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Gutierrez-Camino A, Richer C, Ouimet M, Fuchs C, Langlois S, Khater F, Caron M, Beaulieu P, St-Onge P, Bataille AR, Sinnett D. Characterisation of FLT3 alterations in childhood acute lymphoblastic leukaemia. Br J Cancer 2024; 130:317-326. [PMID: 38049555 PMCID: PMC10803556 DOI: 10.1038/s41416-023-02511-8] [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: 01/03/2023] [Revised: 11/10/2023] [Accepted: 11/15/2023] [Indexed: 12/06/2023] Open
Abstract
BACKGROUND Alterations of FLT3 are among the most common driver events in acute leukaemia with important clinical implications, since it allows patient classification into prognostic groups and the possibility of personalising therapy thanks to the availability of FLT3 inhibitors. Most of the knowledge on FLT3 implications comes from the study of acute myeloid leukaemia and so far, few studies have been performed in other leukaemias. METHODS A comprehensive genomic (DNA-seq in 267 patients) and transcriptomic (RNA-seq in 160 patients) analysis of FLT3 in 342 childhood acute lymphoblastic leukaemia (ALL) patients was performed. Mutations were functionally characterised by in vitro experiments. RESULTS Point mutations (PM) and internal tandem duplications (ITD) were detected in 4.3% and 2.7% of the patients, respectively. A new activating mutation of the TKD, G846D, conferred oncogenic properties and sorafenib resistance. Moreover, a novel alteration involving the circularisation of read-through transcripts (rt-circRNAs) was observed in 10% of the cases. Patients presenting FLT3 alterations exhibited higher levels of the receptor. In addition, patients with ZNF384- and MLL/KMT2A-rearranged ALL, as well as hyperdiploid subtype, overexpressed FLT3. DISCUSSION Our results suggest that specific ALL subgroups may also benefit from a deeper understanding of the biology of FLT3 alterations and their clinical implications.
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Affiliation(s)
- Angela Gutierrez-Camino
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Chantal Richer
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Manon Ouimet
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Claire Fuchs
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Sylvie Langlois
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Fida Khater
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Maxime Caron
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Patrick Beaulieu
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Pascal St-Onge
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Alain R Bataille
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Daniel Sinnett
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, Quebec, Canada.
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Quebec, Canada.
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Gutierrez-Camino A, Caron M, Richer C, Fuchs C, Illarregi U, Poncelet L, St-Onge P, Bataille AR, Tremblay-Dauphinais P, Lopez-Lopez E, Camos M, Ramirez-Orellana M, Astigarraga I, Lécuyer É, Bourque G, Martin-Guerrero I, Sinnett D. CircRNAome of Childhood Acute Lymphoblastic Leukemia: Deciphering Subtype-Specific Expression Profiles and Involvement in TCF3::PBX1 ALL. Int J Mol Sci 2024; 25:1477. [PMID: 38338754 PMCID: PMC10855129 DOI: 10.3390/ijms25031477] [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: 11/10/2023] [Revised: 01/15/2024] [Accepted: 01/18/2024] [Indexed: 02/12/2024] Open
Abstract
Childhood B-cell acute lymphoblastic leukemia (B-ALL) is a heterogeneous disease comprising multiple molecular subgroups with subtype-specific expression profiles. Recently, a new type of ncRNA, termed circular RNA (circRNA), has emerged as a promising biomarker in cancer, but little is known about their role in childhood B-ALL. Here, through RNA-seq analysis in 105 childhood B-ALL patients comprising six genetic subtypes and seven B-cell controls from two independent cohorts we demonstrated that circRNAs properly stratified B-ALL subtypes. By differential expression analysis of each subtype vs. controls, 156 overexpressed and 134 underexpressed circRNAs were identified consistently in at least one subtype, most of them with subtype-specific expression. TCF3::PBX1 subtype was the one with the highest number of unique and overexpressed circRNAs, and the circRNA signature could effectively discriminate new patients with TCF3::PBX1 subtype from others. Our results indicated that NUDT21, an RNA-binding protein (RBP) involved in circRNA biogenesis, may contribute to this circRNA enrichment in TCF3::PBX1 ALL. Further functional characterization using the CRISPR-Cas13d system demonstrated that circBARD1, overexpressed in TCF3::PBX1 patients and regulated by NUDT21, might be involved in leukemogenesis through the activation of p38 via hsa-miR-153-5p. Our results suggest that circRNAs could play a role in the pathogenesis of childhood B-ALL.
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Affiliation(s)
- Angela Gutierrez-Camino
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Maxime Caron
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada;
| | - Chantal Richer
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Claire Fuchs
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Unai Illarregi
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (U.I.); (I.M.-G.)
| | - Lucas Poncelet
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Pascal St-Onge
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Alain R. Bataille
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Pascal Tremblay-Dauphinais
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
| | - Elixabet Lopez-Lopez
- Department of Biochemistry and Molecular Biology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain;
- Pediatric Oncology Group, Biobizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Mireia Camos
- Hematology Laboratory, Sant Joan de Déu Research Institute, Esplugues de Llobregat, 08950 Barcelona, Spain;
| | - Manuel Ramirez-Orellana
- Department of Pediatric Hematology and Oncology, Niño Jesús University Hospital, 28009 Madrid, Spain;
| | - Itziar Astigarraga
- Pediatric Oncology Group, Biobizkaia Health Research Institute, 48903 Barakaldo, Spain;
- Department of Pediatrics, Cruces University Hospital, 48903 Barakaldo, Spain
| | - Éric Lécuyer
- Institut de Recherches Cliniques de Montréal (IRCM), Montreal, QC H2W 1R7, Canada;
- Département de Biochimie et Médecine Moléculaire, Université de Montréal, Montreal, QC H3C 3J7, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC H3A 0G4, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC H3A 0G4, Canada;
| | - Idoia Martin-Guerrero
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), 48940 Leioa, Spain; (U.I.); (I.M.-G.)
- Pediatric Oncology Group, Biobizkaia Health Research Institute, 48903 Barakaldo, Spain;
| | - Daniel Sinnett
- Division of Hematology-Oncology, CHU Sainte-Justine Research Center, Montreal, QC H3T 1C5, Canada; (A.G.-C.); (M.C.); (C.R.); (C.F.); (L.P.); (P.S.-O.); (A.R.B.); (P.T.-D.)
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
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Santos P, Chakraborty N, Salz T, Curry M, Vicioso NL, Mathis NJ, Caron M, Ostroff J, Guttman D, Salner AL, Panoff JE, McIntosh AF, Pfister DG, Yang JT, Snyderman AL, Gillespie EF. Implementation Outcomes of Strategies to Promote Short-Course Radiation for Nonspine Bone Metastases in an Academic-Community Partnership: Survey Results from the ALIGNMENT Trial. Int J Radiat Oncol Biol Phys 2023; 117:S124-S125. [PMID: 37784321 DOI: 10.1016/j.ijrobp.2023.06.466] [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: 10/04/2023]
Abstract
PURPOSE/OBJECTIVE(S) Local treatment of nonspine bone metastases has become increasingly complex, resulting in physician practice variability nationwide. The purpose of this study was to assess physician perceptions of 3 implementation strategies to promote adoption of short course radiotherapy (RT) for nonspine bone metastases. MATERIALS/METHODS ALIGNMENT ("Alliance Group for Bone Metastasis") was a multi-institutional stepped wedge cluster randomized implementation trial testing strategies to increase use of ≤5 fractions for nonspine bone metastases conducted across 3 clinical sites in an academic-community partnership. Strategies included a) multidisciplinary consensus guidelines, b) e-Consults, an email-based consultation platform, and c) personalized audit and feedback (A&F) reports with peer comparison. Using the Proctor et al. framework and validated questions from Weiner et al., physician surveys were used to assess each strategy's usefulness, acceptability (i.e., "I welcome [strategy]"), appropriateness (i.e., "[strategy] seems like a good match"), and feasibility (i.e., "[strategy] seems implementable" or "easy to use"). Survey responses were anonymized, so Fisher's Exact test was used to compare proportions with significance set at p<0.05. RESULTS Overall, 29 of 38 and 30 of 38 physicians participated in the pre- and post-implementation surveys, respectively, with 80% completing both. Pre-implementation, guidelines was most often ranked 1st in terms of usefulness (61%), followed by eConsults (38%) and A&F (3%). Post-implementation, guidelines and eConsults had the most and least favorable acceptability, appropriateness, and feasibility scores, respectively (Table), with 77% of physicians being likely to recommend the guidelines to other oncologists. In contrast, while 43% of physicians reported having at least 1 difficult clinical question regarding bone metastases during the study, only 33% of physicians preferred eConsults, while 50% preferred reaching out to a friend/colleague. Lastly, although A&F had the lowest perceived usefulness pre-implementation, A&F had the greatest increase in acceptability (72%→90%; p = 0.10), appropriateness (66%→90%; p = 0.03) feasibility ("implementable": 59%→93%, p = 0.002; "easy to use": 45%→93%, p<0.001). CONCLUSION In this multicenter trial, all strategies were acceptable, appropriate, and feasible, with guidelines and A&F showing the most favorable outcomes post-implementation. While guidelines were assessed as the most useful, A&F had significant increases in appropriateness and feasibility.
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Affiliation(s)
- P Santos
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY; Harvard T.H. Chan School of Public Health, Boston, MA
| | - N Chakraborty
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - T Salz
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - M Curry
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - N Ledesma Vicioso
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - N J Mathis
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - M Caron
- Strategic Partnerships, Memorial Sloan Kettering Cancer Center, New York, NY
| | - J Ostroff
- Department of Psychiatry and Behavioral Sciences, Memorial Sloan Kettering Cancer Center, New York, NY
| | - D Guttman
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - A L Salner
- Hartford HealthCare Cancer Institute, Hartford, CT
| | - J E Panoff
- Department of Radiation Oncology, Miami Cancer Institute, Baptist Health South Florida, Miami, FL
| | - A F McIntosh
- Allentown Radiation Oncology Associates, Allentown, PA, United States
| | - D G Pfister
- Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - J T Yang
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY; Department of Radiation Oncology, University of Washington, Seattle, WA
| | - A Lipitz Snyderman
- Department of Epidemiology and Biostatistics, Memorial Sloan Kettering Cancer Center, New York, NY
| | - E F Gillespie
- Department of Radiation Oncology, Memorial Sloan Kettering Cancer Center, New York, NY; Department of Radiation Oncology, University of Washington, Seattle, WA
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4
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Beaudry A, Jacques-Ricard S, Darracq A, Sgarioto N, Garcia A, García TR, Lemieux W, Béland K, Haddad E, Cordeiro P, Duval M, McGraw S, Richer C, Caron M, Marois F, St-Onge P, Sinnett D, Banquy X, Raynal NJM. Repurposing disulfiram, an alcohol-abuse drug, in neuroblastoma causes KAT2A downregulation and in vivo activity with a water/oil emulsion. Sci Rep 2023; 13:16443. [PMID: 37777587 PMCID: PMC10543387 DOI: 10.1038/s41598-023-43219-2] [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: 03/09/2023] [Accepted: 09/21/2023] [Indexed: 10/02/2023] Open
Abstract
Neuroblastoma, the most common type of pediatric extracranial solid tumor, causes 10% of childhood cancer deaths. Despite intensive multimodal treatment, the outcomes of high-risk neuroblastoma remain poor. We urgently need to develop new therapies with safe long-term toxicity profiles for rapid testing in clinical trials. Drug repurposing is a promising approach to meet these needs. Here, we investigated disulfiram, a safe and successful chronic alcoholism treatment with known anticancer and epigenetic effects. Disulfiram efficiently induced cell cycle arrest and decreased the viability of six human neuroblastoma cell lines at half-maximal inhibitory concentrations up to 20 times lower than its peak clinical plasma level in patients treated for chronic alcoholism. Disulfiram shifted neuroblastoma transcriptome, decreasing MYCN levels and activating neuronal differentiation. Consistently, disulfiram significantly reduced the protein level of lysine acetyltransferase 2A (KAT2A), drastically reducing acetylation of its target residues on histone H3. To investigate disulfiram's anticancer effects in an in vivo model of high-risk neuroblastoma, we developed a disulfiram-loaded emulsion to deliver the highly liposoluble drug. Treatment with the emulsion significantly delayed neuroblastoma progression in mice. These results identify KAT2A as a novel target of disulfiram, which directly impacts neuroblastoma epigenetics and is a promising candidate for repurposing to treat pediatric neuroblastoma.
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Affiliation(s)
- Annie Beaudry
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Simon Jacques-Ricard
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
- Département de Pharmacologie et de Physiologie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Anaïs Darracq
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
- Département de Pharmacologie et de Physiologie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada
| | - Nicolas Sgarioto
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Araceli Garcia
- Faculté de Pharmacie, Université de Montréal, Montreal, QC, Canada
| | | | - William Lemieux
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Kathie Béland
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Elie Haddad
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Paulo Cordeiro
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Michel Duval
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Serge McGraw
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Chantal Richer
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Maxime Caron
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - François Marois
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Pascal St-Onge
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
| | - Daniel Sinnett
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada
- Département de Pédiatrie, Université de Montréal, Montreal, QC, Canada
| | - Xavier Banquy
- Faculté de Pharmacie, Université de Montréal, Montreal, QC, Canada
| | - Noël J-M Raynal
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montreal, QC, H3T 1C5, Canada.
- Département de Pharmacologie et de Physiologie, Faculté de Médecine, Université de Montréal, Montreal, QC, Canada.
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5
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Tsai HK, Gogakos T, Lip V, Tsai JM, Li YD, Fisch AS, Weiss J, Yang W, Grimmett L, DiToro D, Schaefer EJ, Lindsley RC, Tran TH, Caron M, Langlois S, Sinnett D, Pikman Y, Nardi V, Kim AS, Silverman LB, Harris MH. Outlier Expression of Isoforms by Targeted or Total RNA Sequencing Identifies Clinically Significant Genomic Variants in Hematolymphoid Tumors. J Mol Diagn 2023; 25:665-681. [PMID: 37419244 PMCID: PMC10488324 DOI: 10.1016/j.jmoldx.2023.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [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: 09/28/2022] [Revised: 04/14/2023] [Accepted: 06/01/2023] [Indexed: 07/09/2023] Open
Abstract
Recognition of aberrant gene isoforms due to DNA events can impact risk stratification and molecular classification of hematolymphoid tumors. In myelodysplastic syndromes, KMT2A partial tandem duplication (PTD) was one of the top adverse predictors in the International Prognostic Scoring System-Molecular study. In B-cell acute lymphoblastic leukemia (B-ALL), ERG isoforms have been proposed as markers of favorable-risk DUX4 rearrangements, whereas deletion-mediated IKZF1 isoforms are associated with adverse prognosis and have been extended to the high-risk IKZF1plus signature defined by codeletions, including PAX5. In this limited study, outlier expression of isoforms as markers of IKZF1 intragenic or 3' deletions, DUX4 rearrangements, or PAX5 intragenic deletions were 92.3% (48/52), 90% (9/10), or 100% (9/9) sensitive, respectively, and 98.7% (368/373), 100% (35/35), or 97.1% (102/105) specific, respectively, by targeted RNA sequencing, and 84.0% (21/25), 85.7% (6/7), or 81.8% (9/11) sensitive, respectively, and 98.2% (109/111), 98.4% (127/129), or 98.7% (78/79) specific, respectively, by total RNA sequencing. Comprehensive split-read analysis identified expressed DNA breakpoints, cryptic splice sites associated with IKZF1 3' deletions, PTD of IKZF1 exon 5 spanning N159Y in B-ALL with mutated IKZF1 N159Y, and truncated KMT2A-PTD isoforms. Outlier isoforms were also effective targeted RNA markers for PAX5 intragenic amplifications (B-ALL), KMT2A-PTD (myeloid malignant cancers), and rare NOTCH1 intragenic deletions (T-cell acute lymphoblastic leukemia). These findings support the use of outlier isoform analysis as a robust strategy for detecting clinically significant DNA events.
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Affiliation(s)
- Harrison K Tsai
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts; Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts.
| | - Tasos Gogakos
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Va Lip
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan M Tsai
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Yen-Der Li
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Adam S Fisch
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Jonathan Weiss
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Weiping Yang
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Leslie Grimmett
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Daniel DiToro
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Eva J Schaefer
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - R Coleman Lindsley
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Thai Hoa Tran
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada; Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Maxime Caron
- Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Sylvie Langlois
- Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Daniel Sinnett
- Division of Pediatric Hematology-Oncology, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada; Immune Diseases and Cancers Axis, Centre Hospitalier Universitaire Sainte-Justine, Montreal, Quebec, Canada
| | - Yana Pikman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Valentina Nardi
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, Massachusetts
| | - Annette S Kim
- Department of Pathology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Lewis B Silverman
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts; Division of Hematology/Oncology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts
| | - Marian H Harris
- Department of Pathology, Boston Children's Hospital, Harvard Medical School, Boston, Massachusetts.
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6
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Pelland-Marcotte MC, Rémy MM, Ma Y, Liu J, Jimenez-Cortes C, Sontag T, Caron M, Saint-Onge P, Langlois S, Joly-Beauparlant C, Sinnett D, Droit A, Tran TH, Santiago R. Abstract 3897: Ribosomal translational regulation is a potential mechanism for leukemia-related thrombo-embolic event in childhood acute lymphoblastic leukemia. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3897] [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
Introduction: Thrombo-embolic event (TE) is a frequent complication of childhood acute lymphoblastic leukemia (cALL) and is associated with reduced survival. Overexpression of podoplanin or coagulome genes and coagulation pathway activation have been identified in cancer-induced TE but the role of leukemia environment in TE occurrence has not been fully elucidated in ALL. We assessed whether leukemia gene expression (GE) signature at diagnosis was associated with TE development in cALL.
Methods: We included children aged 0-18 years old (y.o.), from two hospitals, with newly diagnosed ALL and available RNA sequencing data from bone marrow at diagnosis. The primary outcome was the occurrence of grade ≥2 TE during ALL therapy using the Ponte Di Legno Working Group classification. TEs were classified as early (ET) if they occurred within 6 weeks from treatment start, or late (LT) otherwise. We compared differential gene expression (DE) in children with and without TE, adjusted for age (<10 or ≥10 y.o.) and ALL type (T or B-ALL). A secondary analysis stratified children between ET, LT and no TE. Gene set enrichment analysis (GSEA) was performed on KEGG and gene ontology (GO) databases. DE with absolute fold change ≥2 and p-values <0.05 were considered significant.
Results: We included 80 patients (median age: 5 years [interquartile range, IQR: 3-11 years], 53% male, 83% precursor B-cell ALL) of whom 19 (23.8%) developed a TE (7 ET and 12 LT) at a median of 76 days (IQR: 31-133 days) following cancer diagnosis. Patients with TE were more likely to be ≥10 y.o., while other demographic and clinical characteristics were similar. No genes from the coagulome, podoplanin or Hallmark coagulation pathways were differentially expressed in children with and without TE. The KEGG Ribosome pathway was the most upregulated pathway in the group with TE (normalized enrichment score (NES) = 2.35, adjusted p-value= 0.012) and ET (NES = 2.63, adjusted p-value < 0.001). LT was not significantly associated with ribosome pathway dysregulation. Interestingly, prior reports identified functional enrichment in ribosomal pathway as a biomarker for venous TE. A heatmap classification for ribosomal genes revealed 3 distinct signatures: ribosomal downregulation, moderate and high ribosomal activation. High ribosomal activation profile was seen in 6/7 ET and 9/12 LT, corresponding to a positive and negative predictive value of 0.55 and 0.92 for TE, respectively.
Conclusion: TEs in cALL were not associated with dysregulation in coagulation pathways or podoplanin gene at the RNA level. However, ribosomal translational pathway was highly upregulated in the group with thrombosis, particularly with ET. Dysregulation of posttranscriptional machinery might explain the pro-thrombotic effect of leukemia environment in cALL and warrants further investigation including proteomic exploration.
Citation Format: Marie-Claude Pelland-Marcotte, Meredith Michelle Rémy, Yan Ma, Jessica Liu, Camille Jimenez-Cortes, Thomas Sontag, Maxime Caron, Pascal Saint-Onge, Sylvie Langlois, Charles Joly-Beauparlant, Daniel Sinnett, Arnaud Droit, Thai Hoa Tran, Raoul Santiago. Ribosomal translational regulation is a potential mechanism for leukemia-related thrombo-embolic event in childhood acute lymphoblastic leukemia [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 3897.
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Affiliation(s)
| | | | - Yan Ma
- 2Laval University, Quebec, Quebec, Canada
| | - Jessica Liu
- 3Sherbrooke University, Sherbrooke, Quebec, Canada
| | | | - Thomas Sontag
- 5Charles-Bruneau Cancer Center, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Maxime Caron
- 4Charles-Bruneau Cancer Center, CHU Sainte-Justine, Montréal, Quebec, Canada
| | - Pascal Saint-Onge
- 6Charles-Bruneau Cancer Center, CHU Sainte-Justine, Quebec, Quebec, Canada
| | - Sylvie Langlois
- 5Charles-Bruneau Cancer Center, CHU Sainte-Justine, Montreal, Quebec, Canada
| | | | - Daniel Sinnett
- 5Charles-Bruneau Cancer Center, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Arnaud Droit
- 7CHU of Quebec, Laval University, Quebec, Quebec, Canada
| | - Thai Hoa Tran
- 5Charles-Bruneau Cancer Center, CHU Sainte-Justine, Montreal, Quebec, Canada
| | - Raoul Santiago
- 1CHU of Quebec, Laval University - Charles Bruneau Cancer Center, Quebec, Quebec, Canada
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7
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Neveu B, Richer C, Cassart P, Caron M, Jimenez-Cortes C, St-Onge P, Fuchs C, Garnier N, Gobeil S, Sinnett D. Identification of new ETV6 modulators through a high-throughput functional screening. iScience 2022; 25:103858. [PMID: 35198911 PMCID: PMC8851229 DOI: 10.1016/j.isci.2022.103858] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Revised: 01/01/2022] [Accepted: 01/28/2022] [Indexed: 12/02/2022] Open
Abstract
ETV6 transcriptional activity is critical for proper blood cell development in the bone marrow. Despite the accumulating body of evidence linking ETV6 malfunction to hematological malignancies, its regulatory network remains unclear. To uncover genes that modulate ETV6 repressive transcriptional activity, we performed a specifically designed, unbiased genome-wide shRNA screen in pre-B acute lymphoblastic leukemia cells. Following an extensive validation process, we identified 13 shRNAs inducing overexpression of ETV6 transcriptional target genes. We showed that the silencing of AKIRIN1, COMMD9, DYRK4, JUNB, and SRP72 led to an abrogation of ETV6 repressive activity. We identified critical modulators of the ETV6 function which could participate in cellular transformation through the ETV6 transcriptional network. We develop a genome-wide shRNAs screen for ETV6 modulators The screen uncovered 13 novel putative ETV6 modulator genes The modulators demonstrated a broad impact on the ETV6 transcriptional network T-ALL cells results suggest modulators are conserved in other cellular contexts
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Affiliation(s)
- Benjamin Neveu
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Chantal Richer
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Pauline Cassart
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Maxime Caron
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Human Genetics, McGill University, Montréal, QC H3A 0C7, Canada
| | - Camille Jimenez-Cortes
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Molecular Biology Program, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Pascal St-Onge
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Claire Fuchs
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
| | - Nicolas Garnier
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
| | - Stéphane Gobeil
- CHU de Québec-Université Laval Research Center, Quebec City, QC G1V 4G2, Canada
- Department of Molecular Medicine, Faculty of Medicine, Université Laval, Quebec City, QC G1V 0A6, Canada
- Corresponding author
| | - Daniel Sinnett
- Sainte-Justine University Health Center Research Center, Montreal, QC H3T 1C5, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC H3C 3J7, Canada
- Corresponding author
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8
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Legault LM, Doiron K, Breton-Larrivée M, Langford-Avelar A, Lemieux A, Caron M, Jerome-Majewska LA, Sinnett D, McGraw S. Pre-implantation alcohol exposure induces lasting sex-specific DNA methylation programming errors in the developing forebrain. Clin Epigenetics 2021; 13:164. [PMID: 34425890 PMCID: PMC8381495 DOI: 10.1186/s13148-021-01151-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 08/11/2021] [Indexed: 12/26/2022] Open
Abstract
Background Prenatal alcohol exposure is recognized for altering DNA methylation profiles of brain cells during development, and to be part of the molecular basis underpinning Fetal Alcohol Spectrum Disorder (FASD) etiology. However, we have negligible information on the effects of alcohol exposure during pre-implantation, the early embryonic window marked with dynamic DNA methylation reprogramming, and on how this may rewire the brain developmental program. Results Using a pre-clinical in vivo mouse model, we show that a binge-like alcohol exposure during pre-implantation at the 8-cell stage leads to surge in morphological brain defects and adverse developmental outcomes during fetal life. Genome-wide DNA methylation analyses of fetal forebrains uncovered sex-specific alterations, including partial loss of DNA methylation maintenance at imprinting control regions, and abnormal de novo DNA methylation profiles in various biological pathways (e.g., neural/brain development). Conclusion These findings support that alcohol-induced DNA methylation programming deviations during pre-implantation could contribute to the manifestation of neurodevelopmental phenotypes associated with FASD. Supplementary Information The online version contains supplementary material available at 10.1186/s13148-021-01151-0.
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Affiliation(s)
- L M Legault
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - K Doiron
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - M Breton-Larrivée
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - A Langford-Avelar
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - A Lemieux
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - M Caron
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - L A Jerome-Majewska
- McGill University Health Centre Glen Site, 1001 Boulevard Décarie, Montréal, QC, H4A 3J1, Canada.,Department of Pediatrics, McGill University, 1001 Boulevard Décarie, Montréal, QC, H4A 3J1, Canada
| | - D Sinnett
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Department of Pediatrics, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada
| | - S McGraw
- CHU Sainte-Justine Research Center, 3175 Chemin de La Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada. .,Department of Biochemistry and Molecular Medicine, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada. .,Department of Obstetrics and Gynecology, Université de Montréal, 2900 Boulevard Edouard-Montpetit, Montréal, QC, H3T 1J4, Canada.
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9
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Dankner M, Maritan S, Zhuang R, Caron M, Priego N, Valiente M, Petrecca K, Siegel P. BSCI-10. Invasive growth of brain metastases is driven by cancer cell-pSTAT3+ reactive astrocyte crosstalk. Neurooncol Adv 2021. [PMCID: PMC8351176 DOI: 10.1093/noajnl/vdab071.009] [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: 11/22/2022] Open
Abstract
Background Brain metastases (BrM) with a highly invasive (HI) histological growth pattern are associated with poor prognosis compared to minimally invasive (MI) masses. Compared to MI lesions, HI BrM form greater contacts with cells in the peritumoral brain, particularly reactive astrocytes (RAs). RAs expressing phosphorylated STAT3 (pSTAT3+RAs) have been shown to promote BrM colonization. Here, we investigate the role of pSTAT3+RAs in promoting invasive growth of HI BrM. Methods We performed immunohistochemistry to identify pSTAT3+RAs in HI and MI human and patient-derived xenograft BrM. We assessed how pharmacological STAT3 inhibition or RA-specific STAT3 genetic ablation affected HI and MI BrM growth in vivo. scRNA-seq data generated from HI BrM astrocytes were integrated with published RA secretome data to identify STAT3 targets expressed by RAs that may drive invasion. Cancer cell invasion was modeled in vitro using a brain slice-tumor co-culture assay. Results HI BrM display increased pSTAT3-positivity within RAs when compared to MI lesions. Pharmacological STAT3 inhibition with Legasil (Silibinin) or genetic ablation 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 following STAT3 inhibition. Chi3L1 was identified as a STAT3 target expressed by RAs. Cancer cells treated with recombinant Chi3L1 showed greater invasion into brain slice cultures compared to untreated cells. Conclusions pSTAT3+RAs are over-represented in HI BrM, rendering HI BrM preferentially sensitive to STAT3 inhibition. pSTAT3+RAs functionally contribute to BrM invasion within the brain, in part through Chi3L1-mediated activity. This work identifies STAT3 and Chi3L1 as clinically relevant therapeutic targets in management of HI BrM.
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Affiliation(s)
- Matthew Dankner
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Sarah Maritan
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
| | - Rebecca Zhuang
- University of British Columbia, Faculty of Medicine, Vancouver, BC, Canada
| | - Maxime Caron
- McGill University Genome Centre, Department of Human Genetics, Montreal, QC, Canada
| | - Neibla Priego
- Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Manuel Valiente
- Spanish National Cancer Research Center (CNIO), Madrid, Spain
| | - Kevin Petrecca
- Montreal Neurological Institute-Hospital, Department of Neurology and Neurosurgery, Montreal, QC, Canada
| | - Peter Siegel
- Goodman Cancer Research Centre, McGill University, Montreal, QC, Canada
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10
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Huot M, Caron M, Richer C, Djibo R, Najmanovich R, St-Onge P, Sinnett D, Raynal NJM. Repurposing proscillaridin A in combination with decitabine against embryonal rhabdomyosarcoma RD cells. Cancer Chemother Pharmacol 2021; 88:845-856. [PMID: 34331108 DOI: 10.1007/s00280-021-04339-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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: 04/30/2021] [Accepted: 07/15/2021] [Indexed: 12/13/2022]
Abstract
PURPOSE Embryonal rhabdomyosarcoma (eRMS) is the most common type of rhabdomyosarcoma in children. eRMS is characterized by malignant skeletal muscle cells driven by hyperactivation of several oncogenic pathways including the MYC pathway. Targeting MYC in cancer has been extremely challenging. Recently, we have demonstrated that the heart failure drug, proscillaridin A, produced anticancer effects with specificity toward MYC expressing leukemia cells. We also reported that decitabine, a hypomethylating drug, synergizes with proscillaridin A in colon cancer cells. Here, we investigated whether proscillaridin A exhibits epigenetic and anticancer activity against eRMS RD cells, overexpressing MYC oncogene, and its combination with decitabine. METHODS We investigated the anticancer effects of proscillaridin A in eRMS RD cells in vitro. In response to drug treatment, we measured growth inhibition, cell cycle arrest, loss of clonogenicity and self-renewal capacity. We further evaluated the impact of proscillaridin A on MYC expression and its downstream transcriptomic effects by RNA sequencing. Then, we measured protein expression of epigenetic regulators and their associated chromatin post-translational modifications in response to drug treatment. Chromatin immunoprecipitation sequencing data sets were coupled with transcriptomic results to pinpoint the impact of proscillaridin A on gene pathways associated with specific chromatin modifications. Lastly, we evaluated the effect of the combination of proscillaridin A and the DNA demethylating drug decitabine on eRMS RD cell growth and clonogenic potential. RESULTS Clinically relevant concentration of proscillaridin A (5 nM) produced growth inhibition, cell cycle arrest and loss of clonogenicity in eRMS RD cells. Proscillaridin A produced a significant downregulation of MYC protein expression and inhibition of oncogenic transcriptional programs controlled by MYC, involved in cell replication. Interestingly, significant reduction in total histone 3 acetylation and on specific lysine residues (lysine 9, 14, 18, and 27 on histone 3) was associated with significant protein downregulation of a series of lysine acetyltransferases (KAT3A, KAT3B, KAT2A, KAT2B, and KAT5). In addition, proscillaridin A produced synergistic growth inhibition and loss of clonogenicity when combined with the approved DNA demethylating drug decitabine. CONCLUSION Proscillaridin A produces anticancer and epigenetic effects in the low nanomolar range and its combination with decitabine warrants further investigation for the treatment of eRMS.
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Affiliation(s)
- Marielle Huot
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada.,Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Maxime Caron
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Chantal Richer
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Rahinatou Djibo
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada.,Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Rafael Najmanovich
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada
| | - Pascal St-Onge
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada
| | - Daniel Sinnett
- Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.,Département de Pédiatrie, Université de Montréal, Montréal, QC, Canada
| | - Noël J M Raynal
- Département de Pharmacologie et Physiologie, Université de Montréal, Montréal, QC, Canada. .,Sainte-Justine University Hospital Research Center, 3175, Chemin de la Côte-Sainte-Catherine, Montréal, QC, H3T 1C5, Canada.
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11
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MacDonald A, Lu B, Caron M, Caporicci-Dinucci N, Hatrock D, Petrecca K, Bourque G, Stratton JA. Single Cell Transcriptomics of Ependymal Cells Across Age, Region and Species Reveals Cilia-Related and Metal Ion Regulatory Roles as Major Conserved Ependymal Cell Functions. Front Cell Neurosci 2021; 15:703951. [PMID: 34335193 PMCID: PMC8319996 DOI: 10.3389/fncel.2021.703951] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [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: 05/01/2021] [Accepted: 06/22/2021] [Indexed: 11/22/2022] Open
Abstract
Ependymal cells are ciliated-epithelial glial cells that develop from radial glia along the surface of the ventricles of the brain and the spinal canal. They play a critical role in cerebrospinal fluid (CSF) homeostasis, brain metabolism, and the clearance of waste from the brain. These cells have been implicated in disease across the lifespan including developmental disorders, cancer, and neurodegenerative disease. Despite this, ependymal cells remain largely understudied. Using single-cell RNA sequencing data extracted from publicly available datasets, we make key findings regarding the remarkable conservation of ependymal cell gene signatures across age, region, and species. Through this unbiased analysis, we have discovered that one of the most overrepresented ependymal cell functions that we observed relates to a critically understudied role in metal ion homeostasis. Our analysis also revealed distinct subtypes and states of ependymal cells across regions and ages of the nervous system. For example, neonatal ependymal cells maintained a gene signature consistent with developmental processes such as determination of left/right symmetry; while adult ventricular ependymal cells, not spinal canal ependymal cells, appeared to express genes involved in regulating cellular transport and inflammation. Together, these findings highlight underappreciated functions of ependymal cells, which will be important to investigate in order to better understand these cells in health and disease.
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Affiliation(s)
- Adam MacDonald
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Brianna Lu
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Maxime Caron
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Nina Caporicci-Dinucci
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Dale Hatrock
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Kevin Petrecca
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, QC, Canada
| | - Jo Anne Stratton
- Department of Neurology and Neurosurgery, Montreal Neurological Institute, McGill University, Montreal, QC, Canada
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12
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Caron M, St-Onge P, Sontag T, Wang YC, Richer C, Ragoussis I, Sinnett D, Bourque G. Publisher Correction: Single-cell analysis of childhood leukemia reveals a link between developmental states and ribosomal protein expression as a source of intra-individual heterogeneity. Sci Rep 2021; 11:5414. [PMID: 33654212 PMCID: PMC7925584 DOI: 10.1038/s41598-021-85034-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [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
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Maxime Caron
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,CHU Sainte-Justine Research Center, Montréal, Québec, Canada
| | - Pascal St-Onge
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
| | - Thomas Sontag
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
| | | | - Chantal Richer
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada
| | - Ioannis Ragoussis
- Department of Human Genetics, McGill University, Montréal, Québec, Canada.,McGill Genome Centre, Montréal, Québec, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine Research Center, Montréal, Québec, Canada. .,Department of Pediatrics, University of Montreal, Montréal, Québec, Canada.
