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Nguyen HP, Le AQ, Liu E, Cesarano A, DiMeo F, Perna F, Kapur R, Walker BA, Tran NT. Corrigendum: Protein arginine methyltransferase 1 is a therapeutic vulnerability in multiple myeloma. Front Immunol 2023; 14:1334733. [PMID: 38035085 PMCID: PMC10685262 DOI: 10.3389/fimmu.2023.1334733] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 11/10/2023] [Indexed: 12/02/2023] Open
Abstract
[This corrects the article DOI: 10.3389/fimmu.2023.1239614.].
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Affiliation(s)
- Hong Phuong Nguyen
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana School of Medicine, Indianapolