1
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Benoit A, Abraham MJ, Li S, Kim J, Estrada-Tejedor R, Bakadlag R, Subramaniam N, Makhani K, Guilbert C, Tu R, Salaciak M, Klein KO, Coyle KM, Hilton LK, Santiago R, Dmitrienko S, Assouline S, Morin RD, Del Rincon SV, Johnson NA, Mann KK. STAT6 mutations enriched at diffuse large B-cell lymphoma relapse reshape the tumor microenvironment. Int J Hematol 2024; 119:275-290. [PMID: 38285120 PMCID: PMC10920476 DOI: 10.1007/s12185-023-03692-x] [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: 08/24/2023] [Revised: 12/07/2023] [Accepted: 12/20/2023] [Indexed: 01/30/2024]
Abstract
Diffuse large B-cell lymphoma (DLBCL) relapses in approximately 40% of patients following frontline therapy. We reported that STAT6D419 mutations are enriched in relapsed/refractory DLBCL (rrDLBCL) samples, suggesting that JAK/STAT signaling plays a role in therapeutic resistance. We hypothesized that STAT6D419 mutations can improve DLBCL cell survival by reprogramming the microenvironment to sustain STAT6 activation. Thus, we investigated the role of STAT6D419 mutations on DLBCL cell growth and its microenvironment. We found that phospho-STAT6D419N was retained in the nucleus longer than phospho-STAT6WT following IL-4 stimulation, and STAT6D419N recognized a more restricted DNA-consensus sequence than STAT6WT. Upon IL-4 induction, STAT6D419N expression led to a higher magnitude of gene expression changes, but in a more selective list of gene targets compared with STATWT. The most significantly expressed genes induced by STAT6D419N were those implicated in survival, proliferation, migration, and chemotaxis, in particular CCL17. This chemokine, also known as TARC, attracts helper T-cells to the tumor microenvironment, especially in Hodgkin's lymphoma. To this end, in DLBCL, phospho-STAT6+ rrDLBCL cells had a greater proportion of infiltrating CD4+ T-cells than phospho-STAT6- tumors. Our findings suggest that STAT6D419 mutations in DLBCL lead to cell autonomous changes, enhanced signaling, and altered composition of the tumor microenvironment.
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Affiliation(s)
- Alexandre Benoit
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Madelyn J Abraham
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Sheena Li
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - John Kim
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
- University of British Columbia, Vancouver, BC, Canada
| | - Roger Estrada-Tejedor
- Organic and Pharmaceutical Chemistry Department, IQS School of Engineering, Universitat Ramon Llull, Barcelona, Spain
| | - Rowa Bakadlag
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Nivetha Subramaniam
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Kiran Makhani
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Cynthia Guilbert
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Raymond Tu
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada
| | - Matthew Salaciak
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Kathleen Oros Klein
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Krysta Mila Coyle
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Laura K Hilton
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, BC, Canada
| | - Raoul Santiago
- Department of Pediatrics, Faculty of Medicine, Universite Laval, Quebec City, QC, Canada
| | - Svetlana Dmitrienko
- Division of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Sarit Assouline
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Department of Oncology, McGill University, Montreal, QC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sonia V Del Rincon
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Nathalie A Johnson
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada
- Department of Oncology, McGill University, Montreal, QC, Canada
| | - Koren K Mann
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.
- Division of Experimental Medicine, McGill University, Montreal, QC, Canada.
- Department of Pharmacology and Therapeutics, McGill University, Montreal, QC, Canada.
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Hilton LK, Scott DW, Morin RD. Biological heterogeneity in diffuse large B-cell lymphoma. Semin Hematol 2023; 60:267-276. [PMID: 38151380 DOI: 10.1053/j.seminhematol.2023.11.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/19/2023] [Accepted: 11/28/2023] [Indexed: 12/29/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is heterogeneous both in clinical outcomes and the underlying disease biology. Over the last 2 decades, several different approaches for dissecting biological heterogeneity have emerged. Gene expression profiling (GEP) stratifies DLBCL into 3 broad groups (ABC, GCB, and DZsig/MHG), each with parallels to different normal mature B cell developmental states and prognostic implications. More recently, several different genomic approaches have been developed to categorize DLBCL based on the co-occurrence of tumor somatic mutations, identifying more granular biologically unified subgroups that complement GEP-based approaches. We review the molecular approaches and clinical evidence supporting the stratification of DLBCL patients based on tumor biology. By offering a platform for subtype-guided therapy, these divisions remain a promising avenue for improving patient outcomes, especially in subgroups with inferior outcomes with current standard-of-care therapy.
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Affiliation(s)
- Laura K Hilton
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
| | - David W Scott
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.; Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ryan D Morin
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, Canada
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3
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Davies JR, Hilton LK, Jiang A, Barrans S, Burton C, Johnson PWM, Davies AJ, Du MQ, Tooze R, Cucco F, Care MA, Morin RD, Steidl C, Sha C, Westhead DR, Scott DW. Comparison of MHG and DZsig reveals shared biology and a core overlap group with inferior prognosis in DLBCL. Blood Adv 2023; 7:6156-6162. [PMID: 37595057 PMCID: PMC10582343 DOI: 10.1182/bloodadvances.2023010673] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2023] [Revised: 07/13/2023] [Accepted: 07/30/2023] [Indexed: 08/20/2023] Open
Affiliation(s)
- John R. Davies
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - Laura K. Hilton
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Aixiang Jiang
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Sharon Barrans
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds Teaching Hospitals, Leeds, United Kingdom
| | - Catherine Burton
- Haematological Malignancy Diagnostic Service, Leeds Cancer Centre, Leeds Teaching Hospitals, Leeds, United Kingdom
| | - Peter W. M. Johnson
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Andrew J. Davies
- School of Cancer Sciences, Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Ming-Qing Du
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
| | - Reuben Tooze
- Section of Experimental Haematology, University of Leeds, Leeds, United Kingdom
| | - Francesco Cucco
- Department of Pathology, University of Cambridge, Cambridge, United Kingdom
- Institute of Clinical Physiology (IFC), Consiglio Nazionale delle Ricerche, Pisa, Italy
| | - Matthew A. Care
- Section of Experimental Haematology, University of Leeds, Leeds, United Kingdom
| | - Ryan D. Morin
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Centre, Vancouver, BC, Canada
| | - Christian Steidl
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Chulin Sha
- Institute of Basic Medicine and Cancer, Chinese Academy of Science, Hangzhou, China
| | - David R. Westhead
- School of Molecular and Cellular Biology, Faculty of Biological Sciences, University of Leeds, Leeds, United Kingdom
| | - David W. Scott
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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4
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Rushton CK, Dreval K, Morin RD. Concerning data inconsistencies in Burkitt lymphoma genome study. Blood 2023; 142:933-936. [PMID: 36302254 PMCID: PMC10644070 DOI: 10.1182/blood.2022016505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 06/07/2022] [Accepted: 06/16/2022] [Indexed: 11/20/2022] Open
Affiliation(s)
- Christopher K. Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Kostiantyn Dreval
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Ryan D. Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Lymphoid Cancer Research, BC Cancer, Vancouver, BC, Canada
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5
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Hilton LK, Ngu HS, Collinge B, Dreval K, Ben-Neriah S, Rushton CK, Wong JC, Cruz M, Roth A, Boyle M, Meissner B, Slack GW, Farinha P, Craig JW, Gerrie AS, Freeman CL, Villa D, Rodrigo JA, Song K, Crump M, Shepherd L, Hay AE, Kuruvilla J, Savage KJ, Kridel R, Karsan A, Marra MA, Sehn LH, Steidl C, Morin RD, Scott DW. Relapse Timing Is Associated With Distinct Evolutionary Dynamics in Diffuse Large B-Cell Lymphoma. J Clin Oncol 2023; 41:4164-4177. [PMID: 37319384 PMCID: PMC10852398 DOI: 10.1200/jco.23.00570] [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: 03/14/2023] [Revised: 04/17/2023] [Accepted: 05/08/2023] [Indexed: 06/17/2023] Open
Abstract
PURPOSE Diffuse large B-cell lymphoma (DLBCL) is cured in more than 60% of patients, but outcomes remain poor for patients experiencing disease progression or relapse (refractory or relapsed DLBCL [rrDLBCL]), particularly if these events occur early. Although previous studies examining cohorts of rrDLBCL have identified features that are enriched at relapse, few have directly compared serial biopsies to uncover biological and evolutionary dynamics driving rrDLBCL. Here, we sought to confirm the relationship between relapse timing and outcomes after second-line (immuno)chemotherapy and determine the evolutionary dynamics that underpin that relationship. PATIENTS AND METHODS Outcomes were examined in a population-based cohort of 221 patients with DLBCL who experienced progression/relapse after frontline treatment and were treated with second-line (immuno)chemotherapy with an intention-to-treat with autologous stem-cell transplantation (ASCT). Serial DLBCL biopsies from a partially overlapping cohort of 129 patients underwent molecular characterization, including whole-genome or whole-exome sequencing in 73 patients. RESULTS Outcomes to second-line therapy and ASCT are superior for late relapse (>2 years postdiagnosis) versus primary refractory (<9 months) or early relapse (9-24 months). Diagnostic and relapse biopsies were mostly concordant for cell-of-origin classification and genetics-based subgroup. Despite this concordance, the number of mutations exclusive to each biopsy increased with time since diagnosis, and late relapses shared few mutations with their diagnostic counterpart, demonstrating a branching evolution pattern. In patients with highly divergent tumors, many of the same genes acquired new mutations independently in each tumor, suggesting that the earliest mutations in a shared precursor cell constrain tumor evolution toward the same genetics-based subgroups at both diagnosis and relapse. CONCLUSION These results suggest that late relapses commonly represent genetically distinct and chemotherapy-naïve disease and have implications for optimal patient management.
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Affiliation(s)
- Laura K. Hilton
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Henry S. Ngu
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Brett Collinge
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kostiantyn Dreval
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Susana Ben-Neriah
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Christopher K. Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jasper C.H. Wong
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Manuela Cruz
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Andrew Roth
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Barbara Meissner
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
| | - Graham W. Slack
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jeffrey W. Craig
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Alina S. Gerrie
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ciara L. Freeman
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Diego Villa
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Judith A. Rodrigo
- Department of Hematology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Leukemia/BMT Program of BC, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Kevin Song
- Department of Hematology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
- Leukemia/BMT Program of BC, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Michael Crump
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Lois Shepherd
- Canadian Cancer Trials Group, Queens University, Kingston, Ontario, Canada
- Department of Medicine, Queens University, Kingston, Ontario, Canada
| | - Annette E. Hay
- Canadian Cancer Trials Group, Queens University, Kingston, Ontario, Canada
- Department of Medicine, Queens University, Kingston, Ontario, Canada
| | - John Kuruvilla
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Kerry J. Savage
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Robert Kridel
- Princess Margaret Cancer Center, University Health Network, Toronto, Ontario, Canada
| | - Aly Karsan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Laurie H. Sehn
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan D. Morin
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, British Columbia, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, British Columbia, Canada
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Dreval K, Hilton LK, Cruz M, Shaalan H, Ben-Neriah S, Boyle M, Collinge B, Coyle KM, Duns G, Farinha P, Grande BM, Meissner B, Pararajalingam P, Rushton CK, Slack GW, Wong J, Mungall AJ, Marra MA, Connors JM, Steidl C, Scott DW, Morin RD. Genetic subdivisions of follicular lymphoma defined by distinct coding and noncoding mutation patterns. Blood 2023; 142:561-573. [PMID: 37084389 PMCID: PMC10644066 DOI: 10.1182/blood.2022018719] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [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: 10/12/2022] [Revised: 04/06/2023] [Accepted: 04/06/2023] [Indexed: 04/23/2023] Open
Abstract
Follicular lymphoma (FL) accounts for ∼20% of all new lymphoma cases. Increases in cytological grade are a feature of the clinical progression of this malignancy, and eventual histologic transformation (HT) to the aggressive diffuse large B-cell lymphoma (DLBCL) occurs in up to 15% of patients. Clinical or genetic features to predict the risk and timing of HT have not been described comprehensively. In this study, we analyzed whole-genome sequencing data from 423 patients to compare the protein coding and noncoding mutation landscapes of untransformed FL, transformed FL, and de novo DLBCL. This revealed 2 genetically distinct subgroups of FL, which we have named DLBCL-like (dFL) and constrained FL (cFL). Each subgroup has distinguishing mutational patterns, aberrant somatic hypermutation rates, and biological and clinical characteristics. We implemented a machine learning-derived classification approach to stratify patients with FL into cFL and dFL subgroups based on their genomic features. Using separate validation cohorts, we demonstrate that cFL status, whether assigned with this full classifier or a single-gene approximation, is associated with a reduced rate of HT. This implies distinct biological features of cFL that constrain its evolution, and we highlight the potential for this classification to predict HT from genetic features present at diagnosis.
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Affiliation(s)
- Kostiantyn Dreval
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Laura K. Hilton
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Manuela Cruz
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Haya Shaalan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | | | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Brett Collinge
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Krysta M. Coyle
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Gerben Duns
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | | | | | - Prasath Pararajalingam
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher K. Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Graham W. Slack
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Jasper Wong
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | | | | | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Ryan D. Morin
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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7
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Duns G, Winkle M, Chong L, Ennishi D, Morin RD, Diepstra A, Scott DW, Kluiver JL, Steidl C, van den Berg A. Long non-coding RNAs associated with transcriptomic signatures and treatment outcome in diffuse large B-cell lymphoma. Br J Haematol 2023. [PMID: 37190862 DOI: 10.1111/bjh.18870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Revised: 04/29/2023] [Accepted: 05/06/2023] [Indexed: 05/17/2023]
Affiliation(s)
- Gerben Duns
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Melanie Winkle
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Lauren Chong
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Daisuke Ennishi
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Arjan Diepstra
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Joost L Kluiver
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Anke van den Berg
- Department of Pathology and Medical Biology, University of Groningen, University Medical Center Groningen, The Netherlands
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8
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Hilton LK, Ngu HS, Collinge B, Dreval K, Ben-Neriah S, Rushton CK, Wong JC, Cruz M, Roth A, Boyle M, Meissner B, Slack GW, Farinha P, Craig JW, Gerrie AS, Freeman CL, Villa D, Crump M, Shepherd L, Hay AE, Kuruvilla J, Savage KJ, Kridel R, Karsan A, Marra MA, Sehn LH, Steidl C, Morin RD, Scott DW. Relapse timing is associated with distinct evolutionary dynamics in DLBCL. medRxiv 2023:2023.03.06.23286584. [PMID: 36945587 PMCID: PMC10029038 DOI: 10.1101/2023.03.06.23286584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/10/2023]
Abstract
Diffuse large B-cell lymphoma (DLBCL) is cured in over 60% of patients, but outcomes are poor for patients with relapsed or refractory disease (rrDLBCL). Here, we performed whole genome/exome sequencing (WGS/WES) on tumors from 73 serially-biopsied patients with rrDLBCL. Based on the observation that outcomes to salvage therapy/autologous stem cell transplantation are related to time-to-relapse, we stratified patients into groups according to relapse timing to explore the relationship to genetic divergence and sensitivity to salvage immunochemotherapy. The degree of mutational divergence increased with time between biopsies, yet tumor pairs were mostly concordant for cell-of-origin, oncogene rearrangement status and genetics-based subgroup. In patients with highly divergent tumors, several genes acquired exclusive mutations independently in each tumor, which, along with concordance of genetics-based subgroups, suggests that the earliest mutations in a shared precursor cell constrain tumor evolution. These results suggest that late relapses commonly represent genetically distinct and chemotherapy-naïve disease.
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Affiliation(s)
- Laura K. Hilton
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Henry S. Ngu
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Brett Collinge
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Kostiantyn Dreval
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Susana Ben-Neriah
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Christopher K. Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Jasper C.H. Wong
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Manuela Cruz
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Andrew Roth
- Department of Molecular Oncology, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Barbara Meissner
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Graham W. Slack
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Jeffrey W. Craig
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Alina S. Gerrie
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ciara L. Freeman
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Center & Research Institute, Tampa, FL
| | - Diego Villa
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Michael Crump
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Lois Shepherd
- Canadian Cancer Trials Group, Queens University, Kingston, ON, Canada
- Department of Medicine, Queens University, Kingston, ON, Canada
| | - Annette E. Hay
- Canadian Cancer Trials Group, Queens University, Kingston, ON, Canada
- Department of Medicine, Queens University, Kingston, ON, Canada
| | - John Kuruvilla
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Kerry J. Savage
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Robert Kridel
- Princess Margaret Cancer Center, University Health Network, Toronto, ON, Canada
| | - Aly Karsan
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - Marco A. Marra
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Laurie H. Sehn
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ryan D. Morin
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Vancouver, BC, Canada
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer Research Institute, Vancouver, BC, Canada
- Division of Medical Oncology, Department of Medicine, University of British Columbia, Vancouver, BC, Canada
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9
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Thomas N, Dreval K, Gerhard DS, Hilton LK, Abramson JS, Ambinder RF, Barta S, Bartlett NL, Bethony J, Bhatia K, Bowen J, Bryan AC, Cesarman E, Casper C, Chadburn A, Cruz M, Dittmer DP, Dyer MA, Farinha P, Gastier-Foster JM, Gerrie AS, Grande BM, Greiner T, Griner NB, Gross TG, Harris NL, Irvin JD, Jaffe ES, Henry D, Huppi R, Leal FE, Lee MS, Martin JP, Martin MR, Mbulaiteye SM, Mitsuyasu R, Morris V, Mullighan CG, Mungall AJ, Mungall K, Mutyaba I, Nokta M, Namirembe C, Noy A, Ogwang MD, Omoding A, Orem J, Ott G, Petrello H, Pittaluga S, Phelan JD, Ramos JC, Ratner L, Reynolds SJ, Rubinstein PG, Sissolak G, Slack G, Soudi S, Swerdlow SH, Traverse-Glehen A, Wilson WH, Wong J, Yarchoan R, ZenKlusen JC, Marra MA, Staudt LM, Scott DW, Morin RD. Genetic subgroups inform on pathobiology in adult and pediatric Burkitt lymphoma. Blood 2023; 141:904-916. [PMID: 36201743 PMCID: PMC10023728 DOI: 10.1182/blood.2022016534] [Citation(s) in RCA: 16] [Impact Index Per Article: 16.0] [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: 03/31/2022] [Revised: 09/16/2022] [Accepted: 09/19/2022] [Indexed: 11/20/2022] Open
Abstract
Burkitt lymphoma (BL) accounts for most pediatric non-Hodgkin lymphomas, being less common but significantly more lethal when diagnosed in adults. Much of the knowledge of the genetics of BL thus far has originated from the study of pediatric BL (pBL), leaving its relationship to adult BL (aBL) and other adult lymphomas not fully explored. We sought to more thoroughly identify the somatic changes that underlie lymphomagenesis in aBL and any molecular features that associate with clinical disparities within and between pBL and aBL. Through comprehensive whole-genome sequencing of 230 BL and 295 diffuse large B-cell lymphoma (DLBCL) tumors, we identified additional significantly mutated genes, including more genetic features that associate with tumor Epstein-Barr virus status, and unraveled new distinct subgroupings within BL and DLBCL with 3 predominantly comprising BLs: DGG-BL (DDX3X, GNA13, and GNAI2), IC-BL (ID3 and CCND3), and Q53-BL (quiet TP53). Each BL subgroup is characterized by combinations of common driver and noncoding mutations caused by aberrant somatic hypermutation. The largest subgroups of BL cases, IC-BL and DGG-BL, are further characterized by distinct biological and gene expression differences. IC-BL and DGG-BL and their prototypical genetic features (ID3 and TP53) had significant associations with patient outcomes that were different among aBL and pBL cohorts. These findings highlight shared pathogenesis between aBL and pBL, and establish genetic subtypes within BL that serve to delineate tumors with distinct molecular features, providing a new framework for epidemiologic, diagnostic, and therapeutic strategies.
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Affiliation(s)
- Nicole Thomas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Kostiantyn Dreval
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Daniela S. Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Laura K. Hilton
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Jeremy S. Abramson
- Center for Lymphoma, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Richard F. Ambinder
- Department of Oncology, Sidney Kimmel Comprehensive Cancer Center, Johns Hopkins University School of Medicine, Baltimore, MD
| | - Stefan Barta
- University of Pennsylvania Hospital, Philadelphia, PA
| | - Nancy L. Bartlett
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO
| | - Jeffrey Bethony
- Department of Microbiology, Immunology, and Tropical Medicine, George Washington University, Washington, DC
| | | | - Jay Bowen
- Biopathology Center, Nationwide Children's Hospital, Columbus, OH
| | - Anthony C. Bryan
- Biopathology Center, Nationwide Children's Hospital, Columbus, OH
| | - Ethel Cesarman
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, Cornell University, New York, NY
| | - Corey Casper
- Infectious Disease Research Institute, Seattle, WA
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Manuela Cruz
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Dirk P. Dittmer
- Lineberger Comprehensive Cancer Center and Department of Microbiology and Immunology, The University of North Carolina at Chapel Hill School of Medicine, Chapel Hill, NC
| | - Maureen A. Dyer
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Julie M. Gastier-Foster
- Biopathology Center, Nationwide Children's Hospital, Columbus, OH
- Departments of Pathology and Pediatrics, The Ohio State University, Columbus, OH
| | - Alina S. Gerrie
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | | | - Timothy Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Nicholas B. Griner
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Thomas G. Gross
- Center for Global Health, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Nancy L. Harris
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - John D. Irvin
- Foundation for Burkitt Lymphoma Research, Geneva, Switzerland
| | - Elaine S. Jaffe
- Laboratory of Pathology, Clinical Center, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - David Henry
- University of Pennsylvania Hospital, Philadelphia, PA
| | - Rebecca Huppi
- Office of HIV/AIDS Malignancies, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Fabio E. Leal
- Programa de Oncovirologia, Instituto Nacional de Cancer Jose de Alencar, Rio de Janeiro, Brazil
| | - Michael S. Lee
- University of North Carolina at Chapel Hill, Chapel Hill, NC
| | | | | | - Sam M. Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Ronald Mitsuyasu
- Center for Clinical AIDS Research and Education, University of California Los Angeles, Los Angeles, CA
| | - Vivian Morris
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | | | - Andrew J. Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Karen Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | | | - Mostafa Nokta
- Office of HIV/AIDS Malignancies, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | | | - Ariela Noy
- Memorial Sloan Kettering Cancer Center and Weill Cornell Medical College, New York, NY
| | | | | | | | - German Ott
- Department of Clinical Pathology, Robert-Bosch-Krankenhaus and Dr. Margarete Fischer-Bosch Institute of Clinical Pharmacology, Stuttgart, Germany
| | - Hilary Petrello
- Biopathology Center, Nationwide Children's Hospital, Columbus, OH
| | - Stefania Pittaluga
- Laboratory of Pathology, Clinical Center, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - James D. Phelan
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Juan Carlos Ramos
- Department of Medicine, Division of Hematology, University of Miami, Sylvester Comprehensive Cancer Center, Miami, FL
| | - Lee Ratner
- Department of Medicine, Division of Oncology, Washington University School of Medicine, St. Louis, MO
| | - Steven J. Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD
| | - Paul G. Rubinstein
- Section of Hematology/Oncology, John H. Stroger Jr Hospital of Cook County, Chicago, IL
| | - Gerhard Sissolak
- Tygerberg Academic Hospital and Stellenbosch University, Cape Town, South Africa
| | - Graham Slack
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Shaghayegh Soudi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Steven H. Swerdlow
- Division of Hematopathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | - Alexandra Traverse-Glehen
- Hospices Civils de Lyon, Université Lyon 1, Service d'Anatomie Pathologique, Hopital Lyon Sud France
| | - Wyndham H. Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - Jasper Wong
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Robert Yarchoan
- Office of HIV/AIDS Malignancies, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jean C. ZenKlusen
- The Cancer Genome Atlas, Center for Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Marco A. Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Louis M. Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, Bethesda, MD
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Ryan D. Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
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10
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Qureshi QUA, Audas TE, Morin RD, Coyle KM. Emerging roles for heterogeneous ribonuclear proteins in normal and malignant B cells. Biochem Cell Biol 2023; 101:160-171. [PMID: 36745874 DOI: 10.1139/bcb-2022-0332] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
Heterogeneous nuclear ribonucleoproteins (hnRNPs) are among the most abundantly expressed RNA binding proteins in the cell and play major roles in all facets of RNA metabolism. hnRNPs are increasingly appreciated as essential for mammalian B cell development by regulating the carefully ordered expression of specific genes. Due to this tight regulation of the hnRNP-RNA network, it is no surprise that a growing number of genes encoding hnRNPs have been causally associated with the onset or progression of many cancers, including B cell neoplasms. Here we discuss our current understanding of hnRNP-driven regulation in normal, perturbed, and malignant B cells, and the most recent and emerging therapeutic innovations aimed at targeting the hnRNP-RNA network in lymphoma.
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Affiliation(s)
- Qurat Ul Ain Qureshi
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Timothy E Audas
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Ryan D Morin
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC, Canada
| | - Krysta M Coyle
- Department of Molecular Biology & Biochemistry, Simon Fraser University, Burnaby, BC, Canada
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11
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Riley RM, Spencer Miko SE, Morin RD, Morin GB, Negri GL. PeptideRanger: An R Package to Optimize Synthetic Peptide Selection for Mass Spectrometry Applications. J Proteome Res 2023; 22:526-531. [PMID: 36701129 DOI: 10.1021/acs.jproteome.2c00538] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Targeted and semitargeted mass spectrometry-based approaches are reliable methods to consistently detect and quantify low abundance proteins including proteins of clinical significance. Despite their potential, the development of targeted and semitargeted assays is time-consuming and often requires the purchase of costly libraries of synthetic peptides. To improve the efficiency of this rate-limiting step, we developed PeptideRanger, a tool to identify peptides from protein of interest with physiochemical properties that make them more likely to be suitable for mass spectrometry analysis. PeptideRanger is a flexible, extensively annotated, and intuitive R package that uses a random forest model trained on a diverse data set of thousands of MS experiments spanning a variety of sample types profiled with different chromatography setups and instruments. To support a variety of applications and to leverage rapidly growing public MS databases, PeptideRanger can readily be retrained with experiment-specific data sets and customized to prioritize and filter peptides based on selected properties.
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Affiliation(s)
- Ryan M Riley
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver V5Z 1L3, Canada
| | | | - Ryan D Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver V5Z 1L3, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby V5A 1S6, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver V5Z 1L3, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver V6T 1Z4, Canada
| | - Gian Luca Negri
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver V5Z 1L3, Canada
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12
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Dreval K, Boutros PC, Morin RD. Minimal information for reporting a genomics experiment. Blood 2022; 140:2549-2555. [PMID: 36219881 PMCID: PMC10653092 DOI: 10.1182/blood.2022016095] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Revised: 09/08/2022] [Accepted: 09/30/2022] [Indexed: 11/20/2022] Open
Abstract
Exome and genome sequencing has facilitated the identification of hundreds of genes and other regions that are recurrently mutated in hematologic neoplasms. The data sets from these studies theoretically provide opportunities. Quality differences between data sets can confound secondary analyses. We explore the consequences of these on the conclusions from some recent studies of B-cell lymphomas. We highlight the need for a minimum reporting standard to increase transparency in genomic research.
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Affiliation(s)
- Kostiantyn Dreval
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - Paul C. Boutros
- Departments of Human Genetics and Urology, University of California, Los Angeles, CA
| | - Ryan D. Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
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13
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de Leval L, Alizadeh AA, Bergsagel PL, Campo E, Davies A, Dogan A, Fitzgibbon J, Horwitz SM, Melnick AM, Morice WG, Morin RD, Nadel B, Pileri SA, Rosenquist R, Rossi D, Salaverria I, Steidl C, Treon SP, Zelenetz AD, Advani RH, Allen CE, Ansell SM, Chan WC, Cook JR, Cook LB, d’Amore F, Dirnhofer S, Dreyling M, Dunleavy K, Feldman AL, Fend F, Gaulard P, Ghia P, Gribben JG, Hermine O, Hodson DJ, Hsi ED, Inghirami G, Jaffe ES, Karube K, Kataoka K, Klapper W, Kim WS, King RL, Ko YH, LaCasce AS, Lenz G, Martin-Subero JI, Piris MA, Pittaluga S, Pasqualucci L, Quintanilla-Martinez L, Rodig SJ, Rosenwald A, Salles GA, San-Miguel J, Savage KJ, Sehn LH, Semenzato G, Staudt LM, Swerdlow SH, Tam CS, Trotman J, Vose JM, Weigert O, Wilson WH, Winter JN, Wu CJ, Zinzani PL, Zucca E, Bagg A, Scott DW. Genomic profiling for clinical decision making in lymphoid neoplasms. Blood 2022; 140:2193-2227. [PMID: 36001803 PMCID: PMC9837456 DOI: 10.1182/blood.2022015854] [Citation(s) in RCA: 53] [Impact Index Per Article: 26.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Accepted: 08/15/2022] [Indexed: 01/28/2023] Open
Abstract
With the introduction of large-scale molecular profiling methods and high-throughput sequencing technologies, the genomic features of most lymphoid neoplasms have been characterized at an unprecedented scale. Although the principles for the classification and diagnosis of these disorders, founded on a multidimensional definition of disease entities, have been consolidated over the past 25 years, novel genomic data have markedly enhanced our understanding of lymphomagenesis and enriched the description of disease entities at the molecular level. Yet, the current diagnosis of lymphoid tumors is largely based on morphological assessment and immunophenotyping, with only few entities being defined by genomic criteria. This paper, which accompanies the International Consensus Classification of mature lymphoid neoplasms, will address how established assays and newly developed technologies for molecular testing already complement clinical diagnoses and provide a novel lens on disease classification. More specifically, their contributions to diagnosis refinement, risk stratification, and therapy prediction will be considered for the main categories of lymphoid neoplasms. The potential of whole-genome sequencing, circulating tumor DNA analyses, single-cell analyses, and epigenetic profiling will be discussed because these will likely become important future tools for implementing precision medicine approaches in clinical decision making for patients with lymphoid malignancies.
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Affiliation(s)
- Laurence de Leval
- Institute of Pathology, Department of Laboratory Medicine and Pathology, Lausanne University Hospital and Lausanne University, Lausanne, Switzerland
| | - Ash A. Alizadeh
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
- Stanford Cancer Institute, Stanford University, Stanford, CA
- Institute for Stem Cell Biology and Regenerative Medicine, Stanford University, Stanford, CA
- Division of Hematology, Department of Medicine, Stanford University, Stanford, CA
| | - P. Leif Bergsagel
- Division of Hematology, Department of Internal Medicine, Mayo Clinic, Phoenix, AZ
| | - Elias Campo
- Haematopathology Section, Hospital Clínic, Institut d'Investigaciones Biomèdiques August Pi I Sunyer (IDIBAPS), University of Barcelona, Barcelona, Spain
| | - Andrew Davies
- Centre for Cancer Immunology, University of Southampton, Southampton, United Kingdom
| | - Ahmet Dogan
- Department of Pathology and Laboratory Medicine, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jude Fitzgibbon
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Steven M. Horwitz
- Lymphoma Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Ari M. Melnick
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - William G. Morice
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Ryan D. Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Bertrand Nadel
- Aix Marseille University, CNRS, INSERM, CIML, Marseille, France
| | - Stefano A. Pileri
- Haematopathology Division, IRCCS, Istituto Europeo di Oncologia, IEO, Milan, Italy
| | - Richard Rosenquist
- Department of Molecular Medicine and Surgery, Karolinska Institutet, Stockholm, Sweden
- Clinical Genetics, Karolinska University Laboratory, Karolinska University Hospital, Solna, Sweden
| | - Davide Rossi
- Institute of Oncology Research and Oncology Institute of Southern Switzerland, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Itziar Salaverria
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), Barcelona, Spain
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, Vancouver, Canada
| | | | - Andrew D. Zelenetz
- Lymphoma Service, Memorial Sloan Kettering Cancer Center, New York, NY
- Department of Medicine, Weill Cornell Medicine, New York, NY
| | - Ranjana H. Advani
- Division of Oncology, Department of Medicine, Stanford University, Stanford, CA
| | - Carl E. Allen
- Division of Pediatric Hematology-Oncology, Baylor College of Medicine, Houston, TX
| | | | - Wing C. Chan
- Department of Pathology, City of Hope National Medical Center, Duarte, CA
| | - James R. Cook
- Pathology and Laboratory Medicine Institute, Cleveland Clinic, Cleveland, OH
| | - Lucy B. Cook
- Centre for Haematology, Imperial College London, London, United Kingdom
| | - Francesco d’Amore
- Department of Hematology, Aarhus University Hospital, Aarhus, Denmark
| | - Stefan Dirnhofer
- Institute of Medical Genetics and Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Kieron Dunleavy
- Division of Hematology and Oncology, Georgetown Lombardi Comprehensive Cancer Centre, Georgetown University Hospital, Washington, DC
| | - Andrew L. Feldman
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Falko Fend
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | - Philippe Gaulard
- Department of Pathology, University Hospital Henri Mondor, AP-HP, Créteil, France
- Faculty of Medicine, IMRB, INSERM U955, University of Paris-Est Créteil, Créteil, France
| | - Paolo Ghia
- Università Vita-Salute San Raffaele and IRCCS Ospedale San Raffaele, Milan, Italy
| | - John G. Gribben
- Haemato-Oncology, Barts Cancer Institute, Queen Mary University of London, London, United Kingdom
| | - Olivier Hermine
- Service D’hématologie, Hôpital Universitaire Necker, Université René Descartes, Assistance Publique Hôpitaux de Paris, Paris, France
| | - Daniel J. Hodson
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, United Kingdom
- Department of Haematology, University of Cambridge, Cambridge, United Kingdom
| | - Eric D. Hsi
- Department of Pathology, Wake Forest School of Medicine, Winston-Salem, NC
| | - Giorgio Inghirami
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY
| | - Elaine S. Jaffe
- Hematopathology Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Kennosuke Karube
- Department of Pathology and Laboratory Medicine, Nagoya University Graduate School of Medicine, Nagoya, Japan
| | - Keisuke Kataoka
- Division of Molecular Oncology, National Cancer Center Research Institute, Toyko, Japan
- Division of Hematology, Department of Medicine, Keio University School of Medicine, Tokyo, Japan
| | - Wolfram Klapper
- Hematopathology Section and Lymph Node Registry, Department of Pathology, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Won Seog Kim
- Sungkyunkwan University School of Medicine, Samsung Medical Center, Seoul, South Korea
| | - Rebecca L. King
- Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Young H. Ko
- Department of Pathology, Cheju Halla General Hospital, Jeju, Korea
| | | | - Georg Lenz
- Department of Medicine A, Hematology, Oncology and Pneumology, University Hospital Muenster, Muenster, Germany
| | - José I. Martin-Subero
- Institut d'Investigacions Biomèdiques August Pi i Sunyer (IDIBAPS), University of Barcelona, Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | - Miguel A. Piris
- Department of Pathology, Jiménez Díaz Foundation University Hospital, CIBERONC, Madrid, Spain
| | - Stefania Pittaluga
- Hematopathology Section, Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY
- Department of Pathology & Cell Biology, Columbia University, New York, NY
- The Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY
| | - Leticia Quintanilla-Martinez
- Institute of Pathology and Neuropathology, Eberhard Karls University of Tübingen and Comprehensive Cancer Center, University Hospital Tübingen, Tübingen, Germany
| | - Scott J. Rodig
- Department of Pathology, Brigham and Women’s Hospital, Boston, MA
| | | | - Gilles A. Salles
- Lymphoma Service, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Jesus San-Miguel
- Clínica Universidad de Navarra, Navarra, Cancer Center of University of Navarra, Cima Universidad de NavarraI, Instituto de Investigacion Sanitaria de Navarra, Centro de Investigación Biomédica en Red de Céncer, Pamplona, Spain
| | - Kerry J. Savage
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, Vancouver, Canada
| | - Laurie H. Sehn
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, Vancouver, Canada
| | - Gianpietro Semenzato
- Department of Medicine, University of Padua and Veneto Institute of Molecular Medicine, Padova, Italy
| | - Louis M. Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Steven H. Swerdlow
- Department of Pathology, University of Pittsburgh School of Medicine, Pittsburgh, PA
| | | | - Judith Trotman
- Haematology Department, Concord Repatriation General Hospital, Sydney, Australia
| | - Julie M. Vose
- Department of Internal Medicine, Division of Hematology-Oncology, University of Nebraska Medical Center, Omaha, NE
| | - Oliver Weigert
- Department of Medicine III, LMU Hospital, Munich, Germany
| | - Wyndham H. Wilson
- Lymphoid Malignancies Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jane N. Winter
- Feinberg School of Medicine, Northwestern University, Chicago, IL
| | | | - Pier L. Zinzani
- IRCCS Azienda Ospedaliero-Universitaria di Bologna Istitudo di Ematologia “Seràgnoli” and Dipartimento di Medicina Specialistica, Diagnostica e Sperimentale Università di Bologna, Bologna, Italy
| | - Emanuele Zucca
- Institute of Oncology Research and Oncology Institute of Southern Switzerland, Faculty of Biomedical Sciences, Università della Svizzera Italiana, Bellinzona, Switzerland
| | - Adam Bagg
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer and University of British Columbia, Vancouver, Canada
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14
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Bal E, Kumar R, Hadigol M, Holmes AB, Hilton LK, Loh JW, Dreval K, Wong JCH, Vlasevska S, Corinaldesi C, Soni RK, Basso K, Morin RD, Khiabanian H, Pasqualucci L, Dalla-Favera R. Author Correction: Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature 2022; 611:E2. [PMID: 36253470 DOI: 10.1038/s41586-022-05285-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Elodie Bal
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Rahul Kumar
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Mohammad Hadigol
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Laura K Hilton
- Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jui Wan Loh
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Kostiantyn Dreval
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jasper C H Wong
- Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Sofija Vlasevska
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | | | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY, USA.,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.,Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada.,Genome Sciences Center, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Hossein Khiabanian
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA.,Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA. .,Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY, USA. .,Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA. .,Department of Pathology and Cell Biology, Columbia University, New York, NY, USA. .,Department of Genetics & Development, Columbia University, New York, NY, USA. .,Department of Microbiology & Immunology, Columbia University, New York, NY, USA.
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15
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Bal E, Kumar R, Hadigol M, Holmes AB, Hilton LK, Loh JW, Dreval K, Wong J, Vlasevska S, Corinaldesi C, Soni RKS, Basso K, Morin RD, Khiabanian H, Pasqualucci L, Dalla-Favera R. Abstract A12: Pervasive hypermutation of super-enhancer regions dysregulates oncogene expression in diffuse large B-cell lymphoma. Blood Cancer Discov 2022. [DOI: 10.1158/2643-3249.lymphoma22-a12] [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] Open
Abstract
Abstract
Coding-genome sequencing efforts have identified several genes/pathways altered in Diffuse Large B-cell Lymphoma (DLBCL), including new potential therapeutic targets. However, the mutational contribution of the non-coding genome of DLBCL remains largely unexplored. To identify functionally relevant non-coding mutations targeting regulatory domains, we integrated enhancer (E)/super-enhancer (SE) identification, by ChIP-seq analysis of the hallmark H3K27 histone mark, with whole genome sequencing (WGS) and RNA-seq analysis in 29 DLBCL cell lines representative of the major DLBCL subtypes, along with germinal center (GC) B cells representing the normal counterpart of DLBCL. Following validation in 93 normal/tumor DLBCL biopsies, we found that active SEs are specifically hypermutated (≥3 somatic mutations/Kb) in 99% of DLBCLs, as compared to the same loci when not active as SE (in total, 159 hypermutated SEs, with at least 2/case). As evidence of oncogenic relevance, we have shown that the hypermutated SEs linked to the BCL6 and BCL2 proto-oncogenes prevent the binding and transcriptional downregulation by transcriptional repressors. Genetic correction of selected mutations using the CRISPR/Cas9 technology restored repressor DNA-binding, downregulated target gene expression, and led to the counter-selection of cells harboring corrected alleles, indicating oncogenic dependency from the SE mutations. A third recurrently hypermutated SE was the CXCR4-SE, affected in 19% of cases. CXCR4 encodes for a G-protein coupled chemokine receptor involved in cell migration within the GC, and is mutationally activated in 40% of Waldenström macrobulinemia (WM), a post-GC lymphoproliferative disease. We identified a mutational hotspot preventing the binding of the NR3C1 glucocorticoid receptor in 7.5% of DLBCL cases. Correction of the mutations in cell lines led to counter selection and reduced expression of CXCR4. Conversely, the introduction of a mutation disrupting NR3C1 binding in WT DLBCL cells increased CXCR4 expression. Together, these results are consistent with dependency of the mutant cells on the CXCR4-SE mutation, and confirm a direct link between SE mutations in this region and deregulated gene expression through escape from NR3C1-mediated suppression. In primary cases, mutations in the NR3C1 binding site of the CXCR4-SE were observed in the absence of NR3C1 coding mutations and correlated with increased CXCR4 transcript levels, as documented by RNA-seq. Together with the oncogenic role of CXCR4 in WM, these findings reveal this chemokine receptor as a potential oncogenic target in DLBCL. Collectively, these findings reveal a new layer of genetic alterations, which identifies novel mechanisms of dysregulation for known oncogenes, as well as new dysregulated genes and pathways, with implications for precision classification and therapeutic targeting of DLBCL. * Co-senior authors.
Citation Format: Elodie Bal, Rahul Kumar, Mohammad Hadigol, Antony B. Holmes, Laura K. Hilton, Jui Wan Loh, Kostiantyn Dreval, Jasper Wong, Sofija Vlasevska, Clarissa Corinaldesi, Rajesh Kumar Soni Soni, Katia Basso, Ryan D. Morin, Hossein Khiabanian, Laura Pasqualucci, Riccardo Dalla-Favera. Pervasive hypermutation of super-enhancer regions dysregulates oncogene expression in diffuse large B-cell lymphoma [abstract]. In: Proceedings of the Third AACR International Meeting: Advances in Malignant Lymphoma: Maximizing the Basic-Translational Interface for Clinical Application; 2022 Jun 23-26; Boston, MA. Philadelphia (PA): AACR; Blood Cancer Discov 2022;3(5_Suppl):Abstract nr A12.
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Affiliation(s)
- Elodie Bal
- 1Institute for Cancer Genetics, Columbia University, New York, NY,
| | - Rahul Kumar
- 2Institute for Cancer Genetics, Columbia University, New York, NB,
| | - Mohammad Hadigol
- 3Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ,
| | - Antony B. Holmes
- 1Institute for Cancer Genetics, Columbia University, New York, NY,
| | - Laura K. Hilton
- 4Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, BC, Canada,
| | - Jui Wan Loh
- 3Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ,
| | - Kostiantyn Dreval
- 5Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada,
| | - Jasper Wong
- 4Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, BC, Canada,
| | - Sofija Vlasevska
- 1Institute for Cancer Genetics, Columbia University, New York, NY,
| | | | - Rajesh Kumar Soni Soni
- 6Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY
| | - Katia Basso
- 1Institute for Cancer Genetics, Columbia University, New York, NY,
| | - Ryan D. Morin
- 5Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada,
| | - Hossein Khiabanian
- 3Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ,
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16
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Freeman CL, Pararajalingam P, Jin L, Balasubramanian S, Jiang A, Xu W, Grau M, Zapukhlyak M, Boyle M, Hodkinson B, Schaffer M, Enny C, Deshpande S, Sun S, Vermeulen J, Morin RD, Scott DW, Lenz G. Molecular determinants of outcomes in relapsed or refractory mantle cell lymphoma treated with ibrutinib or temsirolimus in the MCL3001 (RAY) trial. Leukemia 2022; 36:2479-2487. [PMID: 35963941 DOI: 10.1038/s41375-022-01658-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/05/2021] [Revised: 07/06/2022] [Accepted: 07/14/2022] [Indexed: 11/10/2022]
Abstract
Mantle cell lymphoma (MCL) is a rare, incurable lymphoma subtype characterized by heterogeneous outcomes. To better understand the clinical behavior and response to treatment, predictive biomarkers are needed. Using residual archived material from patients enrolled in the MCL3001 (RAY) study, we performed detailed analyses of gene expression and targeted genetic sequencing. This phase III clinical trial randomized patients with relapsed or refractory MCL to treatment with either ibrutinib or temsirolimus. We confirmed the prognostic capability of the gene expression proliferation assay MCL35 in this cohort treated with novel agents; it outperformed the simplified MCL International Prognostic Index in discriminating patients with different outcomes. Regardless of treatment arm, our data demonstrated that this assay captures the risk conferred by known biological factors, including increased MYC expression, blastoid morphology, aberrations of TP53, and truncated CCND1 3' untranslated region. We showed the negative impact of BIRC3 mutations/deletions on outcomes in this cohort and identified that deletion of chromosome 8p23.3 also negatively impacts survival. Restricted to patients with deletions/alterations in TP53, ibrutinib appeared to abrogate the deleterious impact on outcome. These data illustrate the potential to perform a molecular analysis of predictive biomarkers on routine patient samples that can meaningfully inform clinical practice.
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Affiliation(s)
- Ciara L Freeman
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada. .,Blood and Marrow Transplant and Cellular Immunotherapy, H. Lee Moffitt Cancer Centre and Research Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA.
| | - Prasath Pararajalingam
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Ling Jin
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | | | - Aixiang Jiang
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Wendan Xu
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Michael Grau
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Myroslav Zapukhlyak
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
| | - Merrill Boyle
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Brendan Hodkinson
- Oncology Translational Research, Janssen Research & Development, Spring House, PA, USA
| | - Michael Schaffer
- Oncology Translational Research, Janssen Research & Development, Spring House, PA, USA
| | - Christopher Enny
- Clinical Oncology, Janssen Research & Development, Raritan, NJ, USA
| | - Sanjay Deshpande
- Clinical Oncology, Janssen Research & Development, Raritan, NJ, USA
| | - Steven Sun
- Clinical Biostats, Janssen Research & Development, Raritan, NJ, USA
| | - Jessica Vermeulen
- Clinical Oncology, Janssen Research & Development, Leiden, The Netherlands
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Georg Lenz
- Medical Department A for Hematology, Oncology and Pneumology, University Hospital Münster, Münster, Germany
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17
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Xia M, David L, Teater M, Gutierrez J, Wang X, Meydan C, Lytle A, Slack GW, Scott DW, Morin RD, Onder O, Elenitoba-Johnson KS, Zamponi N, Cerchietti L, Lu T, Philippar U, Fontan L, Wu H, Melnick AM. BCL10 Mutations Define Distinct Dependencies Guiding Precision Therapy for DLBCL. Cancer Discov 2022; 12:1922-1941. [PMID: 35658124 PMCID: PMC9357155 DOI: 10.1158/2159-8290.cd-21-1566] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2021] [Revised: 05/03/2022] [Accepted: 06/01/2022] [Indexed: 01/09/2023]
Abstract
Activated B cell-like diffuse large B-cell lymphomas (ABC-DLBCL) have unfavorable outcomes and chronic activation of CARD11-BCL10-MALT1 (CBM) signal amplification complexes that form due to polymerization of BCL10 subunits, which is affected by recurrent somatic mutations in ABC-DLBCLs. Herein, we show that BCL10 mutants fall into at least two functionally distinct classes: missense mutations of the BCL10 CARD domain and truncation of its C-terminal tail. Truncating mutations abrogated a motif through which MALT1 inhibits BCL10 polymerization, trapping MALT1 in its activated filament-bound state. CARD missense mutations enhanced BCL10 filament formation, forming glutamine network structures that stabilize BCL10 filaments. Mutant forms of BCL10 were less dependent on upstream CARD11 activation and thus manifested resistance to BTK inhibitors, whereas BCL10 truncating but not CARD mutants were hypersensitive to MALT1 inhibitors. Therefore, BCL10 mutations are potential biomarkers for BTK inhibitor resistance in ABC-DLBCL, and further precision can be achieved by selecting therapy based on specific biochemical effects of distinct mutation classes. SIGNIFICANCE ABC-DLBCLs feature frequent mutations of signaling mediators that converge on the CBM complex. We use structure-function approaches to reveal that BCL10 mutations fall into two distinct biochemical classes. Both classes confer resistance to BTK inhibitors, whereas BCL10 truncations confer hyperresponsiveness to MALT1 inhibitors, providing a road map for precision therapies in ABC-DLBCLs. See related commentary by Phelan and Oellerich, p. 1844. This article is highlighted in the In This Issue feature, p. 1825.
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Affiliation(s)
- Min Xia
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Liron David
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Johana Gutierrez
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Xiang Wang
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Cem Meydan
- Institute for Computational Biomedicine, Department of Physiology and Biophysics, Weill Cornell Medicine, New York, New York
| | - Andrew Lytle
- Centre for Lymphoid Cancer, BC Cancer Research, Vancouver, British Columbia, Canada
| | - Graham W. Slack
- Centre for Lymphoid Cancer, BC Cancer Research, Vancouver, British Columbia, Canada
| | - David W. Scott
- Centre for Lymphoid Cancer, BC Cancer Research, Vancouver, British Columbia, Canada
| | - Ryan D. Morin
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ozlem Onder
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Kojo S.J. Elenitoba-Johnson
- Department of Pathology and Laboratory Medicine, Perelman School of Medicine, University of Pennsylvania, Philadelphia, Pennsylvania
| | - Nahuel Zamponi
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Leandro Cerchietti
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Tianbao Lu
- Janssen Research & Development, Springhouse, Pennsylvania
| | | | - Lorena Fontan
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
| | - Hao Wu
- Department of Biological Chemistry and Molecular Pharmacology, Harvard Medical School, Boston, Massachusetts
- Program in Cellular and Molecular Medicine, Boston Children's Hospital, Boston, Massachusetts
| | - Ari M. Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, New York, New York
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18
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Bal E, Kumar R, Hadigol M, Holmes AB, Hilton LK, Loh JW, Dreval K, Wong JCH, Vlasevska S, Corinaldesi C, Soni RK, Basso K, Morin RD, Khiabanian H, Pasqualucci L, Dalla-Favera R. Super-enhancer hypermutation alters oncogene expression in B cell lymphoma. Nature 2022; 607:808-815. [PMID: 35794478 PMCID: PMC9583699 DOI: 10.1038/s41586-022-04906-8] [Citation(s) in RCA: 43] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2021] [Accepted: 05/25/2022] [Indexed: 12/16/2022]
Abstract
Diffuse large B cell lymphoma (DLBCL) is the most common B cell non-Hodgkin lymphoma and remains incurable in around 40% of patients. Efforts to sequence the coding genome identified several genes and pathways that are altered in this disease, including potential therapeutic targets1-5. However, the non-coding genome of DLBCL remains largely unexplored. Here we show that active super-enhancers are highly and specifically hypermutated in 92% of samples from individuals with DLBCL, display signatures of activation-induced cytidine deaminase activity, and are linked to genes that encode B cell developmental regulators and oncogenes. As evidence of oncogenic relevance, we show that the hypermutated super-enhancers linked to the BCL6, BCL2 and CXCR4 proto-oncogenes prevent the binding and transcriptional downregulation of the corresponding target gene by transcriptional repressors, including BLIMP1 (targeting BCL6) and the steroid receptor NR3C1 (targeting BCL2 and CXCR4). Genetic correction of selected mutations restored repressor DNA binding, downregulated target gene expression and led to the counter-selection of cells containing corrected alleles, indicating an oncogenic dependency on the super-enhancer mutations. This pervasive super-enhancer mutational mechanism reveals a major set of genetic lesions deregulating gene expression, which expands the involvement of known oncogenes in DLBCL pathogenesis and identifies new deregulated gene targets of therapeutic relevance.
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Affiliation(s)
- Elodie Bal
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Rahul Kumar
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Biotechnology, Indian Institute of Technology Hyderabad, Kandi, Telangana, India
| | - Mohammad Hadigol
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Antony B Holmes
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | - Laura K Hilton
- Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Jui Wan Loh
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
| | - Kostiantyn Dreval
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jasper C H Wong
- Centre for Lymphoid Cancer, BC Cancer Research Centre, Vancouver, British Columbia, Canada
| | - Sofija Vlasevska
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
| | | | - Rajesh Kumar Soni
- Proteomics and Macromolecular Crystallography Shared Resource, Columbia University, New York, NY, USA
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA
| | - Katia Basso
- Institute for Cancer Genetics, Columbia University, New York, NY, USA
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
- Genome Sciences Center, BC Cancer Research Institute, Vancouver, British Columbia, Canada
| | - Hossein Khiabanian
- Center for Systems and Computational Biology, Rutgers Cancer Institute of New Jersey, Rutgers University, New Brunswick, NJ, USA
- Department of Pathology and Laboratory Medicine, Rutgers Robert Wood Johnson Medical School, Rutgers University, New Brunswick, NJ, USA
| | - Laura Pasqualucci
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
| | - Riccardo Dalla-Favera
- Institute for Cancer Genetics, Columbia University, New York, NY, USA.
- Herbert Irving Comprehensive Cancer Center, Columbia University, New York, NY, USA.
- Department of Pathology and Cell Biology, Columbia University, New York, NY, USA.
- Department of Genetics & Development, Columbia University, New York, NY, USA.
- Department of Microbiology & Immunology, Columbia University, New York, NY, USA.
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19
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Dodani DD, Nguyen MH, Morin RD, Marra MA, Corbett RD. Combinatorial and Machine Learning Approaches for Improved Somatic Variant Calling From Formalin-Fixed Paraffin-Embedded Genome Sequence Data. Front Genet 2022; 13:834764. [PMID: 35571031 PMCID: PMC9092826 DOI: 10.3389/fgene.2022.834764] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Accepted: 03/18/2022] [Indexed: 11/13/2022] Open
Abstract
Formalin fixation of paraffin-embedded tissue samples is a well-established method for preserving tissue and is routinely used in clinical settings. Although formalin-fixed, paraffin-embedded (FFPE) tissues are deemed crucial for research and clinical applications, the fixation process results in molecular damage to nucleic acids, thus confounding their use in genome sequence analysis. Methods to improve genomic data quality from FFPE tissues have emerged, but there remains significant room for improvement. Here, we use whole-genome sequencing (WGS) data from matched Fresh Frozen (FF) and FFPE tissue samples to optimize a sensitive and precise FFPE single nucleotide variant (SNV) calling approach. We present methods to reduce the prevalence of false-positive SNVs by applying combinatorial techniques to five publicly available variant callers. We also introduce FFPolish, a novel variant classification method that efficiently classifies FFPE-specific false-positive variants. Our combinatorial and statistical techniques improve precision and F1 scores compared to the results of publicly available tools when tested individually.
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Affiliation(s)
- Dollina D Dodani
- The Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Matthew H Nguyen
- The Bioinformatics Graduate Program, University of British Columbia, Vancouver, BC, Canada
| | - Ryan D Morin
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
| | - Richard D Corbett
- Canada's Michael Smith Genome Sciences Centre, BC Cancer Research Institute, Provincial Health Services Authority, Vancouver, BC, Canada
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20
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Benoit A, Bou-Petit E, Chou H, Lu M, Guilbert C, Luo VM, Assouline S, Morin RD, Dmitrienko S, Estrada-Tejedor R, Johnson NA, Mann KK. Mutated RAS-associating proteins and ERK activation in relapse/refractory diffuse large B cell lymphoma. Sci Rep 2022; 12:779. [PMID: 35039569 PMCID: PMC8764096 DOI: 10.1038/s41598-021-04736-0] [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: 07/14/2021] [Accepted: 12/06/2021] [Indexed: 11/16/2022] Open
Abstract
Diffuse large B cell lymphoma (DLBCL) is successfully treated with combination immuno-chemotherapy, but relapse with resistant disease occurs in ~ 40% of patients. However, little is known regarding relapsed/refractory DLBCL (rrDLBCL) genetics and alternative therapies. Based on findings from other tumors, we hypothesized that RAS-MEK-ERK signaling would be upregulated in resistant tumors, potentially correlating with mutations in RAS, RAF, or associated proteins. We analyzed mutations and phospho-ERK levels in tumor samples from rrDLBCL patients. Unlike other tumor types, rrDLBCL is not mutated in any Ras or Raf family members, despite having increased expression of p-ERK. In paired biopsies comparing diagnostic and relapsed specimens, 33% of tumors gained p-ERK expression, suggesting a role in promoting survival. We did find mutations in several Ras-associating proteins, including GEFs, GAPs, and downstream effectors that could account for increased ERK activation. We further investigated mutations in one such protein, RASGRP4. In silico modeling indicated an increased interaction between H-Ras and mutant RASGRP4. In cell lines, mutant RASGRP4 increased basal p-ERK expression and lead to a growth advantage in colony forming assays when challenged with doxorubicin. Relapsed/refractory DLBCL is often associated with increased survival signals downstream of ERK, potentially corresponding with mutations in protein controlling RAS/MEK/ERK signaling.
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Affiliation(s)
- Alexandre Benoit
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Elisabeth Bou-Petit
- Grup de Química Farmacèutica, IQS School of Engineering, Universitat Ramon Llull, Barcelona, Spain
| | - Hsiang Chou
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada
| | - Melissa Lu
- Université de Montréal-Faculté de Médecine, Montreal, Canada
| | - Cynthia Guilbert
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada
| | - Vincent Mingyi Luo
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.,Department of Microbiology and Immunology, McGill University, Montreal, QC, Canada
| | - Sarit Assouline
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Svetlana Dmitrienko
- Division of Pathology, McGill University Health Centre, Montreal, QC, Canada
| | - Roger Estrada-Tejedor
- Grup de Química Farmacèutica, IQS School of Engineering, Universitat Ramon Llull, Barcelona, Spain
| | - Nathalie A Johnson
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada.,Division of Experimental Medicine, McGill University, Montreal, QC, Canada.,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada
| | - Koren K Mann
- Lady Davis Institute, Jewish General Hospital, 3755 Côte Sainte-Catherine Road, Montreal, QC, H3T 1E2, Canada. .,Division of Experimental Medicine, McGill University, Montreal, QC, Canada. .,Gerald Bronfman Department of Oncology, McGill University, Montreal, QC, Canada.
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21
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Lacroix E, Pereira L, Yoo B, Coyle KM, Chandhok S, Zapf R, Marijan D, Morin RD, Vlachos S, Harden N, Audas TE. Evolutionary conservation of systemic and reversible amyloid aggregation. J Cell Sci 2021; 134:273507. [PMID: 34704593 DOI: 10.1242/jcs.258907] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2021] [Accepted: 10/19/2021] [Indexed: 12/30/2022] Open
Abstract
In response to environmental stress, human cells have been shown to form reversible amyloid aggregates within the nucleus, termed amyloid bodies (A-bodies). These protective physiological structures share many of the biophysical characteristics associated with the pathological amyloids found in Alzheimer's and Parkinson's disease. Here, we show that A-bodies are evolutionarily conserved across the eukaryotic domain, with their detection in Drosophila melanogaster and Saccharomyces cerevisiae marking the first examples of these functional amyloids being induced outside of a cultured cell setting. The conditions triggering amyloidogenesis varied significantly among the species tested, with results indicating that A-body formation is a severe, but sublethal, stress response pathway that is tailored to the environmental norms of an organism. RNA-sequencing analyses demonstrate that the regulatory low-complexity long non-coding RNAs that drive A-body aggregation are both conserved and essential in human, mouse and chicken cells. Thus, the identification of these natural and reversible functional amyloids in a variety of evolutionarily diverse species highlights the physiological significance of this protein conformation, and will be informative in advancing our understanding of both functional and pathological amyloid aggregation events. This article has an associated First Person interview with the first author of the paper.
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Affiliation(s)
- Emma Lacroix
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Lionel Pereira
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Byoungjoo Yoo
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Krysta M Coyle
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Sahil Chandhok
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Richard Zapf
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Dane Marijan
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Stephanie Vlachos
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada
| | - Nicholas Harden
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, Burnaby, BC V5A 1S6, Canada.,Center for Cell Biology, Development, and Disease, Burnaby, BC V5A 1S6, Canada
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22
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Yang KC, Kalloger SE, Aird JJ, Lee MKC, Rushton C, Mungall KL, Mungall AJ, Gao D, Chow C, Xu J, Karasinska JM, Colborne S, Jones SJM, Schrader J, Morin RD, Loree JM, Marra MA, Renouf DJ, Morin GB, Schaeffer DF, Gorski SM. Proteotranscriptomic classification and characterization of pancreatic neuroendocrine neoplasms. Cell Rep 2021; 37:109817. [PMID: 34644566 DOI: 10.1016/j.celrep.2021.109817] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [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: 03/09/2021] [Revised: 07/16/2021] [Accepted: 09/20/2021] [Indexed: 12/13/2022] Open
Abstract
Pancreatic neuroendocrine neoplasms (PNENs) are biologically and clinically heterogeneous. Here, we use a multi-omics approach to uncover the molecular factors underlying this heterogeneity. Transcriptomic analysis of 84 PNEN specimens, drawn from two cohorts, is substantiated with proteomic profiling and identifies four subgroups: Proliferative, PDX1-high, Alpha cell-like and Stromal/Mesenchymal. The Proliferative subgroup, consisting of both well- and poorly differentiated specimens, is associated with inferior overall survival probability. The PDX1-high and Alpha cell-like subgroups partially resemble previously described subtypes, and we further uncover distinctive metabolism-related features in the Alpha cell-like subgroup. The Stromal/Mesenchymal subgroup exhibits molecular characteristics of YAP1/WWTR1(TAZ) activation suggestive of Hippo signaling pathway involvement in PNENs. Whole-exome sequencing reveals subgroup-enriched mutational differences, supported by activity inference analysis, and identifies hypermorphic proto-oncogene variants in 14.3% of sequenced PNENs. Our study reveals differences in cellular signaling axes that provide potential directions for PNEN patient stratification and treatment strategies.
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Affiliation(s)
- Kevin C Yang
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Steve E Kalloger
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada; School of Population and Public Health, University of British Columbia, Vancouver, BC V6T 1Z3, Canada; Division of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC V5Z 1M9, Canada; Pancreas Centre BC, Vancouver, BC V5Z 1L8, Canada
| | - John J Aird
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada; Division of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC V5Z 1M9, Canada
| | - Michael K C Lee
- Division of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada
| | - Christopher Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Karen L Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Dongxia Gao
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada; Genetic Pathology Evaluation Centre, Vancouver, BC V6H 3Z6, Canada
| | - Christine Chow
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada; Genetic Pathology Evaluation Centre, Vancouver, BC V6H 3Z6, Canada
| | - Jing Xu
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | - Shane Colborne
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 1L3, Canada
| | - Steven J M Jones
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Jörg Schrader
- Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; I. Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Ryan D Morin
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Jonathan M Loree
- Division of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - Daniel J Renouf
- Pancreas Centre BC, Vancouver, BC V5Z 1L8, Canada; Division of Medical Oncology, BC Cancer, Vancouver, BC V5Z 4E6, Canada
| | - Gregg B Morin
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, BC V6T 1Z4, Canada
| | - David F Schaeffer
- Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, BC V6T 1Z7, Canada; Division of Anatomical Pathology, Vancouver General Hospital, Vancouver, BC V5Z 1M9, Canada; Pancreas Centre BC, Vancouver, BC V5Z 1L8, Canada
| | - Sharon M Gorski
- Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 1L3, Canada; Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada; Centre for Cell Biology, Development, and Disease, Simon Fraser University, Burnaby, BC V5A 1S6, Canada.
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23
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Abstract
The term diffuse large B-cell lymphoma (DLBCL) includes a heterogeneous collection of biologically distinct tumours. This heterogeneity currently presents a barrier to the successful deployment of novel, biologically targeted therapies. Molecular profiling studies have recently proposed new molecular classification systems. These have the potential to resolve the biological heterogeneity of DLBCL into manageable subgroups of tumours that rely on shared oncogenic programmes. In many cases these biological programmes straddle the boundaries of our existing systems for classifying B-cell lymphomas. Here we review the findings from these major molecular profiling studies with a specific focus on those that propose new genetic subgroups of DLBCL. We highlight the areas of consensus and discordance between these studies and discuss the implications for current clinical practice and for clinical trials. Finally, we address the outstanding challenges and solutions to the introduction of genomic subtyping and precision medicine in DLBCL.
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Affiliation(s)
- Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.,BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Sarah E Arthur
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Daniel J Hodson
- Wellcome MRC Cambridge Stem Cell Institute, Cambridge Biomedical Campus, Cambridge, UK.,Department of Haematology, University of Cambridge, Cambridge, UK
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24
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Nowicka M, Hilton LK, Ashton-Key M, Hargreaves CE, Lee C, Foxall R, Carter MJ, Beers SA, Potter KN, Bolen CR, Klein C, Knapp A, Mir F, Rose-Zerilli M, Burton C, Klapper W, Scott DW, Sehn LH, Vitolo U, Martelli M, Trneny M, Rushton CK, Slack GW, Farinha P, Strefford JC, Oestergaard MZ, Morin RD, Cragg MS. Prognostic significance of FCGR2B expression for the response of DLBCL patients to rituximab or obinutuzumab treatment. Blood Adv 2021; 5:2945-2957. [PMID: 34323958 PMCID: PMC8361458 DOI: 10.1182/bloodadvances.2021004770] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Accepted: 04/08/2021] [Indexed: 01/16/2023] Open
Abstract
Fc γ receptor IIB (FcγRIIB) is an inhibitory molecule capable of reducing antibody immunotherapy efficacy. We hypothesized its expression could confer resistance in patients with diffuse large B-cell lymphoma (DLBCL) treated with anti-CD20 monoclonal antibody (mAb) chemoimmunotherapy, with outcomes varying depending on mAb (rituximab [R]/obinutuzumab [G]) because of different mechanisms of action. We evaluated correlates between FCGR2B messenger RNA and/or FcγRIIB protein expression and outcomes in 3 de novo DLBCL discovery cohorts treated with R plus cyclophosphamide, doxorubicin, vincristine, and prednisone (R-CHOP) reported by Arthur, Schmitz, and Reddy, and R-CHOP/G-CHOP-treated patients in the GOYA trial (NCT01287741). In the discovery cohorts, higher FCGR2B expression was associated with significantly shorter progression-free survival (PFS; Arthur: hazard ratio [HR], 1.09; 95% confidence interval [CI], 1.01-1.19; P = .0360; Schmitz: HR, 1.13; 95% CI, 1.02-1.26; P = .0243). Similar results were observed in GOYA with R-CHOP (HR, 1.26; 95% CI, 1.00-1.58; P = .0455), but not G-CHOP (HR, 0.91; 95% CI, 0.69-1.20; P = .50). A nonsignificant trend that high FCGR2B expression favored G-CHOP over R-CHOP was observed (HR, 0.67; 95% CI, 0.44-1.02; P = .0622); however, low FCGR2B expression favored R-CHOP (HR, 1.58; 95% CI, 1.00-2.50; P = .0503). In Arthur and GOYA, FCGR2B expression was associated with tumor FcγRIIB expression; correlating with shorter PFS for R-CHOP (HR, 2.17; 95% CI, 1.04-4.50; P = .0378), but not G-CHOP (HR, 1.37; 95% CI, 0.66-2.87; P = .3997). This effect was independent of established prognostic biomarkers. High FcγRIIB/FCGR2B expression has prognostic value in R-treated patients with DLBCL and may confer differential responsiveness to R-CHOP/G-CHOP.
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Affiliation(s)
| | - Laura K Hilton
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
| | - Margaret Ashton-Key
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
- Southampton University Hospitals NHS Foundation Trust, Southampton, United Kingdom
| | - Chantal E Hargreaves
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
| | - Chern Lee
- Southampton University Hospitals NHS Foundation Trust, Southampton, United Kingdom
| | - Russell Foxall
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton, Faculty of Medicine, Southampton, United Kingdom
| | - Matthew J Carter
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton, Faculty of Medicine, Southampton, United Kingdom
| | - Stephen A Beers
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton, Faculty of Medicine, Southampton, United Kingdom
| | - Kathleen N Potter
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
| | | | | | | | - Farheen Mir
- Royal Marsden Hospital, Sutton, United Kingdom
| | - Matthew Rose-Zerilli
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
| | - Cathy Burton
- St James's Institute of Oncology, Leeds, United Kingdom
| | - Wolfram Klapper
- Department of Hematopathology, University of Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - David W Scott
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Laurie H Sehn
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
- Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Umberto Vitolo
- Multidisciplinary Oncology Outpatient Clinic, Candiolo Cancer Institute, FPO-IRCCS, Candiolo, Italy
| | - Maurizio Martelli
- Department of Translational and Precision Medicine, Hematology, Sapienza University, Rome, Italy
| | - Marek Trneny
- 1st Medical Faculty, Charles University, Prague, Czech Republic; and
| | - Christopher K Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; and
| | - Graham W Slack
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Pedro Farinha
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada
| | - Jonathan C Strefford
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
| | | | - Ryan D Morin
- Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada; and
| | - Mark S Cragg
- School of Cancer Sciences, University of Southampton, Southampton, United Kingdom
- Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton, Faculty of Medicine, Southampton, United Kingdom
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25
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Gebremeskel S, Schanin J, Coyle KM, Butuci M, Luu T, Brock EC, Xu A, Wong A, Leung J, Korver W, Morin RD, Schleimer RP, Bochner BS, Youngblood BA. Mast Cell and Eosinophil Activation Are Associated With COVID-19 and TLR-Mediated Viral Inflammation: Implications for an Anti-Siglec-8 Antibody. Front Immunol 2021; 12:650331. [PMID: 33777047 PMCID: PMC7988091 DOI: 10.3389/fimmu.2021.650331] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [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: 01/06/2021] [Accepted: 02/18/2021] [Indexed: 12/11/2022] Open
Abstract
Coronavirus disease 2019 (COVID-19) caused by SARS-CoV-2 infection represents a global health crisis. Immune cell activation via pattern recognition receptors has been implicated as a driver of the hyperinflammatory response seen in COVID-19. However, our understanding of the specific immune responses to SARS-CoV-2 remains limited. Mast cells (MCs) and eosinophils are innate immune cells that play pathogenic roles in many inflammatory responses. Here we report MC-derived proteases and eosinophil-associated mediators are elevated in COVID-19 patient sera and lung tissues. Stimulation of viral-sensing toll-like receptors in vitro and administration of synthetic viral RNA in vivo induced features of hyperinflammation, including cytokine elevation, immune cell airway infiltration, and MC-protease production—effects suppressed by an anti-Siglec-8 monoclonal antibody which selectively inhibits MCs and depletes eosinophils. Similarly, anti-Siglec-8 treatment reduced disease severity and airway inflammation in a respiratory viral infection model. These results suggest that MC and eosinophil activation are associated with COVID-19 inflammation and anti-Siglec-8 antibodies are a potential therapeutic approach for attenuating excessive inflammation during viral infections.
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Affiliation(s)
| | | | - Krysta M Coyle
- Department of Molecular Biology and Biochemistry, Research Centre, Simon Fraser University, Vancouver, BC, Canada
| | | | - Thuy Luu
- Allakos Inc., Redwood City, CA, United States
| | | | - Alan Xu
- Allakos Inc., Redwood City, CA, United States
| | - Alan Wong
- Allakos Inc., Redwood City, CA, United States
| | - John Leung
- Allakos Inc., Redwood City, CA, United States
| | | | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Research Centre, Simon Fraser University, Vancouver, BC, Canada
| | - Robert P Schleimer
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
| | - Bruce S Bochner
- Division of Allergy and Immunology, Department of Medicine, Northwestern University Feinberg School of Medicine, Chicago, IL, United States
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26
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Hilton LK, Nowicka M, Ashton-Key M, Hargreaves CE, Lee C, Foxall R, Carter MJ, Beers SA, Potter KN, Bolen CR, Klein C, Knapp A, Mir F, Rose-Zerilli M, Burton C, Klapper W, Scott DW, Sehn LH, Vitolo U, Martelli M, Trneny M, Slack GW, Farinha P, Strefford JC, Oestergaard MZ, Morin RD, Cragg MS. Abstract PO-26: Prognostic significance of Fc gamma receptor IIB expression in the response of previously untreated diffuse large B-cell lymphomas to anti-CD20 monoclonal antibodies: Differing impact of rituximab and obinutuzumab. Blood Cancer Discov 2020. [DOI: 10.1158/2643-3249.lymphoma20-po-26] [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] Open
Abstract
Abstract
Background: The anti-CD20 monoclonal antibody (mAb), obinutuzumab (G), has shown improved outcomes versus rituximab (R) in indolent lymphomas; however, no improvement was seen in diffuse large B-cell lymphoma (DLBCL), and the molecular basis is unclear. The inhibitory Fc gamma receptor IIB (Fc γRIIB), expressed on lymphoma cells, can impair the effects of direct targeting mAbs, such as R, by binding and internalizing them, reducing opsonization and limiting FcγR-mediated killing. We hypothesized that FcγRIIB expression on cellular effectors and/or the lymphoma confers treatment resistance in some patients (pts) and evaluated if outcomes differ for therapies involving a non-internalized mAb (G).
Methods: We evaluated correlates between FCGR2B mRNA and/or FcγRIIB protein expression and pt outcomes in two discovery cohorts of de novo DLBCL treated with R-CHOP (Arthur et al. 2018, n=372; Schmitz et al. 2018, n=234), and the phase III GOYA trial (NCT01287741; n=552), which compared R-CHOP with G-CHOP in pts with previously untreated DLBCL. FCGR2B mRNA expression was assessed by RNA-Seq, and protein expression was assessed in evaluable cohorts by immunohistochemistry, using tissue microarrays with macrophages identified by CD68. FCGR2B expression was also measured by a NanoString assay (Arthur cohort). Cox regression analyzed the impact of FcγRIIB/FCGR2B expression on progression-free survival (PFS), with univariate and multivariate models adjusted for International Prognostic Index (IPI), cell of origin (COO), and BCL2 protein expression.
Results: In the discovery cohorts, a higher FCGR2B expression was significantly associated with shorter PFS (Arthur: HR 1.09 [95% CI: 1.01–1.19], P=0.036; Schmitz: HR 1.13 [95% CI: 1.02–1.26], P=0.0243). Expression by NanoString strongly correlated with RNA-Seq, confirming the association with shorter PFS (HR 1.13 [95% CI: 1.04–1.23], P=0.0048). In GOYA, a significant association between PFS and FCGR2B was observed in the R arm (HR 1.26 [95% CI: 1.00–1.58], P=0.0455), with no prognostic effect observed for G (HR 0.91 [95% CI: 0.69–1.20], P=0.5). Pts with high FCGR2B expression appeared to benefit more from G than R (HR 0.67 [95% CI: 0.44–1.02], P=0.0622), in contrast to pts with low FCGR2B expression (HR 1.58 [95% CI: 1.00–2.50], P=0.0503). In both Arthur and GOYA cohorts, FCGR2B expression by RNA-Seq was associated with FcγRIIB on the tumor, which correlated with a shorter PFS for R (HR 2.17 [95% CI: 1.04–4.50], P=0.03), but not G (HR 1.37 [95% CI: 0.66–2.87], P=0.4). This prognostic effect on PFS was independent of established prognostic biomarkers, IPI, COO and BCL2.
Conclusion: High FcγRIIB/FCGR2B expression in pts with DLBCL has prognostic value in those treated with R and may confer differential responsiveness to R or G.
Citation Format: Laura K. Hilton, Malgorzata Nowicka, Margaret Ashton-Key, Chantal E. Hargreaves, Chern Lee, Russell Foxall, Matthew J. Carter, Stephen A. Beers, Kathleen N. Potter, Christopher R. Bolen, Christian Klein, Andrea Knapp, Farheen Mir, Matthew Rose-Zerilli, Cathy Burton, Wolfram Klapper, David W. Scott, Laurie H. Sehn, Umberto Vitolo, Maurizio Martelli, Marek Trneny, Graham W. Slack, Pedro Farinha, Jonathan C. Strefford, Mikkel Z. Oestergaard, Ryan D. Morin, Mark S. Cragg. Prognostic significance of Fc gamma receptor IIB expression in the response of previously untreated diffuse large B-cell lymphomas to anti-CD20 monoclonal antibodies: Differing impact of rituximab and obinutuzumab [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-26.
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Affiliation(s)
- Laura K. Hilton
- 1BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada,
- 2Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
- *Shared first authorship,
| | | | - Margaret Ashton-Key
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
- 5Southampton University Hospitals NHS Foundation Trust, Southampton, United Kingdom,
| | - Chantal E. Hargreaves
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
- 6Nuffield Department of Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom,
| | - Chern Lee
- 5Southampton University Hospitals NHS Foundation Trust, Southampton, United Kingdom,
| | - Russell Foxall
- 7Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom,
| | - Matthew J. Carter
- 7Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom,
| | - Stephen A. Beers
- 7Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom,
| | - Kathleen N. Potter
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
| | | | | | | | - Farheen Mir
- 10Royal Marsden Hospital, Sutton, United Kingdom,
| | - Matthew Rose-Zerilli
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
| | - Cathy Burton
- 11St. James's Institute of Oncology, Leeds, United Kingdom,
| | | | - David W. Scott
- 1BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada,
- 13University of British Columbia, Vancouver, BC, Canada,
| | - Laurie H. Sehn
- 1BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada,
- 13University of British Columbia, Vancouver, BC, Canada,
| | - Umberto Vitolo
- 14Candiolo Cancer Institute, FPO-IRCCS, Candiolo (TO), Italy,
| | - Maurizio Martelli
- 15Department of Translational and Precision Medicine, Hematology, Sapienza University, Rome, Italy,
| | - Marek Trneny
- 16Charles University General Hospital, Prague, Czech Republic,
| | - Graham W. Slack
- 1BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada,
| | - Pedro Farinha
- 1BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada,
| | - Jonathan C. Strefford
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
- #shared senior authorship
| | - Mikkel Z. Oestergaard
- 17F. Hoffmann-La Roche Ltd., Basel, Switzerland (currently, Novo Nordisk, Zurich, Switzerland),
- #shared senior authorship
| | - Ryan D. Morin
- 2Canada's Michael Smith Genome Sciences Centre, Vancouver, BC, Canada,
- 18Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- #shared senior authorship
| | - Mark S. Cragg
- 4School of Cancer Sciences, University of Southampton, Southampton, United Kingdom,
- 7Antibody and Vaccine Group, Centre for Cancer Immunology, School of Cancer Sciences, University of Southampton Faculty of Medicine, Southampton, United Kingdom,
- #shared senior authorship
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Arthur SE, Thomas N, Tang J, Rushton CK, Alcaide M, Telenius A, Healy S, Mottok A, Scott DW, Steidl C, Morin RD. Abstract PO-32: NFKBIZ 3′ UTR mutations confer selective growth advantage and affect drug response in diffuse large B-cell lymphoma. Blood Cancer Discov 2020. [DOI: 10.1158/2643-3249.lymphoma20-po-32] [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] Open
Abstract
Abstract
Introduction: The activated B cell-like (ABC) molecular subgroup of diffuse large B-cell lymphoma (DLBCL) is characterized by activation of NF-κB signaling. Recurrent mutations affecting genes such as MYD88, CD79A/B, and TNFAIP3 contribute to this in some cases, but there remain tumors with no known genetic basis for this pathway activation. This suggests that our understanding of ABC DLBCL drivers remains incomplete. Previously, NFKBIZ was shown to be amplified in 10% of ABC DLBCLs and to contribute to activation of NF-κB signaling. We recently described a novel pattern of mutations affecting the 3′ UTR of NFKBIZ resulting in an overall mutation rate of 30% (UTR or AMP) in ABC DLBCL. These NFKBIZ UTR mutations are mutually exclusive with MYD88 mutations, thus suggesting they may also lead to activation of NF-κB signaling. The NFKBIZ protein interacts with NF-κB transcription factors and is thought to regulate canonical NF-κB signaling. We hypothesized that NFKBIZ UTR mutations affect the normally rapid degradation of this mRNA by disrupting secondary structures recognized by RNA-binding proteins such as ribonucleases. The resulting elevated NFKBIZ mRNA levels would lead to accumulation of protein and may be a novel mechanism to promote cell growth and survival in ABC DLBCL.
Methods: NFKBIZ 3′ UTR mutations were introduced into a DLBCL cell line using the CRISPR-Cas9 system. A competitive growth assay with wild-type (WT) and CRISPR-mutant lines was performed to assess whether UTR mutations provide a growth advantage in culture (in vitro) and in mouse xenografts (in vivo). RNA-sequencing was then performed on WT and a subset of CRISPR-mutant lines and analyses were performed to identify genes upregulated by IκB-ζ in mutant lines. The IC50 of relevant drugs was determined by WST-1 assays after drug treatment on WT and mutant lines.
Results: Introduction of NFKBIZ mutations into a DLBCL cell line confirmed that UTR deletions lead to increased mRNA and protein levels. NFKBIZ UTR deletions give DLBCL cells a selective growth advantage over WT both in vitro and in vivo. RNA-sequencing of mutant and WT lines revealed possible transcriptional targets of NFKBIZ, including NF-κB targets and genes commonly overexpressed in ABC DLBCL. Novel candidate NFKBIZ targets were also discovered through this analysis, including CD274, the gene encoding PD-L1. Mutant cell lines had significantly higher IC50 compared to WT for the drugs ibrutinib, idelalisib, and masitinib, but not bortezomib, suggesting that NKFBIZ UTR mutations make cell lines more resistant to specific NF-κB pathway-targeted drugs.
Conclusions: This work directly establishes a role for NFKBIZ amplifications and 3′ UTR mutations in driving ABC DLBCL through NF-κB signaling. We demonstrate that these mutations can lead to overexpression of NFKBIZ and provide a selective growth advantage to cells both in vitro and in vivo. In addition, we found that these mutant lines were more resistant to some targeted lymphoma drugs but not others.
Citation Format: Sarah E. Arthur, Nicole Thomas, Jeffrey Tang, Christopher K. Rushton, Miguel Alcaide, Adèle Telenius, Shannon Healy, Anja Mottok, David W. Scott, Christian Steidl, Ryan D. Morin. NFKBIZ 3′ UTR mutations confer selective growth advantage and affect drug response in diffuse large B-cell lymphoma [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-32.
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Affiliation(s)
| | | | | | | | | | | | | | - Anja Mottok
- 2BC Cancer Research Centre, Vancouver, BC, Canada
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Coyle KM, Qureshi Q, Pararajalingam P, Thomas N, Audas TE, Morin RD. Abstract PO-04: Noncoding mutations in mantle cell lymphoma disrupt regulation of HNRNPH1 by alternative splicing. Blood Cancer Discov 2020. [DOI: 10.1158/2643-3249.lymphoma20-po-04] [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] Open
Abstract
Abstract
Non-Hodgkin lymphomas (NHL) are a collection of cancers with each malignancy having distinct clinical management and prognosis. Mantle cell lymphoma (MCL) is particularly genetically heterogeneous and is considered incurable. Through a combination of exome, genome, and targeted sequencing of MCL tumors, we identified recurrent mutations in HNRNPH1 (heterogeneous nuclear ribonucleoprotein H1). These mutations are largely intronic or silent and are associated with a putative cis regulatory region involving a single exon. In RNA-seq data from matched cases, we identified variable representation of two distinct HNRNPH1 isoforms. Based on the reading frame of the affected exons, canonical splicing is predicted to produce a functional protein, while alternative splicing introduces a premature termination codon leading to nonsense-mediated decay. We observed a significantly higher proportion of canonical transcripts in MCL tumors bearing HNRNPH1 mutations, leading us to conclude that mutations in HNRNPH1 significantly alter its splicing. Furthermore, increased canonical splicing results in higher HNRNPH1 protein abundance as determined by immunohistochemical analysis of an MCL tissue microarray. HNRNPH1 mutation status and splicing ratio are associated with shorter survival of MCL patients. We developed an in vitro reporter minigene and introduced three specific mutations corresponding to the patient-identified mutations in HNRNPH1. These mutations lead to an increase in canonical splicing and translation of the HNRNPH1 minigene-derived peptide. Additionally, when HNRNPH1 is overexpressed, we observe a decrease of this peptide, implicating HNRNPH1 in the regulation of its own splicing. This is supported by preliminary data indicating that HNRNPH1 binds its own RNA. Beyond its own splicing, HNRNPH1 is likely also involved in the splicing of additional splicing factors. Overexpression of HNRNPH1 affects the splicing of SRSF3 and HNRNPDL, and many other targets are likely to be identified. This work elucidates a functional role for recurrent noncoding HNRNPH1 mutations and implicates HNRNPH1 expression and splicing of its downstream targets in lymphomagenesis. We continue to explore trans regulatory targets of HNRNPH1 using in vitro and cell-based models. While splicing is a growing field of interest in lymphoma biology, the unique pattern and consequences of these largely silent mutations specifically implicate alternative splicing as an oncogenic mechanism in MCL.
Citation Format: Krysta M. Coyle, Quratulain Qureshi, Prasath Pararajalingam, Nicole Thomas, Timothy E. Audas, Ryan D. Morin. Noncoding mutations in mantle cell lymphoma disrupt regulation of HNRNPH1 by alternative splicing [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr PO-04.
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Thomas N, Hilton LK, Michaud N, Bushell K, Rys R, Jain M, Shepherd L, Marra MA, Kuruvilla J, Crump M, Mann K, Assouline S, Steidl C, Cragg MS, Scott DW, Johnson N, Morin RD, Rushton CK, Arthur SE, Alcaide M, Cheung M, Jiang A, Coyle KM, Cleary KLS. Abstract IA42: Detecting and quantifying mutations associated with treatment resistance in aggressive lymphomas using ctDNA. Blood Cancer Discov 2020. [DOI: 10.1158/2643-3249.lymphoma20-ia42] [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] Open
Abstract
Abstract
A significant proportion of diffuse large B-cell lymphoma (DLBCL) patients treated with immunochemotherapy containing rituximab (R-CHOP) exhibit either primary or acquired treatment resistance. The advancement of therapeutics in the relapse setting has likely been encumbered by our limited understanding of the molecular features that underlie resistance to R-CHOP. Unfortunately, our knowledge of DLBCL genetics is mostly limited to analyses conducted on diagnostic tissue biopsies, which have not been exposed to the selective pressures imposed by therapy. Identifying genetic alterations that contribute to treatment resistance may reveal additional treatment options and lead to biomarkers allowing patients to be paired with appropriate treatments. Genetic subgroups are gaining popularity as a new strategy to implement precision medicine in DLBCL (1). The relevance of these and other biomarkers in the relapse setting remains unclear due to limited genetic exploration of relapsed and refractory DLBCL (rrDLBCL). Progress has been limited, in part, by the requirement of tissue biopsies collected after relapse. It is well established that quantitative genomic techniques such as digital PCR and targeted sequencing can be used to determine the proportion of tumor DNA in plasma from lymphoma patients (2). With a sufficiently broad panel, sequencing affords additional opportunities including the ability to identify subclonal structure and population dynamics over time. This presentation will discuss our recent analysis of a large collection of ctDNA primarily comprising DLBCL patients on various clinical trials (3). Targeted sequencing of these samples and comparison to exome data from a meta-cohort of previously characterized untreated DLBCL biopsies revealed six genes significantly enriched for mutations upon relapse. We found both TP53 and KMT2D were mutated in the majority of rrDLBCLs, and these mutations persisted in the dominant clone following relapse, suggesting a role in primary treatment resistance. By inferring subclonal dynamics, we observed recurrent patterns of clonal expansion and contraction following rituximab-based therapy, with MS4A1 mutations representing the only example of consistent clonal expansion. MS4A1 missense mutations within the transmembrane domains led to loss of CD20 expression in vitro, and patient tumors harboring these mutations lacked CD20 protein expression. Our analysis nominates TP53 and KMT2D mutation status as novel prognostic factors that may facilitate the identification of high-risk patients prior to therapy. Moreover, we have demonstrated the potential to identify tumors with loss of CD20 surface expression stemming from MS4A1 mutations. Implementation of noninvasive assays to detect such features of acquired treatment resistance may allow timely transition to more effective treatment regimens. In certain scenarios whole-exome sequencing (WES) or whole-genome sequencing (WGS) can be successfully applied to ctDNA, thereby allowing the identification of mutations, structural variation, and copy number changes. Low-pass sequencing of shotgun libraries can also be used to ascertain course estimates of ctDNA levels as well as the copy number landscape (4). Given the importance of copy number and structural alterations in the inference of genetic subgroups, these methods may allow the exploration of these groups and their stability over time. Through a series of illustrative examples, this presentation will explore the benefits of each of these techniques in the study of tumor evolution and acquired treatment resistance in DLBCL.
References: 1. Morin RD, Scott DW. DLBCL subclassification: Divide and conquer? Blood 2020;135:1722–4. 2. Rossi D et al. The development of liquid biopsy for research and clinical practice in lymphomas: Report of the 15-ICML workshop on ctDNA. Hematol Oncol 2020;38:34–7. 3. Rushton CK et al. Genetic and evolutionary patterns of treatment resistance in relapsed B-cell lymphoma. Blood Adv 2020;4:2886–98. 4. Adalsteinsson VA et al. Scalable whole-exome sequencing of cell-free DNA reveals high concordance with metastatic tumors. Nat Commun 2017;8:1324.
Citation Format: Nicole Thomas, Laura K. Hilton, Neil Michaud, Kevin Bushell, Ryan Rys, Michael Jain, Lois Shepherd, Marco A. Marra, John Kuruvilla, Michael Crump, Koren Mann, Sarit Assouline, Christian Steidl, Mark S. Cragg, David W. Scott, Nathalie Johnson, Ryan D. Morin, Christopher K. Rushton, Sarah E. Arthur, Miguel Alcaide, Matthew Cheung, Aixiang Jiang, Krysta M. Coyle, Kirstie L. S. Cleary. Detecting and quantifying mutations associated with treatment resistance in aggressive lymphomas using ctDNA [abstract]. In: Proceedings of the AACR Virtual Meeting: Advances in Malignant Lymphoma; 2020 Aug 17-19. Philadelphia (PA): AACR; Blood Cancer Discov 2020;1(3_Suppl):Abstract nr IA42.
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Affiliation(s)
| | | | | | | | - Ryan Rys
- 3McGill University, Montreal, QC, Canada,
| | | | | | | | | | - Michael Crump
- 7Princess Margaret Cancer Centre, Toronto, ON, Canada,
| | - Koren Mann
- 3McGill University, Montreal, QC, Canada,
| | | | | | - Mark S. Cragg
- 8University of Southampton, Southampton, United Kingdom
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30
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Jiang A, Hilton LK, Tang J, Rushton CK, Grande BM, Scott DW, Morin RD. PRPS-ST: A protocol-agnostic self-training method for gene expression-based classification of blood cancers. Blood Cancer Discov 2020; 1:244-257. [PMID: 33392514 DOI: 10.1158/2643-3230.bcd-20-0076] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022] Open
Abstract
Gene expression classifiers are gaining increasing popularity for stratifying tumors into subgroups with distinct biological features. A fundamental limitation shared by current classifiers is the requirement for comparable training and testing data sets. Here, we describe a self-training implementation of our probability ratio-based classification prediction score method (PRPS-ST), which facilitates the porting of existing classification models to other gene expression data sets. In comparison to gold standards, we demonstrate favorable performance of PRPS-ST in gene expression-based classification of DLBCL and B-ALL using a diverse variety of gene expression data types and pre-processing methods, including in classifications with a high degree of class imbalance. Tumors classified by our method were significantly enriched for prototypical genetic features of their respective subgroups. Interestingly, this included cases that were unclassifiable by established methods, implying the potential enhanced sensitivity of PRPS-ST.
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Affiliation(s)
- Aixiang Jiang
- Department of Pathology & Laboratory Medicine, University of British Columbia, Vancouver, BC, Canada.,BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Laura K Hilton
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.,Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Jeffrey Tang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher K Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - David W Scott
- BC Cancer Centre for Lymphoid Cancer, Vancouver, BC, Canada.,Department of Medicine, University of British Columbia, Vancouver, BC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
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31
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Pararajalingam P, Coyle KM, Arthur SE, Thomas N, Alcaide M, Meissner B, Boyle M, Qureshi Q, Grande BM, Rushton C, Slack GW, Mungall AJ, Tam CS, Agarwal R, Dawson SJ, Lenz G, Balasubramanian S, Gascoyne RD, Steidl C, Connors J, Villa D, Audas TE, Marra MA, Johnson NA, Scott DW, Morin RD. Coding and noncoding drivers of mantle cell lymphoma identified through exome and genome sequencing. Blood 2020; 136:572-584. [PMID: 32160292 PMCID: PMC7440974 DOI: 10.1182/blood.2019002385] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [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: 07/09/2019] [Accepted: 02/20/2020] [Indexed: 12/11/2022] Open
Abstract
Mantle cell lymphoma (MCL) is an uncommon B-cell non-Hodgkin lymphoma (NHL) that is incurable with standard therapies. The genetic drivers of this cancer have not been firmly established, and the features that contribute to differences in clinical course remain limited. To extend our understanding of the biological pathways involved in this malignancy, we performed a large-scale genomic analysis of MCL using data from 51 exomes and 34 genomes alongside previously published exome cohorts. To confirm our findings, we resequenced the genes identified in the exome cohort in 191 MCL tumors, each having clinical follow-up data. We confirmed the prognostic association of TP53 and NOTCH1 mutations. Our sequencing revealed novel recurrent noncoding mutations surrounding a single exon of the HNRNPH1gene. In RNA-seq data from 103 of these cases, MCL tumors with these mutations had a distinct imbalance of HNRNPH1 isoforms. This altered splicing of HNRNPH1 was associated with inferior outcomes in MCL and showed a significant increase in protein expression by immunohistochemistry. We describe a functional role for these recurrent noncoding mutations in disrupting an autoregulatory feedback mechanism, thereby deregulating HNRNPH1 protein expression. Taken together, these data strongly imply a role for aberrant regulation of messenger RNA processing in MCL pathobiology.
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Affiliation(s)
- Prasath Pararajalingam
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Krysta M Coyle
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sarah E Arthur
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Nicole Thomas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Miguel Alcaide
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Barbara Meissner
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Merrill Boyle
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Quratulain Qureshi
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Christopher Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Graham W Slack
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | | | - Constantine S Tam
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Rishu Agarwal
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
| | - Sarah-Jane Dawson
- Peter MacCallum Cancer Centre, Melbourne, VIC, Australia
- University of Melbourne, Melbourne, VIC, Australia
| | - Georg Lenz
- Department of Medicine A, Hematology, Oncology, and Pneumology, University Hospital Münster, Münster, Germany
| | | | - Randy D Gascoyne
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Christian Steidl
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Joseph Connors
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Diego Villa
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Timothy E Audas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Marco A Marra
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | | | - David W Scott
- BC Cancer Centre for Lymphoid Cancer and
- BC Cancer Research Centre, Vancouver, BC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Michael Smith Genome Sciences Centre, Vancouver, BC, Canada
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Rushton CK, Arthur SE, Alcaide M, Cheung M, Jiang A, Coyle KM, Cleary KLS, Thomas N, Hilton LK, Michaud N, Daigle S, Davidson J, Bushell K, Yu S, Rys RN, Jain M, Shepherd L, Marra MA, Kuruvilla J, Crump M, Mann K, Assouline S, Connors JM, Steidl C, Cragg MS, Scott DW, Johnson NA, Morin RD. Genetic and evolutionary patterns of treatment resistance in relapsed B-cell lymphoma. Blood Adv 2020; 4:2886-2898. [PMID: 32589730 PMCID: PMC7362366 DOI: 10.1182/bloodadvances.2020001696] [Citation(s) in RCA: 54] [Impact Index Per Article: 13.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2020] [Accepted: 05/14/2020] [Indexed: 12/20/2022] Open
Abstract
Diffuse large B-cell lymphoma (DLBCL) patients are typically treated with immunochemotherapy containing rituximab (rituximab, cyclophosphamide, hydroxydaunorubicin-vincristine (Oncovin), and prednisone [R-CHOP]); however, prognosis is extremely poor if R-CHOP fails. To identify genetic mechanisms contributing to primary or acquired R-CHOP resistance, we performed target-panel sequencing of 135 relapsed/refractory DLBCLs (rrDLBCLs), primarily comprising circulating tumor DNA from patients on clinical trials. Comparison with a metacohort of 1670 diagnostic DLBCLs identified 6 genes significantly enriched for mutations upon relapse. TP53 and KMT2D were mutated in the majority of rrDLBCLs, and these mutations remained clonally persistent throughout treatment in paired diagnostic-relapse samples, suggesting a role in primary treatment resistance. Nonsense and missense mutations affecting MS4A1, which encodes CD20, are exceedingly rare in diagnostic samples but show recurrent patterns of clonal expansion following rituximab-based therapy. MS4A1 missense mutations within the transmembrane domains lead to loss of CD20 in vitro, and patient tumors harboring these mutations lacked CD20 protein expression. In a time series from a patient treated with multiple rounds of therapy, tumor heterogeneity and minor MS4A1-harboring subclones contributed to rapid disease recurrence, with MS4A1 mutations as founding events for these subclones. TP53 and KMT2D mutation status, in combination with other prognostic factors, may be used to identify high-risk patients prior to R-CHOP for posttreatment monitoring. Using liquid biopsies, we show the potential to identify tumors with loss of CD20 surface expression stemming from MS4A1 mutations. Implementation of noninvasive assays to detect such features of acquired treatment resistance may allow timely transition to more effective treatment regimens.
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Affiliation(s)
- Christopher K Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sarah E Arthur
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Miguel Alcaide
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Matthew Cheung
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Aixiang Jiang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | - Krysta M Coyle
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Kirstie L S Cleary
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - Nicole Thomas
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Laura K Hilton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | | | | | - Jordan Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Kevin Bushell
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Stephen Yu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | | | - Michael Jain
- Department of Blood and Marrow Transplant and Cellular Immunotherapy, Moffitt Cancer Center, Tampa, FL
| | - Lois Shepherd
- Canadian Cancer Trials Group, Queen's University, Kingston, ON, Canada
| | - Marco A Marra
- Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
| | - John Kuruvilla
- Princess Margaret Cancer Centre, Toronto, ON, Canada; and
| | - Michael Crump
- Princess Margaret Cancer Centre, Toronto, ON, Canada; and
| | - Koren Mann
- Lady Davis Institute for Medical Research
- Jewish General Hospital, Montreal, QC, Canada
| | | | | | | | - Mark S Cragg
- Faculty of Medicine, University of Southampton, Southampton, United Kingdom
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer, Vancouver, BC, Canada
| | | | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada
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Venturutti L, Teater M, Zhai A, Chadburn A, Babiker L, Kim D, Béguelin W, Lee TC, Kim Y, Chin CR, Yewdell WT, Raught B, Phillip JM, Jiang Y, Staudt LM, Green MR, Chaudhuri J, Elemento O, Farinha P, Weng AP, Nissen MD, Steidl C, Morin RD, Scott DW, Privé GG, Melnick AM. TBL1XR1 Mutations Drive Extranodal Lymphoma by Inducing a Pro-tumorigenic Memory Fate. Cell 2020; 182:297-316.e27. [PMID: 32619424 DOI: 10.1016/j.cell.2020.05.049] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 03/24/2020] [Accepted: 05/27/2020] [Indexed: 12/30/2022]
Abstract
The most aggressive B cell lymphomas frequently manifest extranodal distribution and carry somatic mutations in the poorly characterized gene TBL1XR1. Here, we show that TBL1XR1 mutations skew the humoral immune response toward generating abnormal immature memory B cells (MB), while impairing plasma cell differentiation. At the molecular level, TBL1XR1 mutants co-opt SMRT/HDAC3 repressor complexes toward binding the MB cell transcription factor (TF) BACH2 at the expense of the germinal center (GC) TF BCL6, leading to pre-memory transcriptional reprogramming and cell-fate bias. Upon antigen recall, TBL1XR1 mutant MB cells fail to differentiate into plasma cells and instead preferentially reenter new GC reactions, providing evidence for a cyclic reentry lymphomagenesis mechanism. Ultimately, TBL1XR1 alterations lead to a striking extranodal immunoblastic lymphoma phenotype that mimics the human disease. Both human and murine lymphomas feature expanded MB-like cell populations, consistent with a MB-cell origin and delineating an unforeseen pathway for malignant transformation of the immune system.
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Affiliation(s)
- Leandro Venturutti
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Andrew Zhai
- Department of Biochemistry, University of Toronto, Toronto, ON M5S 1A8, Canada
| | - Amy Chadburn
- Department of Pathology and Laboratory Medicine, Weill Cornell Medicine, New York, NY 10065, USA
| | - Leena Babiker
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Daleum Kim
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Tak C Lee
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Youngjun Kim
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA
| | - Christopher R Chin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA; Tri-Institutional Program in Computational Biology and Medicine, New York, NY 10065, USA
| | - William T Yewdell
- Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA
| | - Brian Raught
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada
| | - Jude M Phillip
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Yanwen Jiang
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA
| | - Louis M Staudt
- Center for Cancer Genomics, National Cancer Institute, Bethesda, MD 20892, USA
| | - Michael R Green
- Department of Lymphoma and Myeloma, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA; Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
| | - Jayanta Chaudhuri
- Immunology and Microbial Pathogenesis Program, Weill Cornell Graduate School of Medical Sciences, New York, NY 10065, USA; Immunology Program, Memorial Sloan Kettering Cancer Center, New York, NY 10065, USA; Gerstner Sloan Kettering Graduate School of Biomedical Sciences, New York, NY 10065, USA
| | - Olivier Elemento
- Caryl and Israel Englander Institute for Precision Medicine, Weill Cornell Medicine, New York, NY 10021, USA
| | - Pedro Farinha
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Andrew P Weng
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada; Department of Pathology and Lab Medicine, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Michael D Nissen
- Terry Fox Laboratory, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Christian Steidl
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Ryan D Morin
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, BC Cancer Agency, Vancouver, BC V5Z1L3, Canada
| | - Gilbert G Privé
- Princess Margaret Cancer Centre, University of Toronto, Toronto, ON M5G 1L7, Canada; Department of Medical Biophysics, University of Toronto, and Princess Margaret Cancer Centre, Toronto, ON M5S 1A8, Canada
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medicine, Cornell University, New York, NY 10021, USA.
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34
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Wright GW, Huang DW, Phelan JD, Coulibaly ZA, Roulland S, Young RM, Wang JQ, Schmitz R, Morin RD, Tang J, Jiang A, Bagaev A, Plotnikova O, Kotlov N, Johnson CA, Wilson WH, Scott DW, Staudt LM. A Probabilistic Classification Tool for Genetic Subtypes of Diffuse Large B Cell Lymphoma with Therapeutic Implications. Cancer Cell 2020; 37:551-568.e14. [PMID: 32289277 PMCID: PMC8459709 DOI: 10.1016/j.ccell.2020.03.015] [Citation(s) in RCA: 511] [Impact Index Per Article: 127.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/19/2019] [Revised: 01/03/2020] [Accepted: 03/16/2020] [Indexed: 12/22/2022]
Abstract
The development of precision medicine approaches for diffuse large B cell lymphoma (DLBCL) is confounded by its pronounced genetic, phenotypic, and clinical heterogeneity. Recent multiplatform genomic studies revealed the existence of genetic subtypes of DLBCL using clustering methodologies. Here, we describe an algorithm that determines the probability that a patient's lymphoma belongs to one of seven genetic subtypes based on its genetic features. This classification reveals genetic similarities between these DLBCL subtypes and various indolent and extranodal lymphoma types, suggesting a shared pathogenesis. These genetic subtypes also have distinct gene expression profiles, immune microenvironments, and outcomes following immunochemotherapy. Functional analysis of genetic subtype models highlights distinct vulnerabilities to targeted therapy, supporting the use of this classification in precision medicine trials.
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MESH Headings
- Animals
- Apoptosis
- Biomarkers, Tumor/genetics
- Cell Proliferation
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Genetic Heterogeneity
- Humans
- Lymphoma, Large B-Cell, Diffuse/classification
- Lymphoma, Large B-Cell, Diffuse/drug therapy
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/pathology
- Mice
- Mice, Inbred NOD
- Mice, SCID
- Molecular Targeted Therapy
- Precision Medicine
- Tumor Cells, Cultured
- Tumor Microenvironment
- Xenograft Model Antitumor Assays
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Affiliation(s)
- George W Wright
- Biometric Research Branch, Division of Cancer Diagnosis and Treatment, National Cancer Institute, National Institutes of Health, Bethesda, MD, USA
| | - Da Wei Huang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James D Phelan
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Zana A Coulibaly
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Sandrine Roulland
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan M Young
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - James Q Wang
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Roland Schmitz
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Jeffrey Tang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | - Aixiang Jiang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC V5A 1S6, Canada
| | | | | | | | - Calvin A Johnson
- Office of Intramural Research, Center for Information Technology, National Institutes of Health, Bethesda, MD 20892, USA
| | - Wyndham H Wilson
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA
| | - David W Scott
- British Columbia Cancer, Vancouver, BC V5Z 4E6, Canada
| | - Louis M Staudt
- Lymphoid Malignancies Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA.
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35
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Mendis S, Alcaide M, Topham JT, Johnson B, Morin RD, Chu J, Bosdet I, Kopetz S, Karsan A, Gill S, Laskin J, Jones SJM, Marra MA, Schaeffer DF, Renouf DJ, Loree JM. Integration of Whole-Genome Sequencing With Circulating Tumor DNA Analysis Captures Clonal Evolution and Tumor Heterogeneity in Non-V600 BRAF Mutant Colorectal Cancer. Clin Colorectal Cancer 2020; 19:132-136.e3. [PMID: 32151517 DOI: 10.1016/j.clcc.2020.02.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Revised: 01/22/2020] [Accepted: 02/01/2020] [Indexed: 12/21/2022]
Affiliation(s)
- Shehara Mendis
- Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Miguel Alcaide
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | | | - Benny Johnson
- Department of Gastrointestinal Medical Oncology, The University of M.D. Anderson Cancer Center, Houston, TX
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Jenny Chu
- Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Ian Bosdet
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Scott Kopetz
- Department of Gastrointestinal Medical Oncology, The University of M.D. Anderson Cancer Center, Houston, TX
| | - Aly Karsan
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, British Columbia, Canada
| | - Sharlene Gill
- Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Steven J M Jones
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - Marco A Marra
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada; Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada; Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
| | - David F Schaeffer
- Pancreas Centre BC, Vancouver, British Columbia, Canada; Department of Pathology and Laboratory Medicine, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Daniel J Renouf
- Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada; Pancreas Centre BC, Vancouver, British Columbia, Canada
| | - Jonathan M Loree
- Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada.
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36
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Haile S, Corbett RD, Bilobram S, Mungall K, Grande BM, Kirk H, Pandoh P, MacLeod T, McDonald H, Bala M, Coope RJ, Moore RA, Mungall AJ, Zhao Y, Morin RD, Jones SJ, Marra MA. Evaluation of protocols for rRNA depletion-based RNA sequencing of nanogram inputs of mammalian total RNA. PLoS One 2019; 14:e0224578. [PMID: 31671154 PMCID: PMC6822755 DOI: 10.1371/journal.pone.0224578] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [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: 06/14/2019] [Accepted: 10/16/2019] [Indexed: 12/19/2022] Open
Abstract
Next generation RNA-sequencing (RNA-seq) is a flexible approach that can be applied to a range of applications including global quantification of transcript expression, the characterization of RNA structure such as splicing patterns and profiling of expressed mutations. Many RNA-seq protocols require up to microgram levels of total RNA input amounts to generate high quality data, and thus remain impractical for the limited starting material amounts typically obtained from rare cell populations, such as those from early developmental stages or from laser micro-dissected clinical samples. Here, we present an assessment of the contemporary ribosomal RNA depletion-based protocols, and identify those that are suitable for inputs as low as 1–10 ng of intact total RNA and 100–500 ng of partially degraded RNA from formalin-fixed paraffin-embedded tissues.
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Affiliation(s)
- Simon Haile
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard D. Corbett
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Steve Bilobram
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Karen Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Bruno M. Grande
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Heather Kirk
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Pawan Pandoh
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Tina MacLeod
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Helen McDonald
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Miruna Bala
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Robin J. Coope
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Richard A. Moore
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Andrew J. Mungall
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Yongjun Zhao
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
| | - Ryan D. Morin
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Steven J. Jones
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Marco A. Marra
- Canada’s Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, British Columbia, Canada
- * E-mail:
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37
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Khakabimamaghani S, Kelkar YD, Grande BM, Morin RD, Ester M, Ziemek D. SUBSTRA: Supervised Bayesian Patient Stratification. Bioinformatics 2019; 35:3263-3272. [DOI: 10.1093/bioinformatics/btz112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2018] [Revised: 01/11/2019] [Accepted: 02/13/2019] [Indexed: 11/14/2022] Open
Abstract
Abstract
Motivation
Patient stratification methods are key to the vision of precision medicine. Here, we consider transcriptional data to segment the patient population into subsets relevant to a given phenotype. Whereas most existing patient stratification methods focus either on predictive performance or interpretable features, we developed a method striking a balance between these two important goals.
Results
We introduce a Bayesian method called SUBSTRA that uses regularized biclustering to identify patient subtypes and interpretable subtype-specific transcript clusters. The method iteratively re-weights feature importance to optimize phenotype prediction performance by producing more phenotype-relevant patient subtypes. We investigate the performance of SUBSTRA in finding relevant features using simulated data and successfully benchmark it against state-of-the-art unsupervised stratification methods and supervised alternatives. Moreover, SUBSTRA achieves predictive performance competitive with the supervised benchmark methods and provides interpretable transcriptional features in diverse biological settings, such as drug response prediction, cancer diagnosis, or kidney transplant rejection.
Availability and implementation
The R code of SUBSTRA is available at https://github.com/sahandk/SUBSTRA.
Supplementary information
Supplementary data are available at Bioinformatics online.
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Affiliation(s)
| | - Yogeshwar D Kelkar
- Computational Systems Immunology, Pfizer Worldwide R&D, Cambridge, MA, USA
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Ryan D Morin
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Martin Ester
- School of Computing Science, Simon Fraser University, Burnaby, BC, Canada
| | - Daniel Ziemek
- Computational Systems Immunology, Pfizer Worldwide R&D, Berlin, Germany
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38
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Negri GL, Grande BM, Delaidelli A, El-Naggar A, Cochrane D, Lau CC, Triche TJ, Moore RA, Jones SJ, Montpetit A, Marra MA, Malkin D, Morin RD, Sorensen PH. Integrative genomic analysis of matched primary and metastatic pediatric osteosarcoma. J Pathol 2019; 249:319-331. [PMID: 31236944 DOI: 10.1002/path.5319] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2018] [Revised: 05/23/2019] [Accepted: 06/20/2019] [Indexed: 01/14/2023]
Abstract
Despite being the most common childhood bone tumor, the genomic characterization of osteosarcoma remains incomplete. In particular, very few osteosarcoma metastases have been sequenced to date, critical to better understand mechanisms of progression and evolution in this tumor. We performed an integrated whole genome and exome sequencing analysis of paired primary and metastatic pediatric osteosarcoma specimens to identify recurrent genomic alterations. Sequencing of 13 osteosarcoma patients including 13 primary, 10 metastatic, and 3 locally recurring tumors revealed a highly heterogeneous mutational landscape, including cases of hypermutation and microsatellite instability positivity, but with virtually no recurrent alterations except for mutations involving the tumor suppressor genes RB1 and TP53. At the germline level, we detected alterations in multiple cancer related genes in the majority of the cohort, including those potentially disrupting DNA damage response pathways. Metastases retained only a minimal number of short variants from their corresponding primary tumors, while copy number alterations showed higher conservation. One recurrently amplified gene, KDR, was highly expressed in advanced cases and associated with poor prognosis. © 2019 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd.
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Affiliation(s)
- Gian Luca Negri
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Alberto Delaidelli
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
| | - Amal El-Naggar
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology, Faculty of Medicine, Menoufia University, Shebeen El-Kom, Egypt
| | - Dawn Cochrane
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada
| | - Ching C Lau
- Texas Children's Cancer and Hematology Centers, Department of Pediatrics, Baylor College of Medicine and Texas Children's Hospital, Houston, TX, USA
| | - Timothy J Triche
- Department of Pathology and Laboratory Medicine, Childrens Hospital Los Angeles, Los Angeles, CA, USA.,Department of Pathology, Keck School of Medicine of USC, Los Angeles, CA, USA
| | - Richard A Moore
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Steven Jm Jones
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada
| | - Alexandre Montpetit
- Department of Human Genetics, McGill University and Research Institute, McGill University Health Centre, Montreal, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.,Department of Medical Genetics, University of British Columbia, Vancouver, Canada
| | - David Malkin
- Division of Haematology-Oncology, The Hospital for Sick Children, Department of Pediatrics, University of Toronto, Toronto, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Poul H Sorensen
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, Vancouver, Canada
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39
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Healy S, Ennishi D, Bashashati A, Saberi S, Hother C, Mottok A, Chan FC, Chong L, Kridel R, Boyle M, Meissner B, Aoki T, Takata K, Woolcock BW, Vigano E, Abraham L, Gold M, Telenius A, Farinha P, Slack G, Ben-Neriah S, Lai D, Zhang AW, Salehi S, Shulha HP, Chiu DS, Mostafavi S, Gerrie AS, Villa D, Sehn LH, Savage KJJ, Mungall AJJ, Weng AP, Bally M, Morin RD, Freue GVC, Connors JM, Marra MA, Shah SP, Gascoyne1 RD, Scott DW, Steidl C, Steidl U. Abstract 3480: TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-3480] [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
Diffuse large B-cell lymphoma (DLBCL) is the most common lymphoma subtype worldwide, accounting for 40% of all non-Hodgkin lymphomas. DLBCL presents as an aggressive disease requiring immediate treatment. Although significant improvement in outcome has been achieved, ~40% of patients still experience treatment failure. Here, we characterized the recurrent genetic alterations and transcriptomic signatures in diagnostic biopsies from a population registry-based cohort of 347 patients with de novo DLBCL uniformly treated with R-CHOP. This analysis revealed bi-allelic loss of function mutations of TMEM30A that were associated with favorable treatment outcome. TMEM30A is a chaperone protein, involved in maintaining the asymmetric distribution of phosphatidylethanolamine and phosphatidylserine, an integral component of the plasma membrane and “eat-me” signal recognized by macrophages. Using TMEM30A knockout systems by CRISPR genome editing techniques, we have functionally characterized this loss-of-function mutation in representative human and mouse DLBCL cell line models. We have discovered that TMEM30A loss is associated with increased B-cell signaling following antigen stimulation, including a two-fold increase in the diffusion rate of B-cell receptor (BCR) clustering, using high resolution Single Particle Tracking (SPT) technology. In addition, we have measured three-fold increase in chemotherapeutic drug accumulation in both knockout cell lines and randomly selected patient biopsies with TMEM30A biallelic loss. This observation was validated in a xenograft mouse model, which presented improved survival and limited tumor growth following vincristine treatment in mice injected with TMEM30A null DLBCL cell lines compared with native cell lines. This phenotype explains the improved prognosis observed in DLBCL patients following R-CHOP treatment. Furthermore, we have observed over two fold higher numbers of tumor-associated macrophages in B-cell lymphoma syngeneic mouse models with Tmem30a loss-of-function, prior to any form of treatment, suggesting the existence of “hot” and primed tumors. Our data highlight a multi-faceted role for TMEM30A and plasma membrane physiology in B-cell lymphomagenesis, and characterize intrinsic and extrinsic vulnerabilities of cancer cells that can be therapeutically exploited. Characterization of these mechanisms will address a missing link in the cancer field as related insights in lymphoma will outline therapeutic approaches that can be extended to cancer therapy in general.