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec, Canada. .,McGill Genome Centre, Montréal, Québec, Canada. .,Canadian Center for Computational Genomics, Montréal, Québec, Canada.
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13
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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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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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Dankner M, Caron M, Al-Saadi T, Yu W, Ouellet V, Uyen Le P, Ezzeddine R, Neubarth N, Savage P, Zuo D, Altoukhi H, Bourque G, Ragoussis J, Diaz R, Park M, Guiot MC, Lam S, Petrecca K, Siegel PM. 65. INVASIVE HISTOPATHOLOGY DRIVES POOR OUTCOMES IN SURGICALLY RESECTED BRAIN METASTASES. Neurooncol Adv 2020. [PMCID: PMC7401331 DOI: 10.1093/noajnl/vdaa073.052] [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: 11/13/2022] Open
Abstract
BACKGROUND Brain metastasis (BrM) patients treated with surgery and radiotherapy frequently experience local recurrence (LR), leptomeningeal metastasis (LM), and poor overall survival (OS). We sought to correlate the presence of invasive or circumscribed histopathological growth pattern, observed in the BrM lesion and surrounding brain, with these outcomes, and to study molecular mediators of parenchymal invasion. METHODS We assessed the HGP of H&E-stained slides from 164 surgically resected BrM from 147 patients. HGP was correlated with incidence of LR, LM and OS. Single-cell RNA sequencing (scRNAseq) was performed on three invasive HGP patients, sampling the metastasis center (MC) and surrounding brain (SB) outside of the contrast-enhancing region. Orthotopic patient-derived xenograft models (OPDX) were established from N=30 brain metastasis via intracranial propagation. RESULTS 56/164 BrM specimens (34%) showed a circumscribed growth pattern between the tumor and adjacent brain (cHGP) while 108/164 (66%) showed significant invasion of tumor lobules or single cells into the brain parenchyma (iHGP). iHGP was associated with LR, LM and shortened OS in BrM patients. OPDX models of BrM retain features of patient BrM, including HGP. scRNAseq identified abundant cancer cells in SB that overexpressed a number of genes involved in cell survival, invasion and metastasis 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 iHGP patient and OPDX BrM. Modulation of CIRBP expression in OPDX and cell line models of iHGP BrM delayed BrM progression and extended OS. CONCLUSION iHGP 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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Affiliation(s)
- Matthew Dankner
- McGill University, Montreal, QC, Canada
- Goodman Cancer Research Centre, Montreal, QC, Canada
| | | | - Tariq Al-Saadi
- McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, Montreal, QC, Canada
| | | | - Veronique Ouellet
- 5Centre Hospitalier de l‘Université de Montréal/CRCHUM, Montreal, QC, Canada
| | - Phuong Uyen Le
- McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, Montreal, QC, Canada
| | - Rima Ezzeddine
- McGill University, Montreal, QC, Canada
- Goodman Cancer Research Centre, Montreal, QC, Canada
| | - Noah Neubarth
- McGill University, Montreal, QC, Canada
- Goodman Cancer Research Centre, Montreal, QC, Canada
| | | | - Dongmei Zuo
- McGill University, Montreal, QC, Canada
- Goodman Cancer Research Centre, Montreal, QC, Canada
| | | | | | | | - Roberto Diaz
- McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, Montreal, QC, Canada
| | - Morag Park
- McGill University, Montreal, QC, Canada
- Goodman Cancer Research Centre, Montreal, QC, Canada
| | - Marie-Christine Guiot
- McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, Montreal, QC, Canada
| | | | - Kevin Petrecca
- McGill University, Montreal, QC, Canada
- Montreal Neurological Institute, Montreal, QC, Canada
| | - Peter M Siegel
- McGill University, Montreal, QC, Canada
- Goodman Cancer Research Centre, Montreal, QC, Canada
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16
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Legault LM, Doiron K, Lemieux A, Caron M, Chan D, Lopes FL, Bourque G, Sinnett D, McGraw S. Developmental genome-wide DNA methylation asymmetry between mouse placenta and embryo. Epigenetics 2020; 15:800-815. [PMID: 32056496 PMCID: PMC7518706 DOI: 10.1080/15592294.2020.1722922] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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: 09/23/2019] [Revised: 01/03/2020] [Accepted: 01/15/2020] [Indexed: 12/27/2022] Open
Abstract
In early embryos, DNA methylation is remodelled to initiate the developmental program but for mostly unknown reasons, methylation marks are acquired unequally between embryonic and placental cells. To better understand this, we generated high-resolution DNA methylation maps of mouse mid-gestation (E10.5) embryo and placenta. We uncovered specific subtypes of differentially methylated regions (DMRs) that contribute directly to the developmental asymmetry existing between mid-gestation embryonic and placental DNA methylation patterns. We show that the asymmetry occurs rapidly during the acquisition of marks in the post-implanted conceptus (E3.5-E6.5), and that these patterns are long-lasting across subtypes of DMRs throughout prenatal development and in somatic tissues. We reveal that at the peri-implantation stages, the de novo methyltransferase activity of DNMT3B is the main driver of methylation marks on asymmetric DMRs, and that DNMT3B can largely compensate for lack of DNMT3A in the epiblast and extraembryonic ectoderm, whereas DNMT3A can only partially compensate in the absence of DNMT3B. However, as development progresses and as DNMT3A becomes the principal de novo methyltransferase, the compensatory DNA methylation mechanism of DNMT3B on DMRs becomes less effective.
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Affiliation(s)
- LM Legault
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Université De Montréal, Montreal, Canada
| | - K Doiron
- Research Center of the CHU Sainte-Justine, Montreal, Canada
| | - A Lemieux
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Université De Montréal, Montreal, Canada
| | - M Caron
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - D Chan
- Research Institute of the McGill University Health Centre, Montreal, Quebec, Canada
| | - FL Lopes
- School of Veterinary Medicine, São Paulo State University (Unesp), Aracatuba, Brazil
| | - G Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada
- Canadian Center for Computational Genomics, Montreal, Quebec, Canada
| | - D Sinnett
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Pediatrics, Université De Montréal, Montreal, Canada
| | - S McGraw
- Research Center of the CHU Sainte-Justine, Montreal, Canada
- Department of Biochemistry and Molecular Medicine, Université De Montréal, Montreal, Canada
- Department of Obstetrics and Gynecology, Université De Montréal, Montreal, Canada
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17
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Costa EMD, Armaos G, McInnes G, Beaudry A, Moquin-Beaudry G, Bertrand-Lehouillier V, Caron M, St-Onge P, Jonhson JR, Krogan N, Sai Y, Downey M, Rafei M, Boileau M, Eppert K, Florez-Diaz E, Haman A, Hoang T, Sinnett D, Beausejour C, McGraw S, Raynal NJ. Abstract 4332: Targeting MYC overexpressing leukemia with cardiac glycoside proscillaridin through downregulation of histone acetyltransferases. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-4332] [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
Targeting MYC oncogene remains a major therapeutic goal in anticancer therapies. Here, we demonstrate that proscillaridin, a cardiac glycoside approved for heart failure treatment, causing Na+/K+ pump inhibition, targets efficiently MYC overexpressing cancer cells. At clinically relevant doses, proscillaridin induced rapid downregulation of MYC protein level, and produced growth inhibition preferentially against MYC overexpressing leukemic cell lines including lymphoid and myeloid stem cell populations. Whole transcriptome analysis with RNA sequencing of acute lymphoblastic leukemia cells showed a downregulation of gene sets involved in MYC pathways and cell replication, and an upregulation of genes involved in hematopoietic differentiation induced by proscillaridin treatment. Gene expression changes were associated with an epigenetic remodeling of chromatin active marks. Proscillaridin induced a significant loss of lysine acetylation in histone H3 (at lysine 9, 14, 18 and 27). In addition, mass spectrometry analysis revealed a loss of lysine acetylation in non-histone proteins such as MYC itself, MYC target proteins, and a series of histone acetylation regulators. Global loss of acetylation correlated with the rapid downregulation of histone acetyltransferase proteins (such as CBP, P300, TIP60 and GCN5) involved in histone and MYC acetylation. Overall, these results strongly support the repurposing of proscillaridin in MYC overexpressing leukemia and suggest a novel strategy to target MYC by inducing the downregulation of histone acetyltransferases involved in its stability.
Citation Format: Elodie Marie Da Costa, Gregory Armaos, Gabrielle McInnes, Annie Beaudry, Gael Moquin-Beaudry, Virginie Bertrand-Lehouillier, Maxime Caron, Pascal St-Onge, Jeffrey R. Jonhson, Nevan Krogan, Yuka Sai, Michale Downey, Moutih Rafei, Meaghan Boileau, Kolja Eppert, Ema Florez-Diaz, Andre Haman, Trang Hoang, Daniel Sinnett, Christian Beausejour, Serge McGraw, Noel J. Raynal. Targeting MYC overexpressing leukemia with cardiac glycoside proscillaridin through downregulation of histone acetyltransferases [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 4332.
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Affiliation(s)
| | - Gregory Armaos
- 1Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | - Gabrielle McInnes
- 1Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | - Annie Beaudry
- 1Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | - Gael Moquin-Beaudry
- 1Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | | | - Maxime Caron
- 1Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | - Pascal St-Onge
- 1Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | | | | | - Yuka Sai
- 3Institute of Systems Biology, Ottawa, Ontario, Canada
| | | | - Moutih Rafei
- 4Universite de Montreal, Montreal, Quebec, Canada
| | | | | | - Ema Florez-Diaz
- 6Institute of Research in Immunology and Cancer Universite de Montreal, Montreal, Quebec, Canada
| | - Andre Haman
- 6Institute of Research in Immunology and Cancer Universite de Montreal, Montreal, Quebec, Canada
| | - Trang Hoang
- 6Institute of Research in Immunology and Cancer Universite de Montreal, Montreal, Quebec, Canada
| | - Daniel Sinnett
- 1Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
| | | | - Serge McGraw
- 1Sainte-Justine University Hospital Research Center, Montreal, Quebec, Canada
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18
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Da Costa EM, Armaos G, McInnes G, Beaudry A, Moquin-Beaudry G, Bertrand-Lehouillier V, Caron M, Richer C, St-Onge P, Johnson JR, Krogan N, Sai Y, Downey M, Rafei M, Boileau M, Eppert K, Flores-Díaz E, Haman A, Hoang T, Sinnett D, Beauséjour C, McGraw S, Raynal NJM. Heart failure drug proscillaridin A targets MYC overexpressing leukemia through global loss of lysine acetylation. J Exp Clin Cancer Res 2019; 38:251. [PMID: 31196146 PMCID: PMC6563382 DOI: 10.1186/s13046-019-1242-8] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [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: 03/25/2019] [Accepted: 05/22/2019] [Indexed: 02/07/2023]
Abstract
Background Cardiac glycosides are approved for the treatment of heart failure as Na+/K+ pump inhibitors. Their repurposing in oncology is currently investigated in preclinical and clinical studies. However, the identification of a specific cancer type defined by a molecular signature to design targeted clinical trials with cardiac glycosides remains to be characterized. Here, we demonstrate that cardiac glycoside proscillaridin A specifically targets MYC overexpressing leukemia cells and leukemia stem cells by causing MYC degradation, epigenetic reprogramming and leukemia differentiation through loss of lysine acetylation. Methods Proscillaridin A anticancer activity was investigated against a panel of human leukemia and solid tumor cell lines with different MYC expression levels, overexpression in vitro systems and leukemia stem cells. RNA-sequencing and differentiation studies were used to characterize transcriptional and phenotypic changes. Drug-induced epigenetic changes were studied by chromatin post-translational modification analysis, expression of chromatin regulators, chromatin immunoprecipitation, and mass-spectrometry. Results At a clinically relevant dose, proscillaridin A rapidly altered MYC protein half-life causing MYC degradation and growth inhibition. Transcriptomic profile of leukemic cells after treatment showed a downregulation of genes involved in MYC pathways, cell replication and an upregulation of hematopoietic differentiation genes. Functional studies confirmed cell cycle inhibition and the onset of leukemia differentiation even after drug removal. Proscillaridin A induced a significant loss of lysine acetylation in histone H3 (at lysine 9, 14, 18 and 27) and in non-histone proteins such as MYC itself, MYC target proteins, and a series of histone acetylation regulators. Global loss of acetylation correlated with the rapid downregulation of histone acetyltransferases. Importantly, proscillaridin A demonstrated anticancer activity against lymphoid and myeloid stem cell populations characterized by MYC overexpression. Conclusion Overall, these results strongly support the repurposing of proscillaridin A in MYC overexpressing leukemia. Electronic supplementary material The online version of this article (10.1186/s13046-019-1242-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elodie M Da Costa
- Département de pharmacologie et physiologie, Université de Montréal, Montréal, (Québec), Canada.,Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada
| | - Gregory Armaos
- Département de pharmacologie et physiologie, Université de Montréal, Montréal, (Québec), Canada.,Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada
| | - Gabrielle McInnes
- Département de pharmacologie et physiologie, Université de Montréal, Montréal, (Québec), Canada.,Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada
| | - Annie Beaudry
- Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada
| | - Gaël Moquin-Beaudry
- Département de pharmacologie et physiologie, Université de Montréal, Montréal, (Québec), Canada.,Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada
| | - Virginie Bertrand-Lehouillier
- Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada.,Département de biochimie et biologie moléculaire, Université de Montréal, Montréal, (Québec), Canada
| | - Maxime Caron
- Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada
| | - Chantal Richer
- Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada
| | - Pascal St-Onge
- Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada
| | - Jeffrey R Johnson
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, USA
| | - Nevan Krogan
- Department of Cellular and Molecular Pharmacology, University of California, San Francisco, USA
| | - Yuka Sai
- Department of Cellular and Molecular Medicine, Ottawa Institute of Systems Biology, Ottawa, (Ontario), Canada
| | - Michael Downey
- Department of Cellular and Molecular Medicine, Ottawa Institute of Systems Biology, Ottawa, (Ontario), Canada
| | - Moutih Rafei
- Département de pharmacologie et physiologie, Université de Montréal, Montréal, (Québec), Canada.,Département de Microbiologie, Infectiologie et Immunologie, Université de Montréal, Montréal, (Québec), Canada.,Department of Microbiology and Immunology, McGill University, Montreal, (Québec), Canada
| | - Meaghan Boileau
- Department of Pediatrics, McGill University, Montreal, (Québec), Canada
| | - Kolja Eppert
- Department of Pediatrics, McGill University, Montreal, (Québec), Canada
| | - Ema Flores-Díaz
- Institute of Research in Immunology and Cancer, Université de Montréal, Montreal, (Québec), Canada
| | - André Haman
- Institute of Research in Immunology and Cancer, Université de Montréal, Montreal, (Québec), Canada
| | - Trang Hoang
- Département de pharmacologie et physiologie, Université de Montréal, Montréal, (Québec), Canada.,Institute of Research in Immunology and Cancer, Université de Montréal, Montreal, (Québec), Canada
| | - Daniel Sinnett
- Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada.,Département de pédiatrie, Université de Montréal, Montréal, (Québec), Canada
| | - Christian Beauséjour
- Département de pharmacologie et physiologie, Université de Montréal, Montréal, (Québec), Canada.,Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada
| | - Serge McGraw
- Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada.,Département de biochimie et biologie moléculaire, Université de Montréal, Montréal, (Québec), Canada.,Département Obstétrique-Gynécologie, Université de Montréal, Montréal, (Québec), Canada
| | - Noël J-M Raynal
- Département de pharmacologie et physiologie, Université de Montréal, Montréal, (Québec), Canada. .,Sainte-Justine University Hospital Research Center (7.17.020), 3175, Chemin de la Côte-Sainte-Catherine, Montréal, (Québec), H3T 1C5, Canada.
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19
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Bourgey M, Dali R, Eveleigh R, Chen KC, Letourneau L, Fillon J, Michaud M, Caron M, Sandoval J, Lefebvre F, Leveque G, Mercier E, Bujold D, Marquis P, Van PT, Anderson de Lima Morais D, Tremblay J, Shao X, Henrion E, Gonzalez E, Quirion PO, Caron B, Bourque G. GenPipes: an open-source framework for distributed and scalable genomic analyses. Gigascience 2019; 8:giz037. [PMID: 31185495 PMCID: PMC6559338 DOI: 10.1093/gigascience/giz037] [Citation(s) in RCA: 90] [Impact Index Per Article: 18.0] [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: 06/02/2018] [Revised: 09/28/2018] [Accepted: 03/10/2019] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND With the decreasing cost of sequencing and the rapid developments in genomics technologies and protocols, the need for validated bioinformatics software that enables efficient large-scale data processing is growing. FINDINGS Here we present GenPipes, a flexible Python-based framework that facilitates the development and deployment of multi-step workflows optimized for high-performance computing clusters and the cloud. GenPipes already implements 12 validated and scalable pipelines for various genomics applications, including RNA sequencing, chromatin immunoprecipitation sequencing, DNA sequencing, methylation sequencing, Hi-C, capture Hi-C, metagenomics, and Pacific Biosciences long-read assembly. The software is available under a GPLv3 open source license and is continuously updated to follow recent advances in genomics and bioinformatics. The framework has already been configured on several servers, and a Docker image is also available to facilitate additional installations. CONCLUSIONS GenPipes offers genomics researchers a simple method to analyze different types of data, customizable to their needs and resources, as well as the flexibility to create their own workflows.
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Affiliation(s)
- Mathieu Bourgey
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Rola Dali
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Robert Eveleigh
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Kuang Chung Chen
- McGill HPC Centre, McGill University, Montréal, QC, Canada
- Calcul Québec, QC, Canada
| | - Louis Letourneau
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Joel Fillon
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Marc Michaud
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Maxime Caron
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
| | - Johanna Sandoval
- Beaulieu-Saucier Université de Montréal Pharmacogenomics Centre, Montréal, QC, Canada
| | - Francois Lefebvre
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Gary Leveque
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Eloi Mercier
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - David Bujold
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Pascale Marquis
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Patrick Tran Van
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Julien Tremblay
- Energy, Mining and Environment, National Research Council Canada, Montréal, QC, Canada
| | - Xiaojian Shao
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Edouard Henrion
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Emmanuel Gonzalez
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Pierre-Olivier Quirion
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
| | - Bryan Caron
- McGill HPC Centre, McGill University, Montréal, QC, Canada
- Calcul Québec, QC, Canada
| | - Guillaume Bourque
- Canadian Centre for Computational Genomics, Montréal, QC, Canada
- McGill University and Genome Québec Innovation Center, Montréal, QC, Canada
- Department of Human Genetics, McGill University, Montréal, QC, Canada
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20
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Valois P, Caron M, Gousse-Lessard AS, Talbot D, Renaud JS. Development and validation of five behavioral indices of flood adaptation. BMC Public Health 2019; 19:245. [PMID: 30819122 PMCID: PMC6394037 DOI: 10.1186/s12889-019-6564-0] [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] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2018] [Accepted: 02/19/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In the current context of climate change, climate forecasts for the province of Quebec (Canada) are a lengthening of the thunderstorm season and an increase in episodes of intense precipitations. These changes in the distribution of precipitations could heighten the intensity or frequency of floods, a natural hazard that concerns 80% of Quebec's riverside municipalities. For the health and safety of the at-risk population, it is very important to make sure they have acquired necessary adaptive behaviors against flooding hazard. However, there has been no assessment of these flood adaptation behaviors to date. Thus, the aim of this study was to develop and validate five indices of adaptation to flooding. METHODS A sample of 1951 adults completed a questionnaire by phone. The questionnaire, specifically developed for this study, measured whether they did or did not adopt the behaviors that are proposed by public health officials to protect themselves against flooding. RESULTS The results of the item, confirmatory factor, and multiple correspondence analyses contributed to the development of five indices corresponding to the adaptation behaviors to adopt according to the chronology of events: (a) pre-alert preventive behaviors, (b) behaviors to carry out after the alert is issued, (c) behaviors to adopt during a flood not requiring evacuation, (d) behaviors to adopt during a flood requiring evacuation, and (e) post-flood behaviors. The results of this study also showed that people who perceive a risk of flooding in their home in the next 5 years tend to adopt more preventive behaviors and adaptation behaviors than those who perceive little or no risk at all. They also reveal that people who feel more adverse effects on their physical or mental health tend to adopt more adaptive behaviors than those who feel little or no adverse effects on their health. CONCLUSION Across a series of psychometric analyses, the results showed that these flood adaptation indices could properly measure a vast range of adaptive behaviors according to the chronology of events. Therefore, researchers, public health agencies, and professionals can use them to monitor the evolution of individuals' adaptive behaviors during floods.
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Affiliation(s)
- Pierre Valois
- Faculty of Education, Université Laval, 2320, rue des Bibliothèques, Quebec City, QC G1V 0A6 Canada
| | - Maxime Caron
- Faculty of Education, Université Laval, 2320, rue des Bibliothèques, Quebec City, QC G1V 0A6 Canada
| | | | - Denis Talbot
- Faculty of Medicine, Université Laval, 1050 Avenue de la Médecine, Quebec City, QC G1V 0A6 Canada
| | - Jean-Sébastien Renaud
- Faculty of Medicine, Université Laval, 1050 Avenue de la Médecine, Quebec City, QC G1V 0A6 Canada
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21
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Caron M, St-Onge P, Drouin S, Richer C, Sontag T, Busche S, Bourque G, Pastinen T, Sinnett D. Very long intergenic non-coding RNA transcripts and expression profiles are associated to specific childhood acute lymphoblastic leukemia subtypes. PLoS One 2018; 13:e0207250. [PMID: 30440012 PMCID: PMC6237371 DOI: 10.1371/journal.pone.0207250] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [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: 06/07/2018] [Accepted: 10/26/2018] [Indexed: 11/18/2022] Open
Abstract
Very long intergenic non-coding RNAs (vlincRNAs) are a novel class of long transcripts (~50 kb to 1 Mb) with cell type- or cancer-specific expression. We report the discovery and characterization of 256 vlincRNAs from a cohort of 64 primary childhood pre-B and pre-T acute lymphoblastic leukemia (cALL) samples, of which 61% are novel and specifically expressed in cALL. Validation was performed in 35 pre-B and pre-T cALL primary samples. We show that their expression is cALL immunophenotype and molecular subtype-specific and correlated with epigenetic modifications on their promoters, much like protein-coding genes. While the biological functions of these vlincRNAs are still unknown, our results suggest they could play a role in cALL etiology or progression.
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Affiliation(s)
- Maxime Caron
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Pascal St-Onge
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Simon Drouin
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Chantal Richer
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Thomas Sontag
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
| | - Stephan Busche
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine Research Center, Montreal, Quebec, Canada
- Department of Pediatrics, University of Montreal, Montreal, Quebec, Canada
- * E-mail:
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22
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Piché J, Gosset N, Legault LM, Pacis A, Oneglia A, Caron M, Chetaille P, Barreiro L, Liu D, Qi X, Nattel S, Leclerc S, Breton-Larrivée M, McGraw S, Andelfinger G. Molecular Signature of CAID Syndrome: Noncanonical Roles of SGO1 in Regulation of TGF-β Signaling and Epigenomics. Cell Mol Gastroenterol Hepatol 2018; 7:411-431. [PMID: 30739867 PMCID: PMC6369230 DOI: 10.1016/j.jcmgh.2018.10.011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/23/2018] [Revised: 10/17/2018] [Accepted: 10/17/2018] [Indexed: 01/14/2023]
Abstract
BACKGROUND & AIMS A generalized human pacemaking syndrome, chronic atrial and intestinal dysrhythmia (CAID) (OMIM 616201), is caused by a homozygous SGO1 mutation (K23E), leading to chronic intestinal pseudo-obstruction and arrhythmias. Because CAID patients do not show phenotypes consistent with perturbation of known roles of SGO1, we hypothesized that noncanonical roles of SGO1 drive the clinical manifestations observed. METHODS To identify a molecular signature for CAID syndrome, we achieved unbiased screens in cell lines and gut tissues from CAID patients vs wild-type controls. We performed RNA sequencing along with stable isotope labeling with amino acids in cell culture. In addition, we determined the genome-wide DNA methylation and chromatin accessibility signatures using reduced representative bisulfite sequencing and assay for transposase-accessible chromatin with high-throughput sequencing. Functional studies included patch-clamp, quantitation of transforming growth factor-β (TGF-β) signaling, and immunohistochemistry in CAID patient gut biopsy specimens. RESULTS Proteome and transcriptome studies converge on cell-cycle regulation, cardiac conduction, and smooth muscle regulation as drivers of CAID syndrome. Specifically, the inward rectifier current, an important regulator of cellular function, was disrupted. Immunohistochemistry confirmed overexpression of Budding Uninhibited By Benzimidazoles 1 (BUB1) in patients, implicating the TGF-β pathway in CAID pathogenesis. Canonical TGF-β signaling was up-regulated and uncoupled from noncanonical signaling in CAID patients. Reduced representative bisulfite sequencing and assay for transposase-accessible chromatin with high-throughput sequencing experiments showed significant changes of chromatin states in CAID, pointing to epigenetic regulation as a possible pathologic mechanism. CONCLUSIONS Our findings point to impaired inward rectifier potassium current, dysregulation of canonical TGF-β signaling, and epigenetic regulation as potential drivers of intestinal and cardiac manifestations of CAID syndrome. Transcript profiling and genomics data are as follows: repository URL: https://www.ncbi.nlm.nih.gov/geo; SuperSeries GSE110612 was composed of the following subseries: GSE110309, GSE110576, and GSE110601.
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Affiliation(s)
- Jessica Piché
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Natacha Gosset
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Lisa-Marie Legault
- Department of Biochemistry and Molecular Medicine, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Alain Pacis
- Department of Genetics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada,Department of Biochemistry, Université de Montréal, Montréal, Québec, Canada
| | - Andrea Oneglia
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Maxime Caron
- Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Philippe Chetaille
- Service of Pediatric Cardiology, Department of Pediatrics, Centre Mère Enfants Soleil, Centre Hospitalier de l’Université de Québec, Québec City, Québec, Canada
| | - Luis Barreiro
- Department of Genetics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada,Department of Biochemistry, Université de Montréal, Montréal, Québec, Canada,Department of Pediatrics, Université de Montréal, Québec, Canada
| | - Donghai Liu
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Xioyan Qi
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Stanley Nattel
- Research Center, Montreal Heart Institute, Université de Montréal, Montréal, Québec, Canada
| | - Séverine Leclerc
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Mélanie Breton-Larrivée
- Department of Biochemistry and Molecular Medicine, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | | | - Serge McGraw
- Department of Biochemistry and Molecular Medicine, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada,Departement of Obstetrics and Gynecology, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada
| | - Gregor Andelfinger
- Cardiovascular Genetics, Department of Pediatrics, Centre Hospitalier Universitaire Sainte Justine Research Center, Université de Montréal, Montréal, Québec, Canada,Correspondence Address correspondence to: Gregor Andelfinger, MD, FRCPC, Service of Cardiology, Department of Pediatrics, Cardiovascular Genetics Research Laboratory, Centre Hospitalier Sainte Justine Research Center, Université de Montréal 3175, Chemin Côte Sainte Catherine, Montréal, Québec, H3T 1C5 Canada. fax: (514) 345-4896.
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23
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Abstract
Genetic alterations in the transcriptional repressor ETV6 are associated with hematological malignancies. Notably, the t(12;21) translocation leading to an ETV6-AML1 fusion gene is the most common genetic alteration found in childhood acute lymphoblastic leukemia. Moreover, most of these patients also lack ETV6 expression, suggesting a tumor suppressor function. To gain insights on ETV6 DNA-binding specificity and genome wide transcriptional regulation capacities, we performed chromatin immunoprecipitation experiments coupled to deep sequencing in a t(12;21)-positive pre-B leukemic cell line. This strategy led to the identification of ETV6-bound regions that were further associated to gene expression. ETV6 binding is mostly cell type-specific as only few regions are shared with other blood cell subtypes. Peaks localization and motif enrichment analyses revealed that this unique binding profile could be associated with the ETV6-AML1 fusion protein specific to the t(12;21) background. This study underscores the complexity of ETV6 binding and uncovers ETV6 transcriptional network in pre-B leukemia cells bearing the recurrent t(12;21) translocation.
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Affiliation(s)
- Benjamin Neveu
- Sainte-Justine UHC Research Center, Montreal, Qc, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada
| | - Maxime Caron
- Sainte-Justine UHC Research Center, Montreal, Qc, Canada
| | - Karine Lagacé
- Sainte-Justine UHC Research Center, Montreal, Qc, Canada
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada
| | - Chantal Richer
- Sainte-Justine UHC Research Center, Montreal, Qc, Canada
| | - Daniel Sinnett
- Sainte-Justine UHC Research Center, Montreal, Qc, Canada.
- Department of Biochemistry and Molecular Medicine, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada.
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, Qc, Canada.
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24
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Ouimet M, Drouin S, Lajoie M, Caron M, St-Onge P, Gioia R, Richer C, Sinnett D. A childhood acute lymphoblastic leukemia-specific lncRNA implicated in prednisolone resistance, cell proliferation, and migration. Oncotarget 2018; 8:7477-7488. [PMID: 27980230 PMCID: PMC5352336 DOI: 10.18632/oncotarget.13936] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2016] [Accepted: 12/02/2016] [Indexed: 11/25/2022] Open
Abstract
Childhood acute lymphoblastic leukemia (cALL) is the most common pediatric cancer and, despite an 85% cure rate, still represents a major cause of disease-related death in children. Recent studies have implicated long non-coding RNAs (lncRNAs) in cALL etiology, progression, and treatment response. However, barring some exceptions little is known about the functional impact of lncRNAs on cancer biology, which limits their potential as potential therapeutic targets. We wanted to investigate the functional role of lncRNAs identified as specifically overexpressed in pre-B cALL by whole-transcriptome sequencing. Here we report five lncRNAs specifically upregulated in pre-B cALL that had significant impacts on cancer hallmark traits such as cell proliferation, migration, apoptosis, and treatment response. In particular, silencing of the RP11-137H2.4 lncRNA effectively restored normal glucocorticoid (GC) response in a GC-resistant pre-B cALL cell line and specifically modulated expression of members of both the NRAS/BRAF/NF-?B MAPK cascade and cell cycle pathways. Since GC form the cornerstone of cALL chemotherapy and resistance in cALL confers a dismal prognosis, characterizing RP11-137H2.4sexact role and function in this process will be critical to the development of new therapeutic approaches to overcome GC resistance in children treated for cALL.
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Affiliation(s)
- Manon Ouimet
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Simon Drouin
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Mathieu Lajoie
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Maxime Caron
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Pascal St-Onge
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Romain Gioia
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Chantal Richer
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, Montreal, QC, Canada
| | - Daniel Sinnett
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, Montreal, QC, Canada.,Department of Pediatrics, University of Montreal, Montreal, QC, Canada
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25
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Caron M, Lamarre G, Grégoire P, Simonyan D, Laflamme N. A244 THE FECAL IMMUNOCHEMICAL TEST (FIT): SELECTED ASPECTS REGARDING ITS EFFECTIVENESS FOR COLORECTAL CANCER SCREENING IN QUEBEC CITY. J Can Assoc Gastroenterol 2018. [DOI: 10.1093/jcag/gwy008.245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- M Caron
- Faculty of Medicine, Universite Laval, Quebec, QC, Canada
| | - G Lamarre
- Faculty of Medicine, Universite Laval, Quebec, QC, Canada
| | | | - D Simonyan
- Centre de recherche du CHU de Québec, Quebec, QC, Canada
| | - N Laflamme
- Centre de recherche du CHU de Québec, Quebec, QC, Canada
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26
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Audet-Walsh É, Dufour CR, Yee T, Zouanat FZ, Yan M, Kalloghlian G, Vernier M, Caron M, Bourque G, Scarlata E, Hamel L, Brimo F, Aprikian AG, Lapointe J, Chevalier S, Giguère V. Nuclear mTOR acts as a transcriptional integrator of the androgen signaling pathway in prostate cancer. Genes Dev 2017; 31:1228-1242. [PMID: 28724614 PMCID: PMC5558925 DOI: 10.1101/gad.299958.117] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [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: 04/03/2017] [Accepted: 06/19/2017] [Indexed: 11/30/2022]
Abstract
Audet-Walsh et al. reveal the existence of a nuclear mTOR–androgen receptor transcriptional axis integral to the metabolic rewiring of prostate cancer cells. Androgen receptor (AR) signaling reprograms cellular metabolism to support prostate cancer (PCa) growth and survival. Another key regulator of cellular metabolism is mTOR, a kinase found in diverse protein complexes and cellular localizations, including the nucleus. However, whether nuclear mTOR plays a role in PCa progression and participates in direct transcriptional cross-talk with the AR is unknown. Here, via the intersection of gene expression, genomic, and metabolic studies, we reveal the existence of a nuclear mTOR–AR transcriptional axis integral to the metabolic rewiring of PCa cells. Androgens reprogram mTOR–chromatin associations in an AR-dependent manner in which activation of mTOR-dependent metabolic gene networks is essential for androgen-induced aerobic glycolysis and mitochondrial respiration. In models of castration-resistant PCa cells, mTOR was capable of transcriptionally regulating metabolic gene programs in the absence of androgens, highlighting a potential novel castration resistance mechanism to sustain cell metabolism even without a functional AR. Remarkably, we demonstrate that increased mTOR nuclear localization is indicative of poor prognosis in patients, with the highest levels detected in castration-resistant PCa tumors and metastases. Identification of a functional mTOR targeted multigene signature robustly discriminates between normal prostate tissues, primary tumors, and hormone refractory metastatic samples but is also predictive of cancer recurrence. This study thus underscores a paradigm shift from AR to nuclear mTOR as being the master transcriptional regulator of metabolism in PCa.
