371/journal.pone.0184365] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2017] [Accepted: 08/22/2017] [Indexed: 12/18/2022] Open
Abstract
Recently, a new class of extrachromosomal circular DNA, called microDNA, was identified. They are on average 100 to 400 bp long and are derived from unique non-repetitive genomic regions with high gene density. MicroDNAs are thought to arise from DNA breaks associated with RNA metabolism or replication slippage. Given the paucity of information on this entirely novel phenomenon, we aimed to get an additional insight into microDNA features by performing the microDNA analysis in 20 independent human lymphoblastoid cell lines (LCLs) prior and after treatment with chemotherapeutic drugs. The results showed non-random genesis of microDNA clusters from the active regions of the genome. The size periodicity of 190 bp was observed, which matches DNA fragmentation typical for apoptotic cells. The chemotherapeutic drug-induced apoptosis of LCLs increased both number and size of clusters further suggesting that part of microDNAs could result from the programmed cell death. Interestingly, proportion of identified microDNA sequences has common loci of origin when compared between cell line experiments. While compatible with the original observation that microDNAs originate from a normal physiological process, obtained results imply complementary source of its production. Furthermore, non-random genesis of microDNAs depicted by redundancy between samples makes these entities possible candidates for new biomarker generation.
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Affiliation(s)
- Pamela Mehanna
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | - Vincent Gagné
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | - Mathieu Lajoie
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | | | - Pascal St-Onge
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada
| | - Ivan Brukner
- Molecular Diagnostics Laboratory, Jewish General Hospital, McGill University, Montreal, Montreal, Qc, Canada
| | - Maja Krajinovic
- CHU Sainte-Justine Research Center, University of Montreal, Montreal, Qc, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada
- Department of Pharmacology and Physiology, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada
- * E-mail:
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11
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Neveu B, Spinella JF, Richer C, Lagacé K, Cassart P, Lajoie M, Jananji S, Drouin S, Healy J, Hickson GRX, Sinnett D. CLIC5: a novel ETV6 target gene in childhood acute lymphoblastic leukemia. Haematologica 2016; 101:1534-1543. [PMID: 27540136 PMCID: PMC5479611 DOI: 10.3324/haematol.2016.149740] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [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: 05/19/2016] [Accepted: 08/11/2016] [Indexed: 01/13/2023] Open
Abstract
The most common rearrangement in childhood precursor B-cell acute lymphoblastic leukemia is the t(12;21)(p13;q22) translocation resulting in the ETV6-AML1 fusion gene. A frequent concomitant event is the loss of the residual ETV6 allele suggesting a critical role for the ETV6 transcriptional repressor in the etiology of this cancer. However, the precise mechanism through which loss of functional ETV6 contributes to disease pathogenesis is still unclear. To investigate the impact of ETV6 loss on the transcriptional network and to identify new transcriptional targets of ETV6, we used whole transcriptome analysis of both pre-B leukemic cell lines and patients combined with chromatin immunoprecipitation. Using this integrative approach, we identified 4 novel direct ETV6 target genes: CLIC5, BIRC7, ANGPTL2 and WBP1L To further evaluate the role of chloride intracellular channel protein CLIC5 in leukemogenesis, we generated cell lines overexpressing CLIC5 and demonstrated an increased resistance to hydrogen peroxide-induced apoptosis. We further described the implications of CLIC5's ion channel activity in lysosomal-mediated cell death, possibly by modulating the function of the transferrin receptor with which it colocalizes intracellularly. For the first time, we showed that loss of ETV6 leads to significant overexpression of CLIC5, which in turn leads to decreased lysosome-mediated apoptosis. Our data suggest that heightened CLIC5 activity could promote a permissive environment for oxidative stress-induced DNA damage accumulation, and thereby contribute to leukemogenesis.
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Affiliation(s)
- Benjamin Neveu
- CHU Sainte-Justine Research Center, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, Canada
| | - Jean-François Spinella
- CHU Sainte-Justine Research Center, Montreal, Canada
- Molecular biology program, Faculty of Medicine, University of Montreal, Montreal, Canada
| | | | - Karine Lagacé
- CHU Sainte-Justine Research Center, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, Canada
| | | | | | | | - Simon Drouin
- CHU Sainte-Justine Research Center, Montreal, Canada
| | - Jasmine Healy
- CHU Sainte-Justine Research Center, Montreal, Canada
| | - Gilles R X Hickson
- CHU Sainte-Justine Research Center, Montreal, Canada
- Department of Pathology and Cellular Biology, Faculty of Medicine, University of Montreal, Montreal, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine Research Center, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Canada
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12
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Spinella JF, Mehanna P, Vidal R, Saillour V, Cassart P, Richer C, Ouimet M, Healy J, Sinnett D. SNooPer: a machine learning-based method for somatic variant identification from low-pass next-generation sequencing. BMC Genomics 2016; 17:912. [PMID: 27842494 PMCID: PMC5109690 DOI: 10.1186/s12864-016-3281-2] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [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: 05/26/2016] [Accepted: 11/09/2016] [Indexed: 12/31/2022] Open
Abstract
Background Next-generation sequencing (NGS) allows unbiased, in-depth interrogation of cancer genomes. Many somatic variant callers have been developed yet accurate ascertainment of somatic variants remains a considerable challenge as evidenced by the varying mutation call rates and low concordance among callers. Statistical model-based algorithms that are currently available perform well under ideal scenarios, such as high sequencing depth, homogeneous tumor samples, high somatic variant allele frequency (VAF), but show limited performance with sub-optimal data such as low-pass whole-exome/genome sequencing data. While the goal of any cancer sequencing project is to identify a relevant, and limited, set of somatic variants for further sequence/functional validation, the inherently complex nature of cancer genomes combined with technical issues directly related to sequencing and alignment can affect either the specificity and/or sensitivity of most callers. Results For these reasons, we developed SNooPer, a versatile machine learning approach that uses Random Forest classification models to accurately call somatic variants in low-depth sequencing data. SNooPer uses a subset of variant positions from the sequencing output for which the class, true variation or sequencing error, is known to train the data-specific model. Here, using a real dataset of 40 childhood acute lymphoblastic leukemia patients, we show how the SNooPer algorithm is not affected by low coverage or low VAFs, and can be used to reduce overall sequencing costs while maintaining high specificity and sensitivity to somatic variant calling. When compared to three benchmarked somatic callers, SNooPer demonstrated the best overall performance. Conclusions While the goal of any cancer sequencing project is to identify a relevant, and limited, set of somatic variants for further sequence/functional validation, the inherently complex nature of cancer genomes combined with technical issues directly related to sequencing and alignment can affect either the specificity and/or sensitivity of most callers. The flexibility of SNooPer’s random forest protects against technical bias and systematic errors, and is appealing in that it does not rely on user-defined parameters. The code and user guide can be downloaded at https://sourceforge.net/projects/snooper/. Electronic supplementary material The online version of this article (doi:10.1186/s12864-016-3281-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
| | - Pamela Mehanna
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Ramon Vidal
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Virginie Saillour
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Pauline Cassart
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Chantal Richer
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Manon Ouimet
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Jasmine Healy
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada. .,Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada. .,Division of Hematology-Oncology, CHU Sainte-Justine Research Center, 3175 Côte Sainte-Catherine, Montreal, QC, H3T 1C5, Canada.