Citation Format: Shannon Healy, Daisuke Ennishi, Ali Bashashati, Saeed Saberi, Christoffer Hother, Anja Mottok, Fong Chun Chan, Lauren Chong, Robert Kridel, Merrill Boyle, Barbara Meissner, Tomohiro Aoki, Katsuyoshi Takata, Bruce W. Woolcock, Elena Vigano, Libin Abraham, Michael Gold, Adele Telenius, Pedro Farinha, Graham Slack, Susana Ben-Neriah, Daniel Lai, Allen W. Zhang, Sohrab Salehi, Hennady P. Shulha, Derek S. Chiu, Sara Mostafavi, Alina S. Gerrie, Diego Villa, Laurie H. Sehn, Kerry J. J. Savage, Andrew J. J. Mungall, Andrew P. Weng, Marcel Bally, Ryan D. Morin, Gabriela V. Cohen Freue, Joseph M. Connors, Marco A. Marra, Sohrab P. Shah, Randy D. Gascoyne1, David W. Scott, Christian Steidl, Ulrich Steidl. TMEM30A loss-of-function mutations drive lymphomagenesis and confer therapeutically exploitable vulnerability in B-cell lymphoma [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 3480.
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Affiliation(s)
- Shannon Healy
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | - Saeed Saberi
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Anja Mottok
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Fong Chun Chan
- 2University of British Columbia, Vancouver, British Columbia, Canada
| | - Lauren Chong
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Robert Kridel
- 3University Health Network, Toronto, Ontario, Canada
| | - Merrill Boyle
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Tomohiro Aoki
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | - Elena Vigano
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Libin Abraham
- 2University of British Columbia, Vancouver, British Columbia, Canada
| | - Michael Gold
- 2University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Pedro Farinha
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Graham Slack
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Daniel Lai
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Sohrab Salehi
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | - Derek S. Chiu
- 2University of British Columbia, Vancouver, British Columbia, Canada
| | - Sara Mostafavi
- 2University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Diego Villa
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | | | | | | | | | - Marcel Bally
- 1BC Cancer Agency, Vancouver, British Columbia, Canada
| | - Ryan D. Morin
- 4Simon Fraser University, Vancouver, British Columbia, Canada
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40
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Grande BM, Gerhard DS, Jiang A, Griner NB, Abramson JS, Alexander TB, Allen H, Ayers LW, Bethony JM, Bhatia K, Bowen J, Casper C, Choi JK, Culibrk L, Davidsen TM, Dyer MA, Gastier-Foster JM, Gesuwan P, Greiner TC, Gross TG, Hanf B, Harris NL, He Y, Irvin JD, Jaffe ES, Jones SJM, Kerchan P, Knoetze N, Leal FE, Lichtenberg TM, Ma Y, Martin JP, Martin MR, Mbulaiteye SM, Mullighan CG, Mungall AJ, Namirembe C, Novik K, Noy A, Ogwang MD, Omoding A, Orem J, Reynolds SJ, Rushton CK, Sandlund JT, Schmitz R, Taylor C, Wilson WH, Wright GW, Zhao EY, Marra MA, Morin RD, Staudt LM. Genome-wide discovery of somatic coding and noncoding mutations in pediatric endemic and sporadic Burkitt lymphoma. Blood 2019; 133:1313-1324. [PMID: 30617194 PMCID: PMC6428665 DOI: 10.1182/blood-2018-09-871418] [Citation(s) in RCA: 130] [Impact Index Per Article: 26.0] [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: 09/07/2018] [Accepted: 12/22/2018] [Indexed: 12/12/2022] Open
Abstract
Although generally curable with intensive chemotherapy in resource-rich settings, Burkitt lymphoma (BL) remains a deadly disease in older patients and in sub-Saharan Africa. Epstein-Barr virus (EBV) positivity is a feature in more than 90% of cases in malaria-endemic regions, and up to 30% elsewhere. However, the molecular features of BL have not been comprehensively evaluated when taking into account tumor EBV status or geographic origin. Through an integrative analysis of whole-genome and transcriptome data, we show a striking genome-wide increase in aberrant somatic hypermutation in EBV-positive tumors, supporting a link between EBV and activation-induced cytidine deaminase (AICDA) activity. In addition to identifying novel candidate BL genes such as SIN3A, USP7, and CHD8, we demonstrate that EBV-positive tumors had significantly fewer driver mutations, especially among genes with roles in apoptosis. We also found immunoglobulin variable region genes that were disproportionally used to encode clonal B-cell receptors (BCRs) in the tumors. These include IGHV4-34, known to produce autoreactive antibodies, and IGKV3-20, a feature described in other B-cell malignancies but not yet in BL. Our results suggest that tumor EBV status defines a specific BL phenotype irrespective of geographic origin, with particular molecular properties and distinct pathogenic mechanisms. The novel mutation patterns identified here imply rational use of DNA-damaging chemotherapy in some patients with BL and targeted agents such as the CDK4/6 inhibitor palbociclib in others, whereas the importance of BCR signaling in BL strengthens the potential benefit of inhibitors for PI3K, Syk, and Src family kinases among these patients.
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Affiliation(s)
- Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Daniela S Gerhard
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Aixiang Jiang
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Nicholas B Griner
- Office of Cancer Genomics, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Jeremy S Abramson
- Center for Lymphoma, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Thomas B Alexander
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | | | - Leona W Ayers
- Department of Pathology, The Ohio State University, Columbus, OH
| | | | - Kishor Bhatia
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Jay Bowen
- Nationwide Children's Hospital, Columbus, OH
| | - Corey Casper
- Infectious Disease Research Institute, Seattle, WA
| | - John Kim Choi
- Department of Pathology, St. Jude Children's Research Hospital, Memphis, TN
| | - Luka Culibrk
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Tanja M Davidsen
- Cancer Informatics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Maureen A Dyer
- Clinical Research Directorate, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD
| | - Julie M Gastier-Foster
- Nationwide Children's Hospital, Columbus, OH
- Departments of Pathology and Pediatrics, The Ohio State University, Columbus, OH
| | - Patee Gesuwan
- Cancer Informatics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Timothy C Greiner
- Department of Pathology and Microbiology, University of Nebraska Medical Center, Omaha, NE
| | - Thomas G Gross
- Center for Global Health, National Cancer Institute, National Institutes of Health, Rockville, MD
| | | | - Nancy Lee Harris
- Department of Pathology, Massachusetts General Hospital, Harvard Medical School, Boston, MA
| | - Yiwen He
- Cancer Informatics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - John D Irvin
- Foundation for Burkitt Lymphoma Research, Geneva, Switzerland
| | - Elaine S Jaffe
- Laboratory of Pathology, Clinical Center, National Cancer Institute, National Institutes of Health, Bethesda, MD
| | - Steven J M Jones
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Patrick Kerchan
- EMBLEM Study, African Field Epidemiology Network, Kampala, Uganda
| | - Nicole Knoetze
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Fabio E Leal
- Programa de Oncovirologia, Instituto Nacional de Câncer José de Alencar, Rio de Janeiro, Brazil
| | | | - Yussanne Ma
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | | | - Sam M Mbulaiteye
- Division of Cancer Epidemiology and Genetics, National Cancer Institute, National Institutes of Health, Rockville, MD
| | | | - Andrew J Mungall
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | | | - Karen Novik
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Ariela Noy
- Memorial Sloan Kettering Cancer Center, New York, NY
- Weill Cornell Medical College, New York, NY
| | | | | | | | - Steven J Reynolds
- Division of Intramural Research, National Institute of Allergy and Infectious Diseases, National Institutes of Health, Bethesda, MD; and
| | - Christopher K Rushton
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - John T Sandlund
- Department of Oncology, St. Jude Children's Research Hospital, Memphis, TN
| | - Roland Schmitz
- Lymphoid Malignancies Branch, Center for Cancer Research and
| | | | | | - George W Wright
- Biometric Research Program, Division of Cancer Diagnosis and Treatment, National Cancer Institute, National Institutes of Health, Rockville, MD
| | - Eric Y Zhao
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Marco A Marra
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
- Canada's Michael Smith Genome Sciences Centre, British Columbia Cancer Agency, Vancouver, BC, Canada
| | - Louis M Staudt
- Lymphoid Malignancies Branch, Center for Cancer Research and
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Rey K, Manku S, Enns W, Van Rossum T, Bushell K, Morin RD, Brinkman FSL, Choy JC. Disruption of the Gut Microbiota With Antibiotics Exacerbates Acute Vascular Rejection. Transplantation 2019. [PMID: 29538261 DOI: 10.1097/tp.0000000000002169] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
BACKGROUND The gut microbiota influences many immunological processes but how its disruption affects transplant rejection is poorly understood. METHODS Interposition grafting of aortic segments was used to examine vascular rejection. The gut microbiota was disrupted in graft recipients using an antibiotic cocktail (ampicillin, vancomycin, metronidazole, neomycin sulfate) in their drinking water. RESULTS Treatment of mice with antibiotics severely reduced total bacterial content in the intestine and disrupted the bacterial composition. Short-term treatment of mice for only the first 3 weeks of life resulted in the population of the intestine in mature mice with bacterial communities that were mildly different from untreated mice, containing slightly more Clostridia and less Bacteroides. Antibiotic disruption of the gut microbiota of graft recipients, either for their entire life or only during the first 3 weeks of life, resulted in increased medial injury of allograft arteries that is reflective of acute vascular rejection but did not affect intimal thickening reflective of transplant arteriosclerosis. Exacerbated vascular rejection resulting from disruption of the gut microbiota was related to increased infiltration of allograft arteries by neutrophils. CONCLUSIONS Disruption of the gut microbiota early in life results in exacerbation of immune responses that cause acute vascular rejection.
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Affiliation(s)
- Kevin Rey
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Sukhbir Manku
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Winnie Enns
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Thea Van Rossum
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Kevin Bushell
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Fiona S L Brinkman
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Jonathan C Choy
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
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Ennishi D, Takata K, Béguelin W, Duns G, Mottok A, Farinha P, Bashashati A, Saberi S, Boyle M, Meissner B, Ben-Neriah S, Woolcock BW, Telenius A, Lai D, Teater M, Kridel R, Savage KJ, Sehn LH, Morin RD, Marra MA, Shah SP, Connors JM, Gascoyne RD, Scott DW, Melnick AM, Steidl C. Molecular and Genetic Characterization of MHC Deficiency Identifies EZH2 as Therapeutic Target for Enhancing Immune Recognition. Cancer Discov 2019; 9:546-563. [PMID: 30705065 DOI: 10.1158/2159-8290.cd-18-1090] [Citation(s) in RCA: 178] [Impact Index Per Article: 35.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2018] [Revised: 12/21/2018] [Accepted: 01/28/2019] [Indexed: 12/21/2022]
Abstract
We performed a genomic, transcriptomic, and immunophenotypic study of 347 patients with diffuse large B-cell lymphoma (DLBCL) to uncover the molecular basis underlying acquired deficiency of MHC expression. Low MHC-II expression defines tumors originating from the centroblast-rich dark zone of the germinal center (GC) that was associated with inferior prognosis. MHC-II-deficient tumors were characterized by somatically acquired gene mutations reducing MHC-II expression and a lower amount of tumor-infiltrating lymphocytes. In particular, we demonstrated a strong enrichment of EZH2 mutations in both MHC-I- and MHC-II-negative primary lymphomas, and observed reduced MHC expression and T-cell infiltrates in murine lymphoma models expressing mutant Ezh2 Y641. Of clinical relevance, EZH2 inhibitors significantly restored MHC expression in EZH2-mutated human DLBCL cell lines. Hence, our findings suggest a tumor progression model of acquired immune escape in GC-derived lymphomas and pave the way for development of complementary therapeutic approaches combining immunotherapy with epigenetic reprogramming. SIGNIFICANCE: We demonstrate how MHC-deficient lymphoid tumors evolve in a cell-of-origin-specific context. Specifically, EZH2 mutations were identified as a genetic mechanism underlying acquired MHC deficiency. The paradigmatic restoration of MHC expression by EZH2 inhibitors provides the rationale for synergistic therapies combining immunotherapies with epigenetic reprogramming to enhance tumor recognition and elimination.See related commentary by Velcheti et al., p. 472.This article is highlighted in the In This Issue feature, p. 453.
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Affiliation(s)
- Daisuke Ennishi
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Katsuyoshi Takata
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Wendy Béguelin
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Gerben Duns
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Anja Mottok
- Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Pedro Farinha
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Ali Bashashati
- Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Saeed Saberi
- Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Merrill Boyle
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Barbara Meissner
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Susana Ben-Neriah
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Bruce W Woolcock
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Adèle Telenius
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Daniel Lai
- Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Matt Teater
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Robert Kridel
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Kerry J Savage
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Laurie H Sehn
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, British Columbia, Canada
| | - Marco A Marra
- Genome Science Centre, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Sohrab P Shah
- Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Joseph M Connors
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Randy D Gascoyne
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - David W Scott
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Ari M Melnick
- Division of Hematology/Oncology, Department of Medicine, Weill Cornell Medical College, New York, New York
| | - Christian Steidl
- Centre for Lymphoid Cancer, British Columbia Cancer, Vancouver, British Columbia, Canada.
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Ennishi D, Jiang A, Boyle M, Collinge B, Grande BM, Ben-Neriah S, Rushton C, Tang J, Thomas N, Slack GW, Farinha P, Takata K, Miyata-Takata T, Craig J, Mottok A, Meissner B, Saberi S, Bashashati A, Villa D, Savage KJ, Sehn LH, Kridel R, Mungall AJ, Marra MA, Shah SP, Steidl C, Connors JM, Gascoyne RD, Morin RD, Scott DW. Double-Hit Gene Expression Signature Defines a Distinct Subgroup of Germinal Center B-Cell-Like Diffuse Large B-Cell Lymphoma. J Clin Oncol 2018; 37:190-201. [PMID: 30523716 DOI: 10.1200/jco.18.01583] [Citation(s) in RCA: 218] [Impact Index Per Article: 36.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
PURPOSE High-grade B-cell lymphoma with MYC and BCL2 and/or BCL6 rearrangements (HGBL-DH/TH) has a poor outcome after standard chemoimmunotherapy. We sought to understand the biologic underpinnings of HGBL-DH/TH with BCL2 rearrangements (HGBL-DH/TH- BCL2) and diffuse large B-cell lymphoma (DLBCL) morphology through examination of gene expression. PATIENTS AND METHODS We analyzed RNA sequencing data from 157 de novo germinal center B-cell-like (GCB)-DLBCLs, including 25 with HGBL-DH/TH- BCL2, to define a gene expression signature that distinguishes HGBL-DH/TH- BCL2 from other GCB-DLBCLs. To assess the genetic, molecular, and phenotypic features associated with this signature, we analyzed targeted resequencing, whole-exome sequencing, RNA sequencing, and immunohistochemistry data. RESULTS We developed a 104-gene double-hit signature (DHITsig) that assigned 27% of GCB-DLBCLs to the DHITsig-positive group, with only one half harboring MYC and BCL2 rearrangements (HGBL-DH/TH- BCL2). DHITsig-positive patients had inferior outcomes after rituximab plus cyclophosphamide, doxorubicin, vincristine, and prednisone immunochemotherapy compared with DHITsig-negative patients (5-year time to progression rate, 57% and 81%, respectively; P < .001), irrespective of HGBL-DH/TH- BCL2 status. The prognostic value of DHITsig was confirmed in an independent validation cohort. DHITsig-positive tumors are biologically characterized by a putative non-light zone germinal center cell of origin and a distinct mutational landscape that comprises genes associated with chromatin modification. A new NanoString assay (DLBCL90) recapitulated the prognostic significance and RNA sequencing assignments. Validating the association with HGBL-DH/TH- BCL2, 11 of 25 DHITsig-positive-transformed follicular lymphomas were classified as HGBL-DH/TH- BCL2 compared with zero of 50 in the DHITsig-negative group. Furthermore, the DHITsig was shared with the majority of B-cell lymphomas with high-grade morphology tested. CONCLUSION We have defined a clinically and biologically distinct subgroup of tumors within GCB-DLBCL characterized by a gene expression signature of HGBL-DH/TH- BCL2. This knowledge has been translated into an assay applicable to routinely available biopsy samples, which enables exploration of its utility to guide patient management.
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Affiliation(s)
- Daisuke Ennishi
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Aixiang Jiang
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada.,2 Simon Fraser University, Burnaby, British Columbia, Canada
| | - Merrill Boyle
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Brett Collinge
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Bruno M Grande
- 2 Simon Fraser University, Burnaby, British Columbia, Canada
| | - Susana Ben-Neriah
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | | | - Jeffrey Tang
- 2 Simon Fraser University, Burnaby, British Columbia, Canada
| | - Nicole Thomas
- 2 Simon Fraser University, Burnaby, British Columbia, Canada
| | - Graham W Slack
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Pedro Farinha
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Katsuyoshi Takata
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Tomoko Miyata-Takata
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Jeffrey Craig
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Anja Mottok
- 3 Institute of Human Genetics, Ulm University and Ulm University Medical Center, Ulm, Germany
| | - Barbara Meissner
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Saeed Saberi
- 4 Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Ali Bashashati
- 4 Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Diego Villa
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Kerry J Savage
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Laurie H Sehn
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Robert Kridel
- 5 Princess Margaret Cancer Center-University Health Network, Toronto, Ontario, Canada
| | - Andrew J Mungall
- 6 Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Marco A Marra
- 6 Genome Sciences Center, British Columbia Cancer Agency, Vancouver, British Columbia, Canada
| | - Sohrab P Shah
- 4 Molecular Oncology, British Columbia Cancer, Vancouver, British Columbia, Canada
| | - Christian Steidl
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Joseph M Connors
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Randy D Gascoyne
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- 2 Simon Fraser University, Burnaby, British Columbia, Canada
| | - David W Scott
- 1 British Columbia Cancer Centre for Lymphoid Cancer, Vancouver, British Columbia, Canada
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Wong HL, Zhao EY, Jones MR, Reisle CR, Eirew P, Pleasance E, Grande BM, Karasinska JM, Kalloger SE, Lim HJ, Shen Y, Yip S, Morin RD, Laskin J, Marra MA, Jones SJ, Schrader KA, Schaeffer DF, Renouf DJ. Temporal Dynamics of Genomic Alterations in a BRCA1 Germline-Mutated Pancreatic Cancer With Low Genomic Instability Burden but Exceptional Response to Fluorouracil, Oxaliplatin, Leucovorin, and Irinotecan. JCO Precis Oncol 2018; 2:PO.18.00057. [PMID: 32913994 PMCID: PMC7446469 DOI: 10.1200/po.18.00057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Hui-li Wong
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Eric Y. Zhao
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Martin R. Jones
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Caralyn R. Reisle
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Peter Eirew
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Erin Pleasance
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Bruno M. Grande
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Joanna M. Karasinska
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steve E. Kalloger
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Howard J. Lim
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Yaoqing Shen
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Stephen Yip
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Ryan D. Morin
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Janessa Laskin
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Marco A. Marra
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Steven J.M. Jones
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Kasmintan A. Schrader
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - David F. Schaeffer
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
| | - Daniel J. Renouf
- Hui-li Wong, Eric Y. Zhao, Martin R. Jones, Caralyn R. Reisle, Peter Eirew, Erin Pleasance, Howard J. Lim, Yaoqing Shen, Ryan D. Morin, Janessa Laskin, Marco A. Marra, Steven J.M. Jones, and Daniel J. Renouf, British Columbia Cancer Agency; Hui-li Wong, Joanna M. Karasinska, Steve E. Kalloger, David F. Schaeffer, and Daniel J. Renouf, Pancreas Centre BC; Bruno M. Grande and Ryan D. Morin, Simon Fraser University; Steve E. Kalloger, Stephen Yip, Marco A. Marra, Steven J.M. Jones, Kasmintan A. Schrader, and David F. Schaeffer, University of British Columbia; and David F. Schaeffer, Vancouver General Hospital, Vancouver, British Columbia, Canada
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45
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Taghiyar MJ, Rosner J, Grewal D, Grande BM, Aniba R, Grewal J, Boutros PC, Morin RD, Bashashati A, Shah SP. Kronos: a workflow assembler for genome analytics and informatics. Gigascience 2018; 6:1-10. [PMID: 28655203 PMCID: PMC5569921 DOI: 10.1093/gigascience/gix042] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [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: 03/07/2017] [Accepted: 06/07/2017] [Indexed: 11/25/2022] Open
Abstract
Background: The field of next-generation sequencing informatics has matured to a point where algorithmic advances in sequence alignment and individual feature detection methods have stabilized. Practical and robust implementation of complex analytical workflows (where such tools are structured into “best practices” for automated analysis of next-generation sequencing datasets) still requires significant programming investment and expertise. Results: We present Kronos, a software platform for facilitating the development and execution of modular, auditable, and distributable bioinformatics workflows. Kronos obviates the need for explicit coding of workflows by compiling a text configuration file into executable Python applications. Making analysis modules would still require programming. The framework of each workflow includes a run manager to execute the encoded workflows locally (or on a cluster or cloud), parallelize tasks, and log all runtime events. The resulting workflows are highly modular and configurable by construction, facilitating flexible and extensible meta-applications that can be modified easily through configuration file editing. The workflows are fully encoded for ease of distribution and can be instantiated on external systems, a step toward reproducible research and comparative analyses. We introduce a framework for building Kronos components that function as shareable, modular nodes in Kronos workflows. Conclusions: The Kronos platform provides a standard framework for developers to implement custom tools, reuse existing tools, and contribute to the community at large. Kronos is shipped with both Docker and Amazon Web Services Machine Images. It is free, open source, and available through the Python Package Index and at https://github.com/jtaghiyar/kronos.
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Affiliation(s)
- M Jafar Taghiyar
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, V6T 2B5 Vancouver, BC, Canada
| | - Jamie Rosner
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada
| | - Diljot Grewal
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, V6T 2B5 Vancouver, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6 Burnaby, BC, Canada
| | - Radhouane Aniba
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, V6T 2B5 Vancouver, BC, Canada
| | - Jasleen Grewal
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6 Burnaby, BC, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research (OICR), 661 University Avenue, M5G 0A3 Toronto, ON, Canada.,Department of Medical Biophysics, University of Toronto, 101 College Street, M5G 1L7 Toronto, ON, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, 8888 University Drive, V5A 1S6 Burnaby, BC, Canada
| | - Ali Bashashati
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, V6T 2B5 Vancouver, BC, Canada
| | - Sohrab P Shah
- Department of Molecular Oncology, British Columbia Cancer Agency, 675 West 10th Ave, V5Z 1L3 Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine, University of British Columbia, 2211 Wesbrook Mall, V6T 2B5 Vancouver, BC, Canada
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46
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Albuquerque MA, Grande BM, Ritch EJ, Pararajalingam P, Jessa S, Krzywinski M, Grewal JK, Shah SP, Boutros PC, Morin RD. Enhancing knowledge discovery from cancer genomics data with Galaxy. Gigascience 2018; 6:1-13. [PMID: 28327945 PMCID: PMC5437943 DOI: 10.1093/gigascience/gix015] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 12/04/2016] [Accepted: 03/06/2017] [Indexed: 01/15/2023] Open
Abstract
The field of cancer genomics has demonstrated the power of massively parallel sequencing techniques to inform on the genes and specific alterations that drive tumor onset and progression. Although large comprehensive sequence data sets continue to be made increasingly available, data analysis remains an ongoing challenge, particularly for laboratories lacking dedicated resources and bioinformatics expertise. To address this, we have produced a collection of Galaxy tools that represent many popular algorithms for detecting somatic genetic alterations from cancer genome and exome data. We developed new methods for parallelization of these tools within Galaxy to accelerate runtime and have demonstrated their usability and summarized their runtimes on multiple cloud service providers. Some tools represent extensions or refinement of existing toolkits to yield visualizations suited to cohort-wide cancer genomic analysis. For example, we present Oncocircos and Oncoprintplus, which generate data-rich summaries of exome-derived somatic mutation. Workflows that integrate these to achieve data integration and visualizations are demonstrated on a cohort of 96 diffuse large B-cell lymphomas and enabled the discovery of multiple candidate lymphoma-related genes. Our toolkit is available from our GitHub repository as Galaxy tool and dependency definitions and has been deployed using virtualization on multiple platforms including Docker.
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Affiliation(s)
- Marco A Albuquerque
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Elie J Ritch
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Prasath Pararajalingam
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Selin Jessa
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Martin Krzywinski
- Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC, Canada
| | - Jasleen K Grewal
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sohrab P Shah
- Department of Pathology, University of British Columbia, Vancouver, BC, Canada
| | - Paul C Boutros
- Ontario Institute for Cancer Research, Toronto, ON, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.,Canada's Michael Smith Genome Sciences Center, BC Cancer Agency, Vancouver, BC, Canada
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47
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Wu C, de Miranda NF, Chen L, Wasik AM, Mansouri L, Jurczak W, Galazka K, Dlugosz-Danecka M, Machaczka M, Zhang H, Peng R, Morin RD, Rosenquist R, Sander B, Pan-Hammarström Q. Genetic heterogeneity in primary and relapsed mantle cell lymphomas: Impact of recurrent CARD11 mutations. Oncotarget 2018; 7:38180-38190. [PMID: 27224912 PMCID: PMC5122381 DOI: 10.18632/oncotarget.9500] [Citation(s) in RCA: 102] [Impact Index Per Article: 17.0] [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: 09/19/2015] [Accepted: 05/01/2016] [Indexed: 12/12/2022] Open
Abstract
The genetic mechanisms underlying disease progression, relapse and therapy resistance in mantle cell lymphoma (MCL) remain largely unknown. Whole-exome sequencing was performed in 27 MCL samples from 13 patients, representing the largest analyzed series of consecutive biopsies obtained at diagnosis and/or relapse for this type of lymphoma. Eighteen genes were found to be recurrently mutated in these samples, including known (ATM, MEF2B and MLL2) and novel mutation targets (S1PR1 and CARD11). CARD11, a scaffold protein required for B-cell receptor (BCR)-induced NF-κB activation, was subsequently screened in an additional 173 MCL samples and mutations were observed in 5.5% of cases. Based on in vitro cell line-based experiments, overexpression of CARD11 mutants were demonstrated to confer resistance to the BCR-inhibitor ibrutinib and NF-κB-inhibitor lenalidomide. Genetic alterations acquired in the relapse samples were found to be largely non-recurrent, in line with the branched evolutionary pattern of clonal evolution observed in most cases. In summary, this study highlights the genetic heterogeneity in MCL, in particular at relapse, and provides for the first time genetic evidence of BCR/NF-κB activation in a subset of MCL.
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Affiliation(s)
- Chenglin Wu
- Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden
| | - Noel Fcc de Miranda
- Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden
| | - Longyun Chen
- Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden.,Beijing Genomics Institute, Shenzhen, China
| | - Agata M Wasik
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Wojciech Jurczak
- Department of Hematology, Jagiellonian University Collegium Medicum, Kraków, Poland
| | - Krystyna Galazka
- Department of Pathology, Jagiellonian University Collegium Medicum, Kraków, Poland
| | | | - Maciej Machaczka
- Faculty of Health Sciences, Jagiellonian University Collegium Medicum, Michalowskiego, Poland
| | - Huilai Zhang
- Department of Lymphoma, Tianjin Medical University Cancer Hospital and Institute, Tianjin, China
| | - Roujun Peng
- Department of Medical Oncology, Sun Yat-Sen University Cancer Center, State Key Laboratory of Oncology in South China, Collaborative Innovation Center of Cancer Medicine, Guangzhou, China
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, Canada
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, Uppsala, Sweden
| | - Birgitta Sander
- Division of Pathology, Department of Laboratory Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden
| | - Qiang Pan-Hammarström
- Division of Clinical Immunology and Transfusion Medicine, Karolinska Institutet at Karolinska University Hospital, Huddinge, Sweden
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48
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Wever CM, Geoffrion D, Grande BM, Yu S, Alcaide M, Lemaire M, Riazalhosseini Y, Hébert J, Gavino C, Vinh DC, Petrogiannis-Haliotis T, Dmitrienko S, Mann KK, Morin RD, Johnson NA. The genomic landscape of two Burkitt lymphoma cases and derived cell lines: comparison between primary and relapse samples. Leuk Lymphoma 2018; 59:2159-2174. [PMID: 29295643 DOI: 10.1080/10428194.2017.1413186] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Relapse occurs in 10-40% of Burkitt lymphoma (BL) patients that have completed intensive chemotherapy regimens and is typically fatal. While treatment-naive BL has been characterized, the genomic landscape of BL at the time of relapse (rBL) has never been reported. Here, we present a genomic characterization of two rBL patients. The diagnostic samples had mutations common in BL, including MYC and CCND3. Additional mutations were detected at relapse, affecting important pathways such as NFκB (IKBKB) and MEK/ERK (NRAS) signaling, glutamine metabolism (SIRT4), and RNA processing (ZFP36L2). Genes implicated in drug resistance were also mutated at relapse (TP53, BAX, ALDH3A1, APAF1, FANCI). This concurrent genomic profiling of samples obtained at diagnosis and relapse has revealed mutations not previously reported in this disease. The patient-derived cell lines will be made available and, along with their detailed genetics, will be a valuable resource to examine the role of specific mutations in therapeutic resistance.
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Affiliation(s)
- Claudia M Wever
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | | | - Bruno M Grande
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada.,d Genome Sciences Centre, BC Cancer Agency , Vancouver , Canada
| | - Stephen Yu
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada
| | - Miguel Alcaide
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada
| | - Maryse Lemaire
- b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | - Yasser Riazalhosseini
- e Department of Human Genetics , McGill University , Montreal , Canada.,f McGill University and Genome Quebec Innovation Centre , Montreal , Canada
| | - Josée Hébert
- g Department of Medicine, Faculty of Medicine , Université de Montréal , Montreal , Canada.,h Research Centre and Division of Hematology-Oncology Maisonneuve-Rosemont Hospital , The Québec Leukemia Cell Bank , Montreal , Canada
| | - Christina Gavino
- i Infectious Disease Susceptibility Program (Research Institute-McGill University Health Centre) , Montreal , Canada.,j Department of Medicine , Medical Microbiology and Human Genetics (McGill University Health Centre) , Montreal , Canada
| | - Donald C Vinh
- i Infectious Disease Susceptibility Program (Research Institute-McGill University Health Centre) , Montreal , Canada.,j Department of Medicine , Medical Microbiology and Human Genetics (McGill University Health Centre) , Montreal , Canada
| | | | | | - Koren K Mann
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
| | - Ryan D Morin
- c Department of Molecular Biology and Biochemistry , Simon Fraser University , Burnaby , Canada.,d Genome Sciences Centre, BC Cancer Agency , Vancouver , Canada
| | - Nathalie A Johnson
- a Department of Medicine , McGill University, Lady Davis Institute, Jewish General Hospital , Montreal , Canada.,b Lady Davis Institute, Jewish General Hospital , Montreal , Canada
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49
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Alcaide M, Yu S, Davidson J, Albuquerque M, Bushell K, Fornika D, Arthur S, Grande BM, McNamara S, Tertre MCD, Batist G, Huntsman DG, Cavallone L, Aguilar A, Basik M, Johnson NA, Deyell RJ, Rassekh SR, Morin RD. Targeted error-suppressed quantification of circulating tumor DNA using semi-degenerate barcoded adapters and biotinylated baits. Sci Rep 2017; 7:10574. [PMID: 28874686 PMCID: PMC5585219 DOI: 10.1038/s41598-017-10269-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Accepted: 08/02/2017] [Indexed: 12/12/2022] Open
Abstract
Ultrasensitive methods for rare allele detection are critical to leverage the full potential offered by liquid biopsies. Here, we describe a novel molecular barcoding method for the precise detection and quantification of circulating tumor DNA (ctDNA). The major benefits of our design include straightforward and cost-effective production of barcoded adapters to tag individual DNA molecules before PCR and sequencing, and better control over cross-contamination between experiments. We validated our approach in a cohort of 24 patients with a broad spectrum of cancer diagnoses by targeting and quantifying single-nucleotide variants (SNVs), indels and genomic rearrangements in plasma samples. By using personalized panels targeting a priori known mutations, we demonstrate comprehensive error-suppression capabilities for SNVs and detection thresholds for ctDNA below 0.1%. We also show that our semi-degenerate barcoded adapters hold promise for noninvasive genotyping in the absence of tumor biopsies and monitoring of minimal residual disease in longitudinal plasma samples. The benefits demonstrated here include broad applicability, flexibility, affordability and reproducibility in the research and clinical settings.
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Affiliation(s)
- Miguel Alcaide
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Stephen Yu
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Jordan Davidson
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Marco Albuquerque
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Kevin Bushell
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Daniel Fornika
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Sarah Arthur
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Bruno M Grande
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada
| | - Suzan McNamara
- Quebec Clinical Research Organization in Cancer (Q-CROC), Exactis Innovation and the Segal Cancer Centre, Montreal, QC, Canada
| | - Mathilde Couetoux du Tertre
- Quebec Clinical Research Organization in Cancer (Q-CROC), Exactis Innovation and the Segal Cancer Centre, Montreal, QC, Canada
| | - Gerald Batist
- Quebec Clinical Research Organization in Cancer (Q-CROC), Exactis Innovation and the Segal Cancer Centre, Montreal, QC, Canada
| | - David G Huntsman
- Department of Molecular Oncology, British Columbia Cancer Agency, Vancouver, BC, Canada.,Department of Pathology and Laboratory Medicine and Department of Obstetrics and Gynecology, University of British Columbia, Vancouver, BC, Canada
| | - Luca Cavallone
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Adriana Aguilar
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Mark Basik
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Nathalie A Johnson
- Department of Medicine, Jewish General Hospital, Montreal, Quebec, Canada
| | - Rebecca J Deyell
- Division of Oncology, Hematology and Bone Marrow Transplant, British Columbia Children's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - S Rod Rassekh
- Division of Oncology, Hematology and Bone Marrow Transplant, British Columbia Children's Hospital and University of British Columbia, Vancouver, British Columbia, Canada
| | - Ryan D Morin
- Department of Molecular Biology and Biochemistry, Simon Fraser University, Burnaby, BC, Canada.
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50
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Dewar LJ, Alcaide M, Fornika D, D’Amato L, Shafaatalab S, Stevens CM, Balachandra T, Phillips SM, Sanatani S, Morin RD, Tibbits GF. Investigating the Genetic Causes of Sudden Unexpected Death in Children Through Targeted Next-Generation Sequencing Analysis. ACTA ACUST UNITED AC 2017; 10:CIRCGENETICS.116.001738. [DOI: 10.1161/circgenetics.116.001738] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 04/25/2017] [Indexed: 12/27/2022]
Abstract
Background—
Inherited arrhythmia syndromes are responsible for a significant portion of autopsy-negative sudden unexpected death (SUD) cases, but molecular autopsy used to identify potentially causal variants is not routinely included in SUD investigations. We collaborated with a medical examiner's office to assist in finding a diagnosis for their autopsy-negative child SUD cases.
Methods and Results—
191 child SUD cases (<5 years of age) were selected for analyses. Our next generation sequencing panel incorporated 38 inherited arrhythmia syndrome candidate genes and another 33 genes not previously investigated for variants that may underlie SUDY pathophysiology. Overall, we identified 11 potentially causal disease-associated variants in 12 cases, for an overall yield of 6.3%. We also identified 31 variants of uncertain significance in 36 cases and 16 novel variants predicted to be pathogenic in silico in 15 cases. The disease-associated variants were reported to the medical examiner to notify surviving relatives and recommend clinical assessment.
Conclusions—
We have identified variants that may assist in the diagnosis of at least 6.3% of autopsy-negative child SUD cases and reduce risk of future SUD in surviving relatives. We recommend a cautious approach to variant interpretation. We also suggest inclusion of cardiomyopathy genes as well as other candidate SUD genes in molecular autopsy analyses.
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Affiliation(s)
- Laura J. Dewar
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Miguel Alcaide
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Daniel Fornika
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Luisa D’Amato
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Sanam Shafaatalab
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Charles M. Stevens
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Thambirajah Balachandra
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Susan M. Phillips
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Shubhayan Sanatani
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Ryan D. Morin
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
| | - Glen F. Tibbits
- From the Departments of Biomedical Physiology and Kinesiology (L.J.D., S.S., C.M.S., G.F.T.) and Molecular Biology and Biochemistry (M.A., D.F., L.D., C.M.S., R.D.M., G.F.T.), Simon Fraser University, Burnaby, British Columbia, Canada; BC Children’s Hospital Research Institute, Vancouver, Canada (L.J.D., S.S., C.M.S., G.F.T.); Department of Pathology, Faculty of Medicine, University of Manitoba, Winnipeg, Canada (T.B., S.M.P.); and Division of Pediatric Cardiology, Department of Pediatrics, British
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