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Affiliation(s)
- Étienne Audet-Walsh
- Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A3, Canada
| | - Catherine R Dufour
- Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A3, Canada
| | - Tracey Yee
- Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A3, Canada
| | - Fatima Z Zouanat
- Urologic Oncology Research Group, Cancer Research Program, Research Institute of the McGill University Health Centre (MUHC), Montréal, Québec H4A 3J1, Canada
| | - Ming Yan
- Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A3, Canada
| | - Georges Kalloghlian
- Urologic Oncology Research Group, Cancer Research Program, Research Institute of the McGill University Health Centre (MUHC), Montréal, Québec H4A 3J1, Canada
| | - Mathieu Vernier
- Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A3, Canada
| | - Maxime Caron
- Génome Québec Innovation Centre, McGill University, Montréal, Québec H3A 0G1, Canada
| | - Guillaume Bourque
- Génome Québec Innovation Centre, McGill University, Montréal, Québec H3A 0G1, Canada.,Department of Human Genetics, McGill University, Montréal, Québec H3A 1A3, Canada
| | - Eleonora Scarlata
- Urologic Oncology Research Group, Cancer Research Program, Research Institute of the McGill University Health Centre (MUHC), Montréal, Québec H4A 3J1, Canada
| | - Lucie Hamel
- Urologic Oncology Research Group, Cancer Research Program, Research Institute of the McGill University Health Centre (MUHC), Montréal, Québec H4A 3J1, Canada
| | - Fadi Brimo
- Department of Human Genetics, McGill University, Montréal, Québec H3A 1A3, Canada
| | - Armen G Aprikian
- Urologic Oncology Research Group, Cancer Research Program, Research Institute of the McGill University Health Centre (MUHC), Montréal, Québec H4A 3J1, Canada.,Department of Pathology, McGill University and MUHC, Montréal, Québec H4A 3J1, Canada
| | - Jacques Lapointe
- Department of Surgery (Urology), McGill University and MUHC, Montréal, Québec H4A 3J1, Canada.,Department of Oncology, McGill University and MUHC, Montréal, Québec H4A 3J1, Canada
| | - Simone Chevalier
- Urologic Oncology Research Group, Cancer Research Program, Research Institute of the McGill University Health Centre (MUHC), Montréal, Québec H4A 3J1, Canada.,Department of Pathology, McGill University and MUHC, Montréal, Québec H4A 3J1, Canada.,Department of Medicine, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Oncology, McGill University, Montréal, Québec H3G 1Y6, Canada
| | - Vincent Giguère
- Goodman Cancer Research Centre, McGill University, Montréal, Québec H3A 1A3, Canada.,Department of Medicine, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Oncology, McGill University, Montréal, Québec H3G 1Y6, Canada.,Department of Biochemistry, McGill University, Montréal, Québec H3G 1Y6, Canada
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27
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Costa EMD, Armaos G, Jacques-Ricard S, Beaudry A, St-Onge P, Caron M, Sinnett D, McGraw S, Raynal NJ. Abstract 1375: Loss of C-MYC and chromatin acetylation induce epigenetic reprogramming in acute lymphoblastic leukemia. Cancer Res 2017. [DOI: 10.1158/1538-7445.am2017-1375] [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
Epigenetic modifications play a key role in establishing and maintaining gene expression. In cancer, they are highly altered and responsable of gene expression deregulation. Epigenetic drugs have the ability to reset cancer cell epigenome producing cancer cell differentiation and apoptosis. In a drug screening initiative, we recently reported a series of FDA-approved drugs with unsuspected epigenetic and anticancer activities. Here, we tested in a secondary screen the activity of these drugs against acute lymphoblastic leukemia (ALL) cell lines (MOLT-4 and NALM-6). We found that Proscillaridin A, a cardiac glycoside used for heart failure treatment, was the most active with IC50 values in the low nanomolar range, suggesting drug repositioning potential. Proscillaridin treatments induced a significant decrease in RNA and protein levels of C-MYC, a master oncogenic driver in ALL. Shortly after proscillaridin A treatment, C-MYC exhibited a 75% reduction in lysine acetylation, a post-translational modification known to prevent its degradation. Loss of acetylation was associated with down-regulation of lysine acetyltransferases CBP, P300 and Tip60, which also correlated with a reduction in histone 3 and 4 acetylation levels (H3K14ac, H3K9ac, H3K27ac and H4K5ac). Preliminary analysis with si-RNA experiments reveal that independent HAT activities are not responsible of C-MYC downregulation. RNA sequencing and gene set enrichment analysis in proscillaridin-treated ALL cells (5 nM for 48h) showed that genes associated with cell differentiation and apoptosis pathways were up-regulated whereas down-regulated genes were associated with C-MYC target genes. Altogether, our findings show that acetylation through lysine acetyltransferase down-regulation simultaneously induces loss of C-MYC and H3 acetylation leading to epigenetic reprogramming in ALL cells. This drug repositioning strategy, using proscillaridin A, has the potential to reprogram cancer cells that are driven by MYC overexpression or hyperactivation.
Citation Format: Elodie M. Da Costa, Gregory Armaos, Simon Jacques-Ricard, Annie Beaudry, Pascal St-Onge, Maxime Caron, Daniel Sinnett, Serge McGraw, Noël J. Raynal. Loss of C-MYC and chromatin acetylation induce epigenetic reprogramming in acute lymphoblastic leukemia [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 1375. doi:10.1158/1538-7445.AM2017-1375
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Affiliation(s)
| | - Gregory Armaos
- CHU Sainte-Justine research center, Montreal, Quebec, Canada
| | | | - Annie Beaudry
- CHU Sainte-Justine research center, Montreal, Quebec, Canada
| | - Pascal St-Onge
- CHU Sainte-Justine research center, Montreal, Quebec, Canada
| | - Maxime Caron
- CHU Sainte-Justine research center, Montreal, Quebec, Canada
| | - Daniel Sinnett
- CHU Sainte-Justine research center, Montreal, Quebec, Canada
| | - Serge McGraw
- CHU Sainte-Justine research center, Montreal, Quebec, Canada
| | - Noël J. Raynal
- CHU Sainte-Justine research center, Montreal, Quebec, Canada
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28
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Chen L, Ge B, Casale FP, Vasquez L, Kwan T, Garrido-Martín D, Watt S, Yan Y, Kundu K, Ecker S, Datta A, Richardson D, Burden F, Mead D, Mann AL, Fernandez JM, Rowlston S, Wilder SP, Farrow S, Shao X, Lambourne JJ, Redensek A, Albers CA, Amstislavskiy V, Ashford S, Berentsen K, Bomba L, Bourque G, Bujold D, Busche S, Caron M, Chen SH, Cheung W, Delaneau O, Dermitzakis ET, Elding H, Colgiu I, Bagger FO, Flicek P, Habibi E, Iotchkova V, Janssen-Megens E, Kim B, Lehrach H, Lowy E, Mandoli A, Matarese F, Maurano MT, Morris JA, Pancaldi V, Pourfarzad F, Rehnstrom K, Rendon A, Risch T, Sharifi N, Simon MM, Sultan M, Valencia A, Walter K, Wang SY, Frontini M, Antonarakis SE, Clarke L, Yaspo ML, Beck S, Guigo R, Rico D, Martens JHA, Ouwehand WH, Kuijpers TW, Paul DS, Stunnenberg HG, Stegle O, Downes K, Pastinen T, Soranzo N. Genetic Drivers of Epigenetic and Transcriptional Variation in Human Immune Cells. Cell 2017; 167:1398-1414.e24. [PMID: 27863251 PMCID: PMC5119954 DOI: 10.1016/j.cell.2016.10.026] [Citation(s) in RCA: 389] [Impact Index Per Article: 55.6] [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: 01/31/2016] [Revised: 08/19/2016] [Accepted: 10/14/2016] [Indexed: 12/20/2022]
Abstract
Characterizing the multifaceted contribution of genetic and epigenetic factors to disease phenotypes is a major challenge in human genetics and medicine. We carried out high-resolution genetic, epigenetic, and transcriptomic profiling in three major human immune cell types (CD14+ monocytes, CD16+ neutrophils, and naive CD4+ T cells) from up to 197 individuals. We assess, quantitatively, the relative contribution of cis-genetic and epigenetic factors to transcription and evaluate their impact as potential sources of confounding in epigenome-wide association studies. Further, we characterize highly coordinated genetic effects on gene expression, methylation, and histone variation through quantitative trait locus (QTL) mapping and allele-specific (AS) analyses. Finally, we demonstrate colocalization of molecular trait QTLs at 345 unique immune disease loci. This expansive, high-resolution atlas of multi-omics changes yields insights into cell-type-specific correlation between diverse genomic inputs, more generalizable correlations between these inputs, and defines molecular events that may underpin complex disease risk. Genome, transcriptome, and epigenome reference panel in three human immune cell types Identified 4,418 genes associated with epigenetic changes independent of genetics Described genome-epigenome coordination defining cell-type-specific regulatory events Functionally mapped disease mechanisms at 345 unique autoimmune disease loci
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Affiliation(s)
- Lu Chen
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Bing Ge
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Francesco Paolo Casale
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Louella Vasquez
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Tony Kwan
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Diego Garrido-Martín
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader, 88, Barcelona 8003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Plaça de la Mercè, 10- 12, Barcelona 8002, Spain
| | - Stephen Watt
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Ying Yan
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Kousik Kundu
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Simone Ecker
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain; UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Avik Datta
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - David Richardson
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Frances Burden
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Daniel Mead
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Alice L Mann
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Jose Maria Fernandez
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain
| | - Sophia Rowlston
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Steven P Wilder
- Genome Analysis, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Samantha Farrow
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Xiaojian Shao
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - John J Lambourne
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Adriana Redensek
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Cornelis A Albers
- Human Genetics, Donders Institute for Brain, Cognition and Behaviour, Radboud University Medical Centre, P.O. Box 9101, Nijmegen 6500 HB, the Netherlands; Molecular Developmental Biology, Radboud Institute for Life Sciences, Radboud University, P.O. Box 9101, Nijmegen 6500 HB, the Netherlands
| | - Vyacheslav Amstislavskiy
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Sofie Ashford
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Kim Berentsen
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Lorenzo Bomba
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Guillaume Bourque
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - David Bujold
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Stephan Busche
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Maxime Caron
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Shu-Huang Chen
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Warren Cheung
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Oliver Delaneau
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, Geneva 1211, Switzerland
| | - Emmanouil T Dermitzakis
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, Geneva 1211, Switzerland
| | - Heather Elding
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Irina Colgiu
- Human Genetics Informatics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Frederik O Bagger
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Paul Flicek
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Ehsan Habibi
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Valentina Iotchkova
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Eva Janssen-Megens
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Bowon Kim
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Hans Lehrach
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Ernesto Lowy
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Amit Mandoli
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Filomena Matarese
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Matthew T Maurano
- Institute for Systems Genetics, New York University Langone Medical Center, ACLS West, Room 511, 430 East 29(th) Street, New York, NY 10016, USA
| | - John A Morris
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Vera Pancaldi
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain
| | - Farzin Pourfarzad
- Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Plesmanlaan 125, Amsterdam 1066CX, the Netherlands
| | - Karola Rehnstrom
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Augusto Rendon
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; Bioinformatics, Genomics England, Charterhouse Square, London EC1M 6BQ, UK
| | - Thomas Risch
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Nilofar Sharifi
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Marie-Michelle Simon
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada
| | - Marc Sultan
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Alfonso Valencia
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain
| | - Klaudia Walter
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK
| | - Shuang-Yin Wang
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Mattia Frontini
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK
| | - Stylianos E Antonarakis
- Genetic Medicine and Development, University of Geneva Medical School-CMU, 1 Rue Michel-Servet, Geneva 1211, Switzerland
| | - Laura Clarke
- Vertebrate Genomics, European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Marie-Laure Yaspo
- Department of Vertebrate Genomics, Max Planck Institute for Molecular Genetics, Ihnestr. 63/73, Berlin 14195, Germany
| | - Stephan Beck
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK
| | - Roderic Guigo
- Bioinformatics and Genomics, Centre for Genomic Regulation (CRG), Barcelona Institute of Science and Technology, Carrer del Dr. Aiguader, 88, Barcelona 8003, Spain; Department of Experimental and Health Sciences, Universitat Pompeu Fabra (UPF), Plaça de la Mercè, 10- 12, Barcelona 8002, Spain; Computational Genomics, Institut Hospital del Mar d'Investigacions Mediques (IMIM), Carrer del Dr. Aiguader, 88, Barcelona 8003, Spain
| | - Daniel Rico
- Structural Biology and Biocomputing Programme, Spanish National Cancer Research Centre (CNIO), Melchor Fernandez Almagro, 3, Madrid 28029, Spain; Institute of Cellular Medicine, Newcastle University, Framlington Place, Newcastle upon Tyne NE2 4HH, UK
| | - Joost H A Martens
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Willem H Ouwehand
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK
| | - Taco W Kuijpers
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; Blood Cell Research, Sanquin Research and Landsteiner Laboratory, Plesmanlaan 125, Amsterdam 1066CX, the Netherlands; Emma Children's Hospital, Academic Medical Center (AMC), University of Amsterdam, Location H7-230, Meibergdreef 9, Amsterdam 1105AZ, the Netherlands
| | - Dirk S Paul
- UCL Cancer Institute, University College London, 72 Huntley Street, London WC1E 6BT, UK; Cardiovascular Epidemiology Unit, Department of Public Health and Primary Care, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud University, Nijmegen 6525GA, the Netherlands
| | - Oliver Stegle
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge CB10 1SD, UK
| | - Kate Downes
- Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; National Health Service (NHS) Blood and Transplant, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK
| | - Tomi Pastinen
- Human Genetics, McGill University, 740 Dr. Penfield, Montreal, QC H3A 0G1, Canada.
| | - Nicole Soranzo
- Department of Human Genetics, The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1HH, UK; Department of Haematology, University of Cambridge, Cambridge Biomedical Campus, Long Road, Cambridge CB2 0PT, UK; British Heart Foundation Centre of Excellence, Division of Cardiovascular Medicine, Addenbrooke's Hospital, Hills Road, Cambridge CB2 0QQ, UK; The National Institute for Health Research Blood and Transplant Unit (NIHR BTRU) in Donor Health and Genomics at the University of Cambridge, Strangeways Research Laboratory, University of Cambridge, Wort's Causeway, Cambridge CB1 8RN, UK.
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Lajoie M, Drouin S, Caron M, St-Onge P, Ouimet M, Gioia R, Lafond MH, Vidal R, Richer C, Oualkacha K, Droit A, Sinnett D. Specific expression of novel long non-coding RNAs in high-hyperdiploid childhood acute lymphoblastic leukemia. PLoS One 2017; 12:e0174124. [PMID: 28346506 PMCID: PMC5367703 DOI: 10.1371/journal.pone.0174124] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 02/22/2017] [Indexed: 12/31/2022] Open
Abstract
Pre-B cell childhood acute lymphoblastic leukemia (pre-B cALL) is a heterogeneous disease involving many subtypes typically stratified using a combination of cytogenetic and molecular-based assays. These methods, although widely used, rely on the presence of known chromosomal translocations, which is a limiting factor. There is therefore a need for robust, sensitive, and specific molecular biomarkers unaffected by such limitations that would allow better risk stratification and consequently better clinical outcome. In this study we performed a transcriptome analysis of 56 pre-B cALL patients to identify expression signatures in different subtypes. In both protein-coding and long non-coding RNAs (lncRNA), we identified subtype-specific gene signatures distinguishing pre-B cALL subtypes, particularly in t(12;21) and hyperdiploid cases. The genes up-regulated in pre-B cALL subtypes were enriched in bivalent chromatin marks in their promoters. LncRNAs is a new and under-studied class of transcripts. The subtype-specific nature of lncRNAs suggests they may be suitable clinical biomarkers to guide risk stratification and targeted therapies in pre-B cALL patients.
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Affiliation(s)
- Mathieu Lajoie
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Simon Drouin
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Maxime Caron
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Pascal St-Onge
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Manon Ouimet
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Romain Gioia
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Marie-Hélène Lafond
- Mathematics and Statistics Department, University of Quebec at Montreal (UQAM), 201 President-Kennedy Av., Montreal, QC, Canada
| | - Ramon Vidal
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Chantal Richer
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
| | - Karim Oualkacha
- Mathematics and Statistics Department, University of Quebec at Montreal (UQAM), 201 President-Kennedy Av., Montreal, QC, Canada
| | - Arnaud Droit
- Department of Endocrinology and Nephrology, Laval University, 2705 Laurier Blvd., Quebec City, QC, Canada
| | - Daniel Sinnett
- Division of Hematology-Oncology, Research Center, Sainte-Justine University Health Center, 3175 Chemin de la Côte-Sainte-Catherine, Montréal, QC, Canada
- Department of Pediatrics, Faculty of Medicine, University of Montreal, Montreal, QC, Canada
- * E-mail:
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Ramsay L, Marchetto MC, Caron M, Chen SH, Busche S, Kwan T, Pastinen T, Gage FH, Bourque G. Conserved expression of transposon-derived non-coding transcripts in primate stem cells. BMC Genomics 2017; 18:214. [PMID: 28245871 PMCID: PMC5331655 DOI: 10.1186/s12864-017-3568-y] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [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: 09/01/2016] [Accepted: 02/07/2017] [Indexed: 12/25/2022] Open
Abstract
Background A significant portion of expressed non-coding RNAs in human cells is derived from transposable elements (TEs). Moreover, it has been shown that various long non-coding RNAs (lncRNAs), which come from the human endogenous retrovirus subfamily H (HERVH), are not only expressed but required for pluripotency in human embryonic stem cells (hESCs). Results To identify additional TE-derived functional non-coding transcripts, we generated RNA-seq data from induced pluripotent stem cells (iPSCs) of four primate species (human, chimpanzee, gorilla, and rhesus) and searched for transcripts whose expression was conserved. We observed that about 30% of TE instances expressed in human iPSCs had orthologous TE instances that were also expressed in chimpanzee and gorilla. Notably, our analysis revealed a number of repeat families with highly conserved expression profiles including HERVH but also MER53, which is known to be the source of a placental-specific family of microRNAs (miRNAs). We also identified a number of repeat families from all classes of TEs, including MLT1-type and Tigger families, that contributed a significant amount of sequence to primate lncRNAs whose expression was conserved. Conclusions Together, these results describe TE families and TE-derived lncRNAs whose conserved expression patterns can be used to identify what are likely functional TE-derived non-coding transcripts in primate iPSCs. Electronic supplementary material The online version of this article (doi:10.1186/s12864-017-3568-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- LeeAnn Ramsay
- Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada
| | - Maria C Marchetto
- Lab of Genetics, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Maxime Caron
- Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada.,McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada
| | - Shu-Huang Chen
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada
| | - Stephan Busche
- McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada.,McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada.,McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada
| | - Fred H Gage
- Lab of Genetics, Salk Institute for Biological Studies, 10010 N Torrey Pines Rd, La Jolla, CA 92037, USA
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Dr Penfield Avenue, Montreal, H3A 1B1, Canada. .,McGill University and Genome Quebec Innovation Centre, 740 Dr Penfield Avenue, Montreal, H3A 1A4, Canada.
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Bujold D, Morais DADL, Gauthier C, Côté C, Caron M, Kwan T, Chen KC, Laperle J, Markovits AN, Pastinen T, Caron B, Veilleux A, Jacques PÉ, Bourque G. The International Human Epigenome Consortium Data Portal. Cell Syst 2016; 3:496-499.e2. [PMID: 27863956 DOI: 10.1016/j.cels.2016.10.019] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2016] [Revised: 07/21/2016] [Accepted: 10/19/2016] [Indexed: 10/20/2022]
Abstract
The International Human Epigenome Consortium (IHEC) coordinates the production of reference epigenome maps through the characterization of the regulome, methylome, and transcriptome from a wide range of tissues and cell types. To define conventions ensuring the compatibility of datasets and establish an infrastructure enabling data integration, analysis, and sharing, we developed the IHEC Data Portal (http://epigenomesportal.ca/ihec). The portal provides access to >7,000 reference epigenomic datasets, generated from >600 tissues, which have been contributed by seven international consortia: ENCODE, NIH Roadmap, CEEHRC, Blueprint, DEEP, AMED-CREST, and KNIH. The portal enhances the utility of these reference maps by facilitating the discovery, visualization, analysis, download, and sharing of epigenomics data. The IHEC Data Portal is the official source to navigate through IHEC datasets and represents a strategy for unifying the distributed data produced by international research consortia.
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Affiliation(s)
- David Bujold
- McGill University and Génome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | | | - Carol Gauthier
- Centre de Calcul Scientifique, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Catherine Côté
- McGill University and Génome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Maxime Caron
- McGill University and Génome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Tony Kwan
- McGill University and Génome Québec Innovation Center, Montréal, QC H3A 0G1, Canada
| | - Kuang Chung Chen
- McGill High Performance Computing Centre, McGill University, Montréal, QC H3C 1K3, Canada
| | - Jonathan Laperle
- Département d'Informatique, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | | | - Tomi Pastinen
- McGill University and Génome Québec Innovation Center, Montréal, QC H3A 0G1, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0G1, Canada
| | - Bryan Caron
- McGill High Performance Computing Centre, McGill University, Montréal, QC H3C 1K3, Canada
| | - Alain Veilleux
- Centre de Calcul Scientifique, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada
| | - Pierre-Étienne Jacques
- Centre de Calcul Scientifique, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département d'Informatique, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Département de Biologie, Université de Sherbrooke, Sherbrooke, QC J1K 2R1, Canada; Centre de Recherche du Centre Hospitalier Universitaire de Sherbrooke, Sherbrooke, QC J1H 5N4, Canada
| | - Guillaume Bourque
- McGill University and Génome Québec Innovation Center, Montréal, QC H3A 0G1, Canada; Department of Human Genetics, McGill University, Montréal, QC H3A 0G1, Canada.
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Morin A, Kwan T, Ge B, Letourneau L, Ban M, Tandre K, Caron M, Sandling JK, Carlsson J, Bourque G, Laprise C, Montpetit A, Syvanen AC, Ronnblom L, Sawcer SJ, Lathrop MG, Pastinen T. Immunoseq: the identification of functionally relevant variants through targeted capture and sequencing of active regulatory regions in human immune cells. BMC Med Genomics 2016; 9:59. [PMID: 27624058 PMCID: PMC5022205 DOI: 10.1186/s12920-016-0220-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2015] [Accepted: 09/01/2016] [Indexed: 12/14/2022] Open
Abstract
Background The observation that the genetic variants identified in genome-wide association studies (GWAS) frequently lie in non-coding regions of the genome that contain cis-regulatory elements suggests that altered gene expression underlies the development of many complex traits. In order to efficiently make a comprehensive assessment of the impact of non-coding genetic variation in immune related diseases we emulated the whole-exome sequencing paradigm and developed a custom capture panel for the known DNase I hypersensitive site (DHS) in immune cells – “Immunoseq”. Results We performed Immunoseq in 30 healthy individuals where we had existing transcriptome data from T cells. We identified a large number of novel non-coding variants in these samples. Relying on allele specific expression measurements, we also showed that our selected capture regions are enriched for functional variants that have an impact on differential allelic gene expression. The results from a replication set with 180 samples confirmed our observations. Conclusions We show that Immunoseq is a powerful approach to detect novel rare variants in regulatory regions. We also demonstrate that these novel variants have a potential functional role in immune cells. Electronic supplementary material The online version of this article (doi:10.1186/s12920-016-0220-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Andréanne Morin
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Bing Ge
- McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Louis Letourneau
- McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Maria Ban
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Karolina Tandre
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
| | - Maxime Caron
- McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Johanna K Sandling
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden.,Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Jonas Carlsson
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Catherine Laprise
- Département des sciences fondamentales, Université du Québec à Chicoutimi, Saguenay, Quebec, Canada
| | - Alexandre Montpetit
- McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Ann-Christine Syvanen
- Department of Medical Sciences, Molecular Medicine and Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Lars Ronnblom
- Department of Medical Sciences, Section of Rheumatology, Uppsala University, Uppsala, Sweden
| | - Stephen J Sawcer
- Department of Clinical Neurosciences, University of Cambridge, Cambridge, UK
| | - Mark G Lathrop
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada.,McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, Montréal, Quebec, Canada. .,McGill University and Genome Québec Innovation Centre, Montréal, Quebec, Canada.
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Deblois G, Smith HW, Tam IS, Gravel SP, Caron M, Savage P, Labbé DP, Bégin LR, Tremblay ML, Park M, Bourque G, St-Pierre J, Muller WJ, Giguère V. ERRα mediates metabolic adaptations driving lapatinib resistance in breast cancer. Nat Commun 2016; 7:12156. [PMID: 27402251 PMCID: PMC4945959 DOI: 10.1038/ncomms12156] [Citation(s) in RCA: 80] [Impact Index Per Article: 10.0] [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: 10/09/2015] [Accepted: 06/06/2016] [Indexed: 12/27/2022] Open
Abstract
Despite the initial benefits of treating HER2-amplified breast cancer patients with the tyrosine kinase inhibitor lapatinib, resistance inevitably develops. Here we report that lapatinib induces the degradation of the nuclear receptor ERRα, a master regulator of cellular metabolism, and that the expression of ERRα is restored in lapatinib-resistant breast cancer cells through reactivation of mTOR signalling. Re-expression of ERRα in resistant cells triggers metabolic adaptations favouring mitochondrial energy metabolism through increased glutamine metabolism, as well as ROS detoxification required for cell survival under therapeutic stress conditions. An ERRα inverse agonist counteracts these metabolic adaptations and overcomes lapatinib resistance in a HER2-induced mammary tumour mouse model. This work reveals a molecular mechanism by which ERRα-induced metabolic reprogramming promotes survival of lapatinib-resistant cancer cells and demonstrates the potential of ERRα inhibition as an effective adjuvant therapy in poor outcome HER2-positive breast cancer.
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Affiliation(s)
- Geneviève Deblois
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada H3A 1A3
- Department of Biochemistry, McGill University, Montréal, Québec, Canada H3G 1Y6
| | - Harvey W. Smith
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada H3A 1A3
| | - Ingrid S. Tam
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada H3A 1A3
| | - Simon-Pierre Gravel
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada H3A 1A3
| | - Maxime Caron
- Department of Human Genetics, McGill University, Montréal, Québec, Canada H3G 1Y6
| | - Paul Savage
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada H3A 1A3
- Department of Medicine, McGill University, Montréal, Québec, Canada H3A 1A3
| | - David P. Labbé
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada H3A 1A3
- Department of Medicine, McGill University, Montréal, Québec, Canada H3A 1A3
| | - Louis R. Bégin
- Service d'anatomopathologie, Hôpital du Sacré-Cœur de Montréal, 5400 Boulevard Gouin Ouest, Montréal, Québec, Canada H4J 1C5
| | - Michel L. Tremblay
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada H3A 1A3
- Department of Biochemistry, McGill University, Montréal, Québec, Canada H3G 1Y6
- Department of Medicine, McGill University, Montréal, Québec, Canada H3A 1A3
- Department of Oncology, McGill University, Montréal, Québec, Canada H2W 1S6
| | - Morag Park
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada H3A 1A3
- Department of Biochemistry, McGill University, Montréal, Québec, Canada H3G 1Y6
- Department of Medicine, McGill University, Montréal, Québec, Canada H3A 1A3
- Department of Oncology, McGill University, Montréal, Québec, Canada H2W 1S6
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, Montréal, Québec, Canada H3G 1Y6
| | - Julie St-Pierre
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada H3A 1A3
- Department of Biochemistry, McGill University, Montréal, Québec, Canada H3G 1Y6
| | - William J. Muller
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada H3A 1A3
- Department of Biochemistry, McGill University, Montréal, Québec, Canada H3G 1Y6
- Department of Medicine, McGill University, Montréal, Québec, Canada H3A 1A3
| | - Vincent Giguère
- Goodman Cancer Research Centre, McGill University, Montréal, Québec, Canada H3A 1A3
- Department of Biochemistry, McGill University, Montréal, Québec, Canada H3G 1Y6
- Department of Medicine, McGill University, Montréal, Québec, Canada H3A 1A3
- Department of Oncology, McGill University, Montréal, Québec, Canada H2W 1S6
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34
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Audet-Walsh É, Papadopoli DJ, Gravel SP, Yee T, Bridon G, Caron M, Bourque G, Giguère V, St-Pierre J. The PGC-1α/ERRα Axis Represses One-Carbon Metabolism and Promotes Sensitivity to Anti-folate Therapy in Breast Cancer. Cell Rep 2016; 14:920-931. [PMID: 26804918 DOI: 10.1016/j.celrep.2015.12.086] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [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: 06/22/2015] [Revised: 11/02/2015] [Accepted: 12/18/2015] [Indexed: 01/18/2023] Open
Abstract
Reprogramming of cellular metabolism plays a central role in fueling malignant transformation, and AMPK and the PGC-1α/ERRα axis are key regulators of this process. The intersection of gene-expression and binding-event datasets for breast cancer cells shows that activation of AMPK significantly increases the expression of PGC-1α/ERRα and promotes the binding of ERRα to its cognate sites. Unexpectedly, the data also reveal that ERRα, in concert with PGC-1α, negatively regulates the expression of several one-carbon metabolism genes, resulting in substantial perturbations in purine biosynthesis. This PGC-1α/ERRα-mediated repression of one-carbon metabolism promotes the sensitivity of breast cancer cells and tumors to the anti-folate drug methotrexate. These data implicate the PGC-1α/ERRα axis as a core regulatory node of folate cycle metabolism and further suggest that activators of AMPK could be used to modulate this pathway in cancer.
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Affiliation(s)
- Étienne Audet-Walsh
- Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - David J Papadopoli
- Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Simon-Pierre Gravel
- Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - Tracey Yee
- Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Gaëlle Bridon
- Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada
| | - Maxime Caron
- McGill University and Génome Québec Innovation Centre, Montréal, QC H3A 0G1, Canada
| | - Guillaume Bourque
- McGill University and Génome Québec Innovation Centre, Montréal, QC H3A 0G1, Canada; Department of Human Genetics, McGill University, Montréal, QC H3G 1Y6, Canada
| | - Vincent Giguère
- Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada; Departments of Medicine and Oncology, McGill University, Montréal, QC H3G 1Y6, Canada.
| | - Julie St-Pierre
- Goodman Cancer Research Centre, McGill University, Montréal, QC H3A 1A3, Canada; Department of Biochemistry, McGill University, Montréal, QC H3G 1Y6, Canada.
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35
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Busche S, Shao X, Caron M, Kwan T, Allum F, Cheung WA, Ge B, Westfall S, Simon MM, Barrett A, Bell JT, McCarthy MI, Deloukas P, Blanchette M, Bourque G, Spector TD, Lathrop M, Pastinen T, Grundberg E. Population whole-genome bisulfite sequencing across two tissues highlights the environment as the principal source of human methylome variation. Genome Biol 2015; 16:290. [PMID: 26699896 PMCID: PMC4699357 DOI: 10.1186/s13059-015-0856-1] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Accepted: 12/09/2015] [Indexed: 12/24/2022] Open
Abstract
Background CpG methylation variation is involved in human trait formation and disease susceptibility. Analyses within populations have been biased towards CpG-dense regions through the application of targeted arrays. We generate whole-genome bisulfite sequencing data for approximately 30 adipose and blood samples from monozygotic and dizygotic twins for the characterization of non-genetic and genetic effects at single-site resolution. Results Purely invariable CpGs display a bimodal distribution with enrichment of unmethylated CpGs and depletion of fully methylated CpGs in promoter and enhancer regions. Population-variable CpGs account for approximately 15–20 % of total CpGs per tissue, are enriched in enhancer-associated regions and depleted in promoters, and single nucleotide polymorphisms at CpGs are a frequent confounder of extreme methylation variation. Differential methylation is primarily non-genetic in origin, with non-shared environment accounting for most of the variance. These non-genetic effects are mainly tissue-specific. Tobacco smoking is associated with differential methylation in blood with no evidence of this exposure impacting cell counts. Opposite to non-genetic effects, genetic effects of CpG methylation are shared across tissues and thus limit inter-tissue epigenetic drift. CpH methylation is rare, and shows similar characteristics of variation patterns as CpGs. Conclusions Our study highlights the utility of low pass whole-genome bisulfite sequencing in identifying methylome variation beyond promoter regions, and suggests that targeting the population dynamic methylome of tissues requires assessment of understudied intergenic CpGs distal to gene promoters to reveal the full extent of inter-individual variation. Electronic supplementary material The online version of this article (doi:10.1186/s13059-015-0856-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephan Busche
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Xiaojian Shao
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Maxime Caron
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Tony Kwan
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Fiona Allum
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Warren A Cheung
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Bing Ge
- McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Susan Westfall
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada.
| | - Marie-Michelle Simon
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | | | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, UK.
| | - Jordana T Bell
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Mark I McCarthy
- Oxford Centre for Diabetes, Endocrinology & Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford, UK. .,Wellcome Trust Centre for Human Genetics, University of Oxford, Oxford, UK. .,Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Headington, Oxford, UK.
| | - Panos Deloukas
- William Harvey Research Institute, Queen Mary University of London, London, UK. .,Wellcome Trust Sanger Institute, Hinxton, Cambridge, UK.
| | - Mathieu Blanchette
- School of Computer Science, McGill University, Montreal, Quebec, Canada.
| | - Guillaume Bourque
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Timothy D Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, London, UK.
| | - Mark Lathrop
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
| | - Elin Grundberg
- Department of Human Genetics, McGill University, 740 Dr. Penfield Avenue, H3A 0G1, Montreal, Quebec, Canada. .,McGill University and Genome Quebec Innovation Centre, Montreal, Quebec, Canada.
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Caron M, Bédard L, Latreille J, Buckeridge DL. An exploratory analysis of individuals with multiple episodes of different reportable diseases, Montreal, 1990-2012. Public Health 2015; 131:49-55. [PMID: 26715312 DOI: 10.1016/j.puhe.2015.10.032] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2015] [Revised: 08/28/2015] [Accepted: 10/29/2015] [Indexed: 11/17/2022]
Abstract
OBJECTIVES Studies of public health reporting have only examined multiple episodes of the same communicable disease within an individual. We aimed to characterize Montreal residents with multiple reportable disease episodes from 1990 to 2012, while accounting for all types of reportable diseases. STUDY DESIGN Retrospective cohort study. METHODS We performed an exploratory analysis using descriptive statistics, contingency tables, and logistic regression. RESULTS There were 157,839 individuals with at least one disease report and a total of 179,455 disease reports. The 9.8% of subjects with more than one episode accounted for 20.7% of all reported episodes. Among subjects with four or fewer episodes, 54.0% were women, while 74.3% of subjects with five or more episodes were men. Subjects with multiple episodes were more likely to be reported for sexually transmitted infections than were persons with a single episode [difference of proportions: 10.4% (95% CI: 10.0%-10.9%)] and to reside in the neighbourhood encompassing Montreal's gay village. CONCLUSIONS Individuals with multiple communicable disease reports place a large burden on public health officials. These results may help guide investigation and prevention efforts to reduce the number of excess episodes.
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Affiliation(s)
- M Caron
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada
| | - L Bédard
- Direction de santé publique, CIUSSS du Centre-Est-de-l'Île-de-Montréal, Montreal, QC, Canada; École de santé publique, Université de Montréal, Montreal, QC, Canada
| | - J Latreille
- Direction de santé publique, CIUSSS du Centre-Est-de-l'Île-de-Montréal, Montreal, QC, Canada
| | - D L Buckeridge
- Department of Epidemiology, Biostatistics and Occupational Health, McGill University, Montreal, QC, Canada; Direction de santé publique, CIUSSS du Centre-Est-de-l'Île-de-Montréal, Montreal, QC, Canada.
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Castrejon I, Carmona L, Agrinier N, Andres M, Briot K, Caron M, Christensen R, Consolaro A, Curbelo R, Ferrer M, Foltz V, Gonzalez C, Guillemin F, Machado PM, Prodinger B, Ravelli A, Scholte-Voshaar M, Uhlig T, van Tuyl LHD, Zink A, Gossec L. The EULAR Outcome Measures Library: development and an example from a systematic review for systemic lupus erythematous instruments. Clin Exp Rheumatol 2015; 33:910-916. [PMID: 25797345] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2014] [Accepted: 01/09/2015] [Indexed: 06/04/2023]
Abstract
OBJECTIVES Patient reported outcomes (PROs) are relevant in rheumatology. Variable accessibility and validity of commonly used PROs are obstacles to homogeneity in evidence synthesis. The objective of this project was to provide a comprehensive library of "validated PROs". METHODS A launch meeting with rheumatologists, PROs methodological experts, and patients, was held to define the library's aims and scope, and basic requirements. To feed the library we performed systematic reviews on selected diseases and domains. Relevant information on PROs was collected using standardised data collection forms based on the COSMIN checklist. RESULTS The EULAR Outcomes Measures Library (OML), whose aims are to provide and to advise on PROs on a user-friendly manner albeit based on scientific grounds, has been launched and made accessible to all. PROs currently included cover any domain and, are generic or specifically target to the following diseases: rheumatoid arthritis, osteoarthritis, spondyloarthritis, low back pain, systemic lupus erythematosus, gout, osteoporosis, juvenile idiopathic arthritis, and fibromyalgia. Up to 236 instruments (106 generic and 130 specific) have been identified, evaluated, and included. The systematic review for SLE, which yielded 10 specific instruments, is presented here as an example. The OML website includes, for each PRO, information on the construct being measured and the extent of validation, recommendations for use, and available versions; it also contains a glossary on common validation terms. CONCLUSIONS The OML is an in progress library led by rheumatologists, related professionals and patients, that will help to better understand and apply PROs in rheumatic and musculoskeletal diseases.
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Affiliation(s)
- I Castrejon
- Division of Rheumatology, Rush University Medical Center, Chicago, USA.
| | - L Carmona
- Instituto de Salud Musculoesquelética, Madrid, Spain
| | - N Agrinier
- University of Lorraine, APEMAC EA 4360, Nancy, F-54500; France & Inserm CIC-EC, 1433, Nancy, F-54500, France
| | - M Andres
- Seccion de Reumatologia. Hospital, General Universitario de Alicante, Alicante, Spain
| | - K Briot
- Paris-Descartes University, Medicine Faculty, Cochin Hospital, Paris, France
| | | | - R Christensen
- Musculoskeletal Statistics Unit, The Parker Institute, Department of Rheumatology, Copenhagen University Hospital, Bispebjerg and Frederiksberg, Denmark
| | | | - R Curbelo
- Instituto de Salud Musculoesquelética and Universidad de Valladolid, Spain
| | - Montserrat Ferrer
- Health Services Research Group, Medical Research Institute (Hospital del Mar), Barcelona, Spain. Coordinator of BiblioPRO
| | - Violaine Foltz
- UPMC Univ Paris 06, GRC-UPMC 08 (EEMOIS); AP-HP, Pitié Salpêtrière Hospital, Department of Rheumatology, Paris, France
| | - C Gonzalez
- Universidad Camilo José Cela, Madrid, Spain
| | - F Guillemin
- University of Lorraine, APEMAC EA 4360, Nancy, F-54500; France & Inserm CIC-EC, 1433, Nancy, F-54500, France
| | - P M Machado
- Coimbra University Hospital, Coimbra, Portugal; and MRC Centre for Neuromuscular Diseases, University College London, London, UK
| | | | - A Ravelli
- University of Genoa and Institute Giannina Gaslini, Genoa, Italy
| | - M Scholte-Voshaar
- Department of Psychology, Health and Technology, University of Twente, Enschede, The Netherlands
| | - T Uhlig
- National Resource Center for Rehabilitation in Rheumatology, Department of Rheumatology, Diakonhjemmet Hospital, Oslo, Norway
| | - L H D van Tuyl
- Department of Rheumatology, VU University Medical Center, Amsterdam, The Netherlands
| | - A Zink
- German Rheumatism Research Centre and Charité University Medicine, Berlin, Germany
| | - L Gossec
- UPMC Univ Paris 06, GRC-UPMC 08 (EEMOIS); AP-HP, Pitié Salpêtrière Hospital, Department of Rheumatology, Paris, France
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38
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Riahi M, Naim C, Gobeil F, Mansour S, Matteau A, Essiambre R, Montigny M, Caron M, Sareault I, Potter B. IMPACT OF A MULTI-PRONGED INTERVENTION ON THE RATE OF INAPPROPRIATE CATHETERIZATION LABORATORY ACTIVATION USING AN AUTOMATED SYSTEM OF PRE-HOSPITAL STEMI DIAGNOSIS. Can J Cardiol 2015. [DOI: 10.1016/j.cjca.2015.07.056] [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: 11/15/2022] Open
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39
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Naim C, Riahi M, Gobeil F, Matteau A, Mansour S, Essiambre R, Montigny M, Caron M, Sareault I, Potter B. SUSTAINABILITY OF “PHYSICIAN-LESS” AUTOMATED PRE-HOSPITAL STEMI DIAGNOSIS AND CATHETERIZATION LABORATORY ACTIVATION TO ENSURE DOOR-TO-BALLOON TIMES: UPDATE AT 5 YEARS. Can J Cardiol 2015. [DOI: 10.1016/j.cjca.2015.07.194] [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: 10/22/2022] Open
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40
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Aarabi M, San Gabriel MC, Chan D, Behan NA, Caron M, Pastinen T, Bourque G, MacFarlane AJ, Zini A, Trasler J. High-dose folic acid supplementation alters the human sperm methylome and is influenced by the MTHFR C677T polymorphism. Hum Mol Genet 2015; 24:6301-13. [PMID: 26307085 DOI: 10.1093/hmg/ddv338] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2015] [Accepted: 08/17/2015] [Indexed: 12/24/2022] Open
Abstract
Dietary folate is a major source of methyl groups required for DNA methylation, an epigenetic modification that is actively maintained and remodeled during spermatogenesis. While high-dose folic acid supplementation (up to 10 times the daily recommended dose) has been shown to improve sperm parameters in infertile men, the effects of supplementation on the sperm epigenome are unknown. To assess the impact of 6 months of high-dose folic acid supplementation on the sperm epigenome, we studied 30 men with idiopathic infertility. Blood folate concentrations increased significantly after supplementation with no significant improvements in sperm parameters. Methylation levels of the differentially methylated regions of several imprinted loci (H19, DLK1/GTL2, MEST, SNRPN, PLAGL1, KCNQ1OT1) were normal both before and after supplementation. Reduced representation bisulfite sequencing (RRBS) revealed a significant global loss of methylation across different regions of the sperm genome. The most marked loss of DNA methylation was found in sperm from patients homozygous for the methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism, a common polymorphism in a key enzyme required for folate metabolism. RRBS analysis also showed that most of the differentially methylated tiles were located in DNA repeats, low CpG-density and intergenic regions. Ingenuity Pathway Analysis revealed that methylation of promoter regions was altered in several genes involved in cancer and neurobehavioral disorders including CBFA2T3, PTPN6, COL18A1, ALDH2, UBE4B, ERBB2, GABRB3, CNTNAP4 and NIPA1. Our data reveal alterations of the human sperm epigenome associated with high-dose folic acid supplementation, effects that were exacerbated by a common polymorphism in MTHFR.
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Affiliation(s)
- Mahmoud Aarabi
- Department of Human Genetics, Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada H4A 3J1
| | - Maria C San Gabriel
- Division of Urology, Department of Surgery and, Research Institute of the McGill University Health Centre, Montreal, QC, Canada H4A 3J1
| | - Donovan Chan
- Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada H4A 3J1
| | - Nathalie A Behan
- Nutrition Research Division, Health Canada, Ottawa, ON, Canada K1A 0K9 and
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada H3A 1A4
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada H3A 1A4
| | - Guillaume Bourque
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada H3A 1A4
| | | | - Armand Zini
- Division of Urology, Department of Surgery and, Research Institute of the McGill University Health Centre, Montreal, QC, Canada H4A 3J1
| | - Jacquetta Trasler
- Department of Human Genetics, Departments of Pediatrics and Pharmacology & Therapeutics, McGill University, Montreal, QC, Canada H4A 3J1, Montreal Children's Hospital and Research Institute of the McGill University Health Centre, Montreal, QC, Canada H4A 3J1,
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41
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Allum F, Shao X, Guénard F, Simon MM, Busche S, Caron M, Lambourne J, Lessard J, Tandre K, Hedman ÅK, Kwan T, Ge B, Rönnblom L, McCarthy MI, Deloukas P, Richmond T, Burgess D, Spector TD, Tchernof A, Marceau S, Lathrop M, Vohl MC, Pastinen T, Grundberg E. Erratum: Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nat Commun 2015. [PMID: 26219997 DOI: 10.1038/ncomms9016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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42
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Dyke SOM, Cheung WA, Joly Y, Ammerpohl O, Lutsik P, Rothstein MA, Caron M, Busche S, Bourque G, Rönnblom L, Flicek P, Beck S, Hirst M, Stunnenberg H, Siebert R, Walter J, Pastinen T. Epigenome data release: a participant-centered approach to privacy protection. Genome Biol 2015; 16:142. [PMID: 26185018 PMCID: PMC4504083 DOI: 10.1186/s13059-015-0723-0] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [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: 05/04/2015] [Accepted: 07/09/2015] [Indexed: 11/10/2022] Open
Abstract
Large-scale epigenome mapping by the NIH Roadmap Epigenomics Project, the ENCODE Consortium and the International Human Epigenome Consortium (IHEC) produces genome-wide DNA methylation data at one base-pair resolution. We examine how such data can be made open-access while balancing appropriate interpretation and genomic privacy. We propose guidelines for data release that both reduce ambiguity in the interpretation of open-access data and limit immediate access to genetic variation data that are made available through controlled access.
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Affiliation(s)
- Stephanie O M Dyke
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC, H3A 0G1, Canada.
| | - Warren A Cheung
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Yann Joly
- Centre of Genomics and Policy, Department of Human Genetics, McGill University, Montreal, QC, H3A 0G1, Canada
| | - Ole Ammerpohl
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel & Christian-Albrechts-University Kiel, 24105, Kiel, Germany
| | - Pavlo Lutsik
- Saarland University, 66123, Saarbrücken, Germany
| | - Mark A Rothstein
- Institute for Bioethics, Health Policy and Law, University of Louisville School of Medicine, Louisville, KY, 40202, USA
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Stephan Busche
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada
| | - Lars Rönnblom
- Department of Medical Sciences, Science for Life Laboratory, Uppsala University, SE-751 85, Uppsala, Sweden
| | - Paul Flicek
- European Molecular Biology Laboratory, European Bioinformatics Institute, Wellcome Genome Campus, Hinxton, Cambridge, CB10 1SD, UK
| | - Stephan Beck
- Medical Genomics, UCL Cancer Institute, University College London, London, WC1E 6BT, UK
| | - Martin Hirst
- Centre for High-Throughput Biology, University of British Columbia and Canada's Michael Smith Genome Sciences Centre, BC Cancer Agency, Vancouver, British Columbia, V5Z 4S6, Canada
| | - Henk Stunnenberg
- Department of Molecular Biology, RIMLS, Faculty of Science, Radboud University, 6500 HB, Nijmegen, The Netherlands
| | - Reiner Siebert
- Institute of Human Genetics, University Hospital Schleswig-Holstein, Campus Kiel & Christian-Albrechts-University Kiel, 24105, Kiel, Germany
| | - Jörn Walter
- Saarland University, 66123, Saarbrücken, Germany
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, H3A 0G1, Canada.
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43
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Allum F, Shao X, Guénard F, Simon MM, Busche S, Caron M, Lambourne J, Lessard J, Tandre K, Hedman ÅK, Kwan T, Ge B, Rönnblom L, McCarthy MI, Deloukas P, Richmond T, Burgess D, Spector TD, Tchernof A, Marceau S, Lathrop M, Vohl MC, Pastinen T, Grundberg E. Characterization of functional methylomes by next-generation capture sequencing identifies novel disease-associated variants. Nat Commun 2015; 6:7211. [PMID: 26021296 PMCID: PMC4544751 DOI: 10.1038/ncomms8211] [Citation(s) in RCA: 72] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2014] [Accepted: 04/17/2015] [Indexed: 02/02/2023] Open
Abstract
Most genome-wide methylation studies (EWAS) of multifactorial disease traits use targeted arrays or enrichment methodologies preferentially covering CpG-dense regions, to characterize sufficiently large samples. To overcome this limitation, we present here a new customizable, cost-effective approach, methylC-capture sequencing (MCC-Seq), for sequencing functional methylomes, while simultaneously providing genetic variation information. To illustrate MCC-Seq, we use whole-genome bisulfite sequencing on adipose tissue (AT) samples and public databases to design AT-specific panels. We establish its efficiency for high-density interrogation of methylome variability by systematic comparisons with other approaches and demonstrate its applicability by identifying novel methylation variation within enhancers strongly correlated to plasma triglyceride and HDL-cholesterol, including at CD36. Our more comprehensive AT panel assesses tissue methylation and genotypes in parallel at ∼4 and ∼3 M sites, respectively. Our study demonstrates that MCC-Seq provides comparable accuracy to alternative approaches but enables more efficient cataloguing of functional and disease-relevant epigenetic and genetic variants for large-scale EWAS.
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Affiliation(s)
- Fiona Allum
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Xiaojian Shao
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Frédéric Guénard
- Institute of Nutrition and Functional Foods (INAF), Université Laval, 2440 Hochelaga Boulevard, Québec, Québec, Canada G1V 0A6
| | - Marie-Michelle Simon
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Stephan Busche
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Maxime Caron
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - John Lambourne
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Julie Lessard
- Québec Heart and Lung Institute, Université Laval, 2725 Sainte-Foy Road, Québec, Québec, Canada G1V 4G5
| | - Karolina Tandre
- Department of Medical Sciences, Uppsala University, Akademiska sjukhuset Ingång 40, Uppsala 75185, Sweden
| | - Åsa K. Hedman
- Department of Medical Sciences, Molecular Epidemiology, Uppsala University, Dag Hammarskjölds väg 14B, Uppsala 75185, Sweden,Science for Life Laboratory, Uppsala University, Dag Hammarskjölds väg 14B, Uppsala 75185, Sweden
| | - Tony Kwan
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Bing Ge
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Lars Rönnblom
- Department of Medical Sciences, Uppsala University, Akademiska sjukhuset Ingång 40, Uppsala 75185, Sweden
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, Roosevelt Drive, Oxford OX3 7BN, UK,Oxford Centre for Diabetes, Endocrinology and Metabolism, University of Oxford, Churchill Hospital, Headington, Oxford OX3 7JU, UK,Oxford National Institute for Health Research Biomedical Research Centre, Churchill Hospital, Headington, Oxford OX3 7JU, UK
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK,William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, Charterhouse Square, London EC1M 6BQ, UK
| | - Todd Richmond
- Roche NimbleGen, 500 South Rosa Road, Madison, Wisconsin 53719, USA
| | - Daniel Burgess
- Roche NimbleGen, 500 South Rosa Road, Madison, Wisconsin 53719, USA
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King's College London, St Thomas' Campus, Lambeth Palace Road, London SE17EH, UK
| | - André Tchernof
- Québec Heart and Lung Institute, Université Laval, 2725 Sainte-Foy Road, Québec, Québec, Canada G1V 4G5
| | - Simon Marceau
- Québec Heart and Lung Institute, Université Laval, 2725 Sainte-Foy Road, Québec, Québec, Canada G1V 4G5
| | - Mark Lathrop
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Marie-Claude Vohl
- Institute of Nutrition and Functional Foods (INAF), Université Laval, 2440 Hochelaga Boulevard, Québec, Québec, Canada G1V 0A6
| | - Tomi Pastinen
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1
| | - Elin Grundberg
- Department of Human Genetics, McGill University, 740 Docteur-Penfield Avenue, Montreal, Québec , Canada H3A 0G1,McGill University and Genome Quebec Innovation Centre, 740 Docteur-Penfield Avenue, Montreal, Québec, Canada H3A 0G1,
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44
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McGraw S, Zhang JX, Farag M, Chan D, Caron M, Konermann C, Oakes CC, Mohan KN, Plass C, Pastinen T, Bourque G, Chaillet JR, Trasler JM. Transient DNMT1 suppression reveals hidden heritable marks in the genome. Nucleic Acids Res 2015; 43:1485-97. [PMID: 25578964 PMCID: PMC4330356 DOI: 10.1093/nar/gku1386] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [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: 11/14/2022] Open
Abstract
Genome-wide demethylation and remethylation of DNA during early embryogenesis is essential for development. Imprinted germline differentially methylated domains (gDMDs) established by sex-specific methylation in either male or female germ cells, must escape these dynamic changes and sustain precise inheritance of both methylated and unmethylated parental alleles. To identify other, gDMD-like sequences with the same epigenetic inheritance properties, we used a modified embryonic stem (ES) cell line that emulates the early embryonic demethylation and remethylation waves. Transient DNMT1 suppression revealed gDMD-like sequences requiring continuous DNMT1 activity to sustain a highly methylated state. Remethylation of these sequences was also compromised in vivo in a mouse model of transient DNMT1 loss in the preimplantation embryo. These novel regions, possessing heritable epigenetic features similar to imprinted-gDMDs are required for normal physiological and developmental processes and when disrupted are associated with disorders such as cancer and autism spectrum disorders. This study presents new perspectives on DNA methylation heritability during early embryo development that extend beyond conventional imprinted-gDMDs.
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Affiliation(s)
- Serge McGraw
- Departments of Pediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and the Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, QC H3Z 2Z3, Canada
| | - Jacques X Zhang
- Departments of Pediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and the Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, QC H3Z 2Z3, Canada
| | - Mena Farag
- Departments of Pediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and the Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, QC H3Z 2Z3, Canada
| | - Donovan Chan
- Departments of Pediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and the Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, QC H3Z 2Z3, Canada
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 1A4, Canada
| | - Carolin Konermann
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg 69120, Germany
| | - Christopher C Oakes
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg 69120, Germany
| | - K Naga Mohan
- Department of Biological Sciences, Birla Institute of Technology and Science Pilani, Hyderabad 500 078, India
| | - Christoph Plass
- Division of Epigenomics and Cancer Risk Factors, German Cancer Research Center, Heidelberg 69120, Germany
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 1A4, Canada
| | - Guillaume Bourque
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A 1A4, Canada
| | - J Richard Chaillet
- Department of Microbiology and Molecular Genetics, University of Pittsburgh, Pittsburgh, PA 15213-3005, USA
| | - Jacquetta M Trasler
- Departments of Pediatrics, Human Genetics and Pharmacology & Therapeutics, McGill University and the Research Institute of the McGill University Health Centre at the Montreal Children's Hospital, Montreal, QC H3Z 2Z3, Canada
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45
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Adoue V, Schiavi A, Light N, Almlöf JC, Lundmark P, Ge B, Kwan T, Caron M, Rönnblom L, Wang C, Chen SH, Goodall AH, Cambien F, Deloukas P, Ouwehand WH, Syvänen AC, Pastinen T. Allelic expression mapping across cellular lineages to establish impact of non-coding SNPs. Mol Syst Biol 2014; 10:754. [PMID: 25326100 PMCID: PMC4299376 DOI: 10.15252/msb.20145114] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [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] [Indexed: 02/06/2023] Open
Abstract
Most complex disease-associated genetic variants are located in non-coding regions and are
therefore thought to be regulatory in nature. Association mapping of differential allelic expression
(AE) is a powerful method to identify SNPs with direct cis-regulatory impact
(cis-rSNPs). We used AE mapping to identify cis-rSNPs regulating
gene expression in 55 and 63 HapMap lymphoblastoid cell lines from a Caucasian and an African
population, respectively, 70 fibroblast cell lines, and 188 purified monocyte samples and found
40–60% of these cis-rSNPs to be shared across cell types. We uncover
a new class of cis-rSNPs, which disrupt footprint-derived de novo
motifs that are predominantly bound by repressive factors and are implicated in disease
susceptibility through overlaps with GWAS SNPs. Finally, we provide the proof-of-principle for a new
approach for genome-wide functional validation of transcription factor–SNP interactions. By
perturbing NFκB action in lymphoblasts, we identified 489 cis-regulated
transcripts with altered AE after NFκB perturbation. Altogether, we perform a comprehensive
analysis of cis-variation in four cell populations and provide new tools for the
identification of functional variants associated to complex diseases.
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Affiliation(s)
- Veronique Adoue
- Institute National de la Santé et de la Recherche Médicale (INSERM), U1043, Toulouse, France
| | - Alicia Schiavi
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Nicholas Light
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Jonas Carlsson Almlöf
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Per Lundmark
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Bing Ge
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Tony Kwan
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Lars Rönnblom
- Rheumatology, Department of Medical Sciences, Uppsala University, Uppsala, Sweden
| | - Chuan Wang
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Shu-Huang Chen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
| | - Alison H Goodall
- Department of Cardiovascular Science, University of Leicester, Leicester, UK Leicester NIHR Biomedical Research Unit in Cardiovascular Disease, Glenfield Hospital, Leicester, UK Cardiogenics Consortium
| | - Francois Cambien
- Cardiogenics Consortium INSERM UMRS 937 Pierre and Marie Curie University and Medical School, Paris, France
| | - Panos Deloukas
- Cardiogenics Consortium Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Cambridge, UK
| | - Willem H Ouwehand
- Cardiogenics Consortium Department of Haematology, University of Cambridge, Cambridge, UK National Health Service Blood and Transplant, Cambridge Centre, Cambridge, UK
| | - Ann-Christine Syvänen
- Department of Medical Sciences, Molecular Medicine, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Tomi Pastinen
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC, Canada
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46
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Kleinman CL, Gerges N, Papillon-Cavanagh S, Sin-Chan P, Pramatarova A, Quang DAK, Adoue V, Busche S, Caron M, Djambazian H, Bemmo A, Fontebasso AM, Spence T, Schwartzentruber J, Albrecht S, Hauser P, Garami M, Klekner A, Bognar L, Montes JL, Staffa A, Montpetit A, Berube P, Zakrzewska M, Zakrzewski K, Liberski PP, Dong Z, Siegel PM, Duchaine T, Perotti C, Fleming A, Faury D, Remke M, Gallo M, Dirks P, Taylor MD, Sladek R, Pastinen T, Chan JA, Huang A, Majewski J, Jabado N. Fusion of TTYH1 with the C19MC microRNA cluster drives expression of a brain-specific DNMT3B isoform in the embryonal brain tumor ETMR. Nat Genet 2014; 46:39-44. [PMID: 24316981 DOI: 10.1038/ng.2849] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2013] [Accepted: 11/13/2013] [Indexed: 12/20/2022]
Abstract
Embryonal tumors with multilayered rosettes (ETMRs) are rare, deadly pediatric brain tumors characterized by high-level amplification of the microRNA cluster C19MC. We performed integrated genetic and epigenetic analyses of 12 ETMR samples and identified, in all cases, C19MC fusions to TTYH1 driving expression of the microRNAs. ETMR tumors, cell lines and xenografts showed a specific DNA methylation pattern distinct from those of other tumors and normal tissues. We detected extreme overexpression of a previously uncharacterized isoform of DNMT3B originating at an alternative promoter that is active only in the first weeks of neural tube development. Transcriptional and immunohistochemical analyses suggest that C19MC-dependent DNMT3B deregulation is mediated by RBL2, a known repressor of DNMT3B. Transfection with individual C19MC microRNAs resulted in DNMT3B upregulation and RBL2 downregulation in cultured cells. Our data suggest a potential oncogenic re-engagement of an early developmental program in ETMR via epigenetic alteration mediated by an embryonic, brain-specific DNMT3B isoform.
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Affiliation(s)
- Claudia L Kleinman
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [3]
| | - Noha Gerges
- 1] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [2]
| | | | - Patrick Sin-Chan
- Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Albena Pramatarova
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | | | - Véronique Adoue
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Stephan Busche
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Maxime Caron
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Haig Djambazian
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Amandine Bemmo
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Adam M Fontebasso
- Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada
| | - Tara Spence
- Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | | | - Steffen Albrecht
- Department of Pathology, McGill University Health Centre, Montreal, Quebec, Canada
| | - Peter Hauser
- Second Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Miklos Garami
- Second Department of Paediatrics, Semmelweis University, Budapest, Hungary
| | - Almos Klekner
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Laszlo Bognar
- Department of Neurosurgery, Medical and Health Science Center, University of Debrecen, Debrecen, Hungary
| | - Jose-Luis Montes
- Division of Neurosurgery, Department of Surgery, Montreal Children's Hospital, McGill University Health Centre, Montreal, Quebec, Canada
| | - Alfredo Staffa
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Alexandre Montpetit
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Pierre Berube
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Magdalena Zakrzewska
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Krzysztof Zakrzewski
- Department of Neurosurgery, Polish Mother's Memorial Hospital Research Institute, Lodz, Poland
| | - Pawel P Liberski
- Department of Molecular Pathology and Neuropathology, Medical University of Lodz, Lodz, Poland
| | - Zhifeng Dong
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Peter M Siegel
- Rosalind and Morris Goodman Cancer Research Centre, McGill University, Montreal, Quebec, Canada
| | - Thomas Duchaine
- Department of Biochemistry, McGill University, Montreal, Quebec, Canada
| | - Christian Perotti
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Adam Fleming
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, McGill University and the McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Damien Faury
- Division of Pediatric Hematology-Oncology, Department of Pediatrics, McGill University and the McGill University Health Centre Research Institute, Montreal, Quebec, Canada
| | - Marc Remke
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Marco Gallo
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Peter Dirks
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Michael D Taylor
- Division of Neurosurgery, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada
| | - Robert Sladek
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada
| | - Tomi Pastinen
- McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada
| | - Jennifer A Chan
- Department of Pathology & Laboratory Medicine, University of Calgary, Calgary, Alberta, Canada
| | - Annie Huang
- 1] Division of Hematology-Oncology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Toronto, Ontario, Canada. [2] Program in Cell Biology, Arthur & Sonia Labatt Brain Tumour Research Centre, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Ontario, Canada. [3]
| | - Jacek Majewski
- 1] McGill University and Génome Québec Innovation Centre, Montreal, Quebec, Canada. [2] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [3]
| | - Nada Jabado
- 1] Department of Human Genetics, McGill University, Montreal, Quebec, Canada. [2] Division of Experimental Medicine, McGill University, Montreal, Quebec, Canada. [3]
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Grundberg E, Meduri E, Sandling JK, Hedman ÅK, Keildson S, Buil A, Busche S, Yuan W, Nisbet J, Sekowska M, Wilk A, Barrett A, Small KS, Ge B, Caron M, Shin SY, Lathrop M, Dermitzakis ET, McCarthy MI, Spector TD, Bell JT, Deloukas P, Ahmadi KR, Ainali C, Barrett A, Bataille V, Bell JT, Buil A, Deloukas P, Dermitzakis ET, Dimas AS, Durbin R, Glass D, Grundberg E, Hassanali N, Hedman ÅK, Ingle C, Knowles D, Krestyaninova M, Lindgren CM, Lowe CE, McCarthy MI, Meduri E, di Meglio P, Min JL, Montgomery SB, Nestle FO, Nica AC, Nisbet J, O’Rahilly S, Parts L, Potter S, Sandling J, Sekowska M, Shin SY, Small KS, Soranzo N, Spector TD, Surdulescu G, Travers ME, Tsaprouni L, Tsoka S, Wilk A, Yang TP, Zondervan KT. Global Analysis of DNA Methylation Variation in Adipose Tissue from Twins Reveals Links to Disease-Associated Variants in Distal Regulatory Elements. Am J Hum Genet 2013. [DOI: 10.1016/j.ajhg.2013.11.003] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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Grundberg E, Meduri E, Sandling J, Hedman Å, Keildson S, Buil A, Busche S, Yuan W, Nisbet J, Sekowska M, Wilk A, Barrett A, Small K, Ge B, Caron M, Shin SY, Lathrop M, Dermitzakis ET, McCarthy MI, Spector TD, Bell JT, Deloukas P. Global analysis of DNA methylation variation in adipose tissue from twins reveals links to disease-associated variants in distal regulatory elements. Am J Hum Genet 2013; 93:876-90. [PMID: 24183450 PMCID: PMC3824131 DOI: 10.1016/j.ajhg.2013.10.004] [Citation(s) in RCA: 288] [Impact Index Per Article: 26.2] [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: 05/13/2013] [Revised: 08/13/2013] [Accepted: 10/04/2013] [Indexed: 12/28/2022] Open
Abstract
Epigenetic modifications such as DNA methylation play a key role in gene regulation and disease susceptibility. However, little is known about the genome-wide frequency, localization, and function of methylation variation and how it is regulated by genetic and environmental factors. We utilized the Multiple Tissue Human Expression Resource (MuTHER) and generated Illumina 450K adipose methylome data from 648 twins. We found that individual CpGs had low variance and that variability was suppressed in promoters. We noted that DNA methylation variation was highly heritable (h(2)median = 0.34) and that shared environmental effects correlated with metabolic phenotype-associated CpGs. Analysis of methylation quantitative-trait loci (metQTL) revealed that 28% of CpGs were associated with nearby SNPs, and when overlapping them with adipose expression quantitative-trait loci (eQTL) from the same individuals, we found that 6% of the loci played a role in regulating both gene expression and DNA methylation. These associations were bidirectional, but there were pronounced negative associations for promoter CpGs. Integration of metQTL with adipose reference epigenomes and disease associations revealed significant enrichment of metQTL overlapping metabolic-trait or disease loci in enhancers (the strongest effects were for high-density lipoprotein cholesterol and body mass index [BMI]). We followed up with the BMI SNP rs713586, a cg01884057 metQTL that overlaps an enhancer upstream of ADCY3, and used bisulphite sequencing to refine this region. Our results showed widespread population invariability yet sequence dependence on adipose DNA methylation but that incorporating maps of regulatory elements aid in linking CpG variation to gene regulation and disease risk in a tissue-dependent manner.
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Affiliation(s)
- Elin Grundberg
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Eshwar Meduri
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Johanna K. Sandling
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- Molecular Medicine, Department of Medical Sciences, Uppsala University, 751 85 Uppsala, Sweden
- Science for Life Laboratory, Uppsala University, 751 23 Uppsala, Sweden
| | - Åsa K. Hedman
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
| | - Sarah Keildson
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
| | - Alfonso Buil
- Department of Genetic Medicine and Development and Institute for Genetics and Genomics in Geneva, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Stephan Busche
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Wei Yuan
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - James Nisbet
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | | | - Alicja Wilk
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | - Amy Barrett
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, OX37LJ Oxford, UK
| | - Kerrin S. Small
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Bing Ge
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Maxime Caron
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - So-Youn Shin
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
| | - Mark Lathrop
- Department of Human Genetics, McGill University and Genome Quebec Innovation Centre, Montreal, QC H3A1A5, Canada
| | - Emmanouil T. Dermitzakis
- Department of Genetic Medicine and Development and Institute for Genetics and Genomics in Geneva, University of Geneva Medical School, 1211 Geneva, Switzerland
| | - Mark I. McCarthy
- Wellcome Trust Centre for Human Genetics, University of Oxford, OX37BN Oxford, UK
- Oxford Centre for Diabetes, Endocrinology, & Metabolism, University of Oxford, Churchill Hospital, OX37LJ Oxford, UK
- NIHR Oxford Biomedical Research Centre, Churchill Hospital, OX3 7LE Oxford, UK
| | - Timothy D. Spector
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Jordana T. Bell
- Department of Twin Research and Genetic Epidemiology, King’s College London, SE17EH London, UK
| | - Panos Deloukas
- Wellcome Trust Sanger Institute, CB101SA Hinxton, UK
- William Harvey Research Institute, Barts and The London School of Medicine and Dentistry, Queen Mary University of London, EC1M 6BQ London, UK
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Kitchen H, Rofail D, Caron M, Emery MP. Oncology patient-reported claims: maximising the chance for success. Ecancermedicalscience 2012; 5:212. [PMID: 22276055 PMCID: PMC3260907 DOI: 10.3332/ecancer.2011.212] [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] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2011] [Indexed: 12/01/2022] Open
Abstract
Objectives/purpose: To review Patient Reported Outcome (PRO) labelling claims achieved in oncology in Europe and in the United States and consider the benefits, and challenges faced. Methods: PROLabels database was searched to identify oncology products with PRO labelling approved in Europe since 1995 or in the United States since 1998. The US Food and Drug Administration (FDA) and the European Medicines Agency (EMA) websites and guidance documents were reviewed. PUBMED was searched for articles on PRO claims in oncology. Results: Among all oncology products approved, 22 were identified with PRO claims; 10 in the United States, 7 in Europe, and 5 in both. The language used in the labelling was limited to benefit (e.g. “…resulted in symptom benefits by significantly prolonging time to deterioration in cough, dyspnoea, and pain, versus placebo”) and equivalence (e.g. “no statistical differences were observed between treatment groups for global QoL”). Seven products used a validated HRQoL tool; two used symptom tools; two used both; seven used single-item symptom measures (one was unknown). The following emerged as likely reasons for success: ensuring systematic PRO data collection; clear rationale for pre-specified endpoints; adequately powered trials to detect differences and clinically significant changes; adjusting for multiplicity; developing an a priori statistical analysis plan including primary and subgroup analyses, dealing with missing data, pooling multiple-site data; establishing clinical versus statistical significance; interpreting failure to detect change. End-stage patient drop-out rates and cessation of trials due to exceptional therapeutic benefit pose significant challenges to demonstrating treatment PRO improvement. Conclusions: PRO labelling claims demonstrate treatment impact and the trade-off between efficacy and side effects ultimately facilitating product differentiation. Reliable and valid instruments specific to the desired language, claim, and target population are required. Practical considerations include rationale for study endpoints, transparency in assumptions, and attention to subtle variations in data.
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Grard G, Drexler JF, Lekana-Douki S, Caron M, Lukashev A, Nkoghe D, Gonzalez JP, Drosten C, Leroy E. Type 1 wild poliovirus and putative enterovirus 109 in an outbreak of acute flaccid paralysis in Congo, October-November 2010. ACTA ACUST UNITED AC 2010; 15. [PMID: 21144443 DOI: 10.2807/ese.15.47.19723-en] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
An outbreak of flaccid paralysis syndrome in adults is ongoing in Congo. Molecular analysis of faecal, throat and cerebrospinal samples identified wildtype 1 poliovirus and an additional enterovirus C strain related to enterovirus 109 as the cause. As of 22 November, the cumulative number of cases was 409, of which 169 (41.3%) were fatal. This is one of the largest wild type 1 poliovirus outbreaks ever described associated with an unusually high case fatality rate.
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Affiliation(s)
- G Grard
- Centre International de Recherches Medicales de Franceville (CIRMF, International Centre of Medical Research of Francville), Franceville, Gabon
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