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13
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Spinella JF, Cassart P, Richer C, Saillour V, Ouimet M, Langlois S, St-Onge P, Sontag T, Healy J, Minden MD, Sinnett D. Genomic characterization of pediatric T-cell acute lymphoblastic leukemia reveals novel recurrent driver mutations. Oncotarget 2016; 7:65485-65503. [PMID: 27602765 PMCID: PMC5323170 DOI: 10.18632/oncotarget.11796] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Accepted: 08/24/2016] [Indexed: 11/25/2022] Open
Abstract
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with variable prognosis. It represents 15% of diagnosed pediatric ALL cases and has a threefold higher incidence among males. Many recurrent alterations have been identified and help define molecular subgroups of T-ALL, however the full range of events involved in driving transformation remain to be defined. Using an integrative approach combining genomic and transcriptomic data, we molecularly characterized 30 pediatric T-ALLs and identified common recurrent T-ALL targets such as FBXW7, JAK1, JAK3, PHF6, KDM6A and NOTCH1 as well as novel candidate T-ALL driver mutations including the p.R35L missense mutation in splicesome factor U2AF1 found in 3 patients and loss of function mutations in the X-linked tumor suppressor genes MED12 (frameshit mutation p.V167fs, splice site mutation g.chrX:70339329T>C, missense mutation p.R1989H) and USP9X (nonsense mutation p.Q117*). In vitro functional studies further supported the putative role of these novel T-ALL genes in driving transformation. U2AF1 p.R35L was shown to induce aberrant splicing of downstream target genes, and shRNA knockdown of MED12 and USP9X was shown to confer resistance to apoptosis following T-ALL relevant chemotherapy drug treatment in Jurkat leukemia cells. Interestingly, nearly 60% of novel candidate driver events were identified among immature T-ALL cases, highlighting the underlying genomic complexity of pediatric T-ALL, and the need for larger integrative studies to decipher the mechanisms that contribute to its various subtypes and provide opportunities to refine patient stratification and treatment.
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Affiliation(s)
| | - Pauline Cassart
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Chantal Richer
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Virginie Saillour
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Manon Ouimet
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Sylvie Langlois
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Pascal St-Onge
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Thomas Sontag
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Jasmine Healy
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
| | - Mark D. Minden
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine Research Center, Université de Montréal, Montreal, QC, Canada
- Department of Pediatrics, Faculty of Medicine, Université de Montréal, Montreal, QC, Canada
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14
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Spinella JF, Cassart P, Garnier N, Rousseau P, Drullion C, Richer C, Ouimet M, Saillour V, Healy J, Autexier C, Sinnett D. A novel somatic mutation in ACD induces telomere lengthening and apoptosis resistance in leukemia cells. BMC Cancer 2015; 15:621. [PMID: 26345285 PMCID: PMC4562123 DOI: 10.1186/s12885-015-1639-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [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: 12/22/2014] [Accepted: 09/01/2015] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND The identification of oncogenic driver mutations has largely relied on the assumption that genes that exhibit more mutations than expected by chance are more likely to play an active role in tumorigenesis. Major cancer sequencing initiatives have therefore focused on recurrent mutations that are more likely to be drivers. However, in specific genetic contexts, low frequency mutations may also be capable of participating in oncogenic processes. Reliable strategies for identifying these rare or even patient-specific (private) mutations are needed in order to elucidate more personalized approaches to cancer diagnosis and treatment. METHODS Here we performed whole-exome sequencing on three cases of childhood pre-B acute lymphoblastic leukemia (cALL), representing three cytogenetically-defined subgroups (high hyperdiploid, t(12;21) translocation, and cytogenetically normal). We applied a data reduction strategy to identify both common and rare/private somatic events with high functional potential. Top-ranked candidate mutations were subsequently validated at high sequencing depth on an independent platform and in vitro expression assays were performed to evaluate the impact of identified mutations on cell growth and survival. RESULTS We identified 6 putatively damaging non-synonymous somatic mutations among the three cALL patients. Three of these mutations were well-characterized common cALL mutations involved in constitutive activation of the mitogen-activated protein kinase pathway (FLT3 p.D835Y, NRAS p.G13D, BRAF p.G466A). The remaining three patient-specific mutations (ACD p.G223V, DOT1L p.V114F, HCFC1 p.Y103H) were novel mutations previously undescribed in public cancer databases. Cytotoxicity assays demonstrated a protective effect of the ACD p.G223V mutation against apoptosis in leukemia cells. ACD plays a key role in protecting telomeres and recruiting telomerase. Using a telomere restriction fragment assay, we also showed that this novel mutation in ACD leads to increased telomere length in leukemia cells. CONCLUSION This study identified ACD as a novel gene involved in cALL and points to a functional role for ACD in enhancing leukemia cell survival. These results highlight the importance of rare/private somatic mutations in understanding cALL etiology, even within well-characterized molecular subgroups.
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Affiliation(s)
- Jean-François Spinella
- Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, H3T 1C5, Montréal, Québec, Canada.
| | - Pauline Cassart
- Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, H3T 1C5, Montréal, Québec, Canada.
| | - Nicolas Garnier
- Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, H3T 1C5, Montréal, Québec, Canada.
| | | | - Claire Drullion
- Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, H3T 1C5, Montréal, Québec, Canada.
| | - Chantal Richer
- Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, H3T 1C5, Montréal, Québec, Canada.
| | - Manon Ouimet
- Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, H3T 1C5, Montréal, Québec, Canada.
| | - Virginie Saillour
- Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, H3T 1C5, Montréal, Québec, Canada.
| | - Jasmine Healy
- Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, H3T 1C5, Montréal, Québec, Canada.
| | - Chantal Autexier
- Lady Davis Institute Jewish General Hospital, Montreal, Qc, Canada. .,Departments of Anatomy, Cell Biology and Medicine, McGill University, Montreal, Qc, Canada.
| | - Daniel Sinnett
- Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, H3T 1C5, Montréal, Québec, Canada. .,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada.
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15
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Spinella JF, Healy J, Saillour V, Richer C, Cassart P, Ouimet M, Sinnett D. Whole-exome sequencing of a rare case of familial childhood acute lymphoblastic leukemia reveals putative predisposing mutations in Fanconi anemia genes. BMC Cancer 2015. [PMID: 26201965 PMCID: PMC4512039 DOI: 10.1186/s12885-015-1549-6] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Acute lymphoblastic leukemia (ALL) is the most common pediatric cancer. While the multi-step model of pediatric leukemogenesis suggests interplay between constitutional and somatic genomes, the role of inherited genetic variability remains largely undescribed. Nonsyndromic familial ALL, although extremely rare, provides the ideal setting to study inherited contributions to ALL. Toward this goal, we sequenced the exomes of a childhood ALL family consisting of mother, father and two non-twinned siblings diagnosed with concordant pre-B hyperdiploid ALL and previously shown to have inherited a rare form of PRDM9, a histone H3 methyltransferase involved in crossing-over at recombination hotspots and Holliday junctions. We postulated that inheritance of additional rare disadvantaging variants in predisposing cancer genes could affect genomic stability and lead to increased risk of hyperdiploid ALL within this family. METHODS Whole exomes were captured using Agilent's SureSelect kit and sequenced on the Life Technologies SOLiD System. We applied a data reduction strategy to identify candidate variants shared by both affected siblings. Under a recessive disease model, we focused on rare non-synonymous or frame-shift variants in leukemia predisposing pathways. RESULTS Though the family was nonsyndromic, we identified a combination of rare variants in Fanconi anemia (FA) genes FANCP/SLX4 (compound heterozygote - rs137976282/rs79842542) and FANCA (rs61753269) and a rare homozygous variant in the Holliday junction resolvase GEN1 (rs16981869). These variants, predicted to affect protein function, were previously identified in familial breast cancer cases. Based on our in-house database of 369 childhood ALL exomes, the sibs were the only patients to carry this particularly rare combination and only a single hyperdiploid patient was heterozygote at both FANCP/SLX4 positions, while no FANCA variant allele carriers were identified. FANCA is the most commonly mutated gene in FA and is essential for resolving DNA interstrand cross-links during replication. FANCP/SLX4 and GEN1 are involved in the cleavage of Holliday junctions and their mutated forms, in combination with the rare allele of PRDM9, could alter Holliday junction resolution leading to nondisjunction of chromosomes and segregation defects. CONCLUSION Taken together, these results suggest that concomitant inheritance of rare variants in FANCA, FANCP/SLX4 and GEN1 on the specific genetic background of this familial case, could lead to increased genomic instability, hematopoietic dysfunction, and higher risk of childhood leukemia.
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Affiliation(s)
| | - Jasmine Healy
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada.
| | - Virginie Saillour
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada.
| | - Chantal Richer
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada.
| | - Pauline Cassart
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada.
| | - Manon Ouimet
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada.
| | - Daniel Sinnett
- Sainte-Justine UHC Research Center, University of Montreal, Montreal, Qc, Canada. .,Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada. .,Division of Hematology-Oncology, Sainte-Justine UHC Research Center, 3175 Côte Ste-Catherine, Montréal (Québec), H3T 1C5, Canada.
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16
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Casals F, Hodgkinson A, Hussin J, Idaghdour Y, Bruat V, de Maillard T, Grenier JC, Gbeha E, Hamdan FF, Girard S, Spinella JF, Larivière M, Saillour V, Healy J, Fernández I, Sinnett D, Michaud JL, Rouleau GA, Haddad E, Le Deist F, Awadalla P. Whole-exome sequencing reveals a rapid change in the frequency of rare functional variants in a founding population of humans. PLoS Genet 2013; 9:e1003815. [PMID: 24086152 PMCID: PMC3784517 DOI: 10.1371/journal.pgen.1003815] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2013] [Accepted: 08/08/2013] [Indexed: 11/18/2022] Open
Abstract
Whole-exome or gene targeted resequencing in hundreds to thousands of individuals has shown that the majority of genetic variants are at low frequency in human populations. Rare variants are enriched for functional mutations and are expected to explain an important fraction of the genetic etiology of human disease, therefore having a potential medical interest. In this work, we analyze the whole-exome sequences of French-Canadian individuals, a founder population with a unique demographic history that includes an original population bottleneck less than 20 generations ago, followed by a demographic explosion, and the whole exomes of French individuals sampled from France. We show that in less than 20 generations of genetic isolation from the French population, the genetic pool of French-Canadians shows reduced levels of diversity, higher homozygosity, and an excess of rare variants with low variant sharing with Europeans. Furthermore, the French-Canadian population contains a larger proportion of putatively damaging functional variants, which could partially explain the increased incidence of genetic disease in the province. Our results highlight the impact of population demography on genetic fitness and the contribution of rare variants to the human genetic variation landscape, emphasizing the need for deep cataloguing of genetic variants by resequencing worldwide human populations in order to truly assess disease risk.
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Affiliation(s)
- Ferran Casals
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Alan Hodgkinson
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Julie Hussin
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Youssef Idaghdour
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Vanessa Bruat
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Thibault de Maillard
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Jean-Cristophe Grenier
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Elias Gbeha
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Fadi F. Hamdan
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Simon Girard
- Centre d'Excellence en Neuromique de l'Université de Montréal, Centre de Recherche du Centre Hospitalier de l'Université de Montréal, Montréal, Québec, Canada
| | - Jean-François Spinella
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Mathieu Larivière
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Virginie Saillour
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Jasmine Healy
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Isabel Fernández
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Microbiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Daniel Sinnett
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Pédiatrie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Jacques L. Michaud
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
| | - Guy A. Rouleau
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Médecine, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
- Montreal Neurological Institute and Hospital, McGill University, Montréal, Québec, Canada
| | - Elie Haddad
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Microbiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
- Département de Pédiatrie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Françoise Le Deist
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Microbiologie et Immunologie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
| | - Philip Awadalla
- Centre de Recherche du Centre Hospitalier Universitaire Sainte-Justine, Université de Montréal, Montréal, Québec, Canada
- Département de Pédiatrie, Faculté de Médecine, Université de Montréal, Montréal, Québec, Canada
- Department of Biochemistry, McGill University, Montréal, Québec, Canada
- * E-mail:
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17
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Busche S, Ge B, Vidal R, Spinella JF, Saillour V, Richer C, Healy J, Chen SH, Droit A, Sinnett D, Pastinen T. Integration of high-resolution methylome and transcriptome analyses to dissect epigenomic changes in childhood acute lymphoblastic leukemia. Cancer Res 2013; 73:4323-36. [PMID: 23722552 DOI: 10.1158/0008-5472.can-12-4367] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
B-cell precursor acute lymphoblastic leukemia (pre-B ALL) is the most common pediatric cancer. Although the genetic determinants underlying disease onset remain unclear, epigenetic modifications including DNA methylation are suggested to contribute significantly to leukemogenesis. Using the Illumina 450K array, we assessed DNA methylation in matched tumor-normal samples of 46 childhood patients with pre-B ALL, extending single CpG-site resolution analysis of the pre-B ALL methylome beyond CpG-islands (CGI). Unsupervised hierarchical clustering of CpG-site neighborhood, gene, or microRNA (miRNA) gene-associated methylation levels separated the tumor cohort according to major pre-B ALL subtypes, and methylation in CGIs, CGI shores, and in regions around the transcription start site was found to significantly correlate with transcript expression. Focusing on samples carrying the t(12;21) ETV6-RUNX1 fusion, we identified 119 subtype-specific high-confidence marker CpG-loci. Pathway analyses linked the CpG-loci-associated genes with hematopoiesis and cancer. Further integration with whole-transcriptome data showed the effects of methylation on expression of 17 potential drivers of leukemogenesis. Independent validation of array methylation and sequencing-derived transcript expression with Sequenom Epityper technology and real-time quantitative reverse transcriptase PCR, respectively, indicates more than 80% empirical accuracy of our genome-wide findings. In summary, genome-wide DNA methylation profiling enabled us to separate pre-B ALL according to major subtypes, to map epigenetic biomarkers specific for the t(12;21) subtype, and through a combined methylome and transcriptome approach to identify downstream effects on candidate drivers of leukemogenesis.
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Affiliation(s)
- Stephan Busche
- Department of Human Genetics, McGill University, Montréal, Canada
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18
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Abstract
The joint sequencing of related genomes has become an important means to discover rare variants. Normal-tumor genome pairs are routinely sequenced together to find somatic mutations and their associations with different cancers. Parental and sibling genomes reveal de novo germline mutations and inheritance patterns related to Mendelian diseases.Acute lymphoblastic leukemia (ALL) is the most common paediatric cancer and the leading cause of cancer-related death among children. With the aim of uncovering the full spectrum of germline and somatic genetic alterations in childhood ALL genomes, we conducted whole-exome re-sequencing on a unique cohort of over 120 exomes of childhood ALL quartets, each comprising a patient's tumor and matched-normal material, and DNA from both parents. We developed a general probabilistic model for such quartet sequencing reads mapped to the reference human genome. The model is used to infer joint genotypes at homologous loci across a normal-tumor genome pair and two parental genomes.We describe the algorithms and data structures for genotype inference, model parameter training. We implemented the methods in an open-source software package (QUADGT) that uses the standard file formats of the 1000 Genomes Project. Our method's utility is illustrated on quartets from the ALL cohort.
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Affiliation(s)
- Eric Bareke
- Department of Computer Science and Operations Research, University of Montréal, QC, Canada
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19
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Hussin J, Sinnett D, Casals F, Idaghdour Y, Bruat V, Saillour V, Healy J, Grenier JC, de Malliard T, Busche S, Spinella JF, Larivière M, Gibson G, Andersson A, Holmfeldt L, Ma J, Wei L, Zhang J, Andelfinger G, Downing JR, Mullighan CG, Awadalla P. Rare allelic forms of PRDM9 associated with childhood leukemogenesis. Genome Res 2012; 23:419-30. [PMID: 23222848 PMCID: PMC3589531 DOI: 10.1101/gr.144188.112] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [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: 01/22/2023]
Abstract
One of the most rapidly evolving genes in humans, PRDM9, is a key determinant of the distribution of meiotic recombination events. Mutations in this meiotic-specific gene have previously been associated with male infertility in humans and recent studies suggest that PRDM9 may be involved in pathological genomic rearrangements. In studying genomes from families with children affected by B-cell precursor acute lymphoblastic leukemia (B-ALL), we characterized meiotic recombination patterns within a family with two siblings having hyperdiploid childhood B-ALL and observed unusual localization of maternal recombination events. The mother of the family carries a rare PRDM9 allele, potentially explaining the unusual patterns found. From exomes sequenced in 44 additional parents of children affected with B-ALL, we discovered a substantial and significant excess of rare allelic forms of PRDM9. The rare PRDM9 alleles are transmitted to the affected children in half the cases; nonetheless there remains a significant excess of rare alleles among patients relative to controls. We successfully replicated this latter observation in an independent cohort of 50 children with B-ALL, where we found an excess of rare PRDM9 alleles in aneuploid and infant B-ALL patients. PRDM9 variability in humans is thought to influence genomic instability, and these data support a potential role for PRDM9 variation in risk of acquiring aneuploidies or genomic rearrangements associated with childhood leukemogenesis.
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Affiliation(s)
- Julie Hussin
- Department of Biochemistry, Faculty of Medicine, University of Montreal, Montreal H3C 3J7, Canada
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