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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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2
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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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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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5
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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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6
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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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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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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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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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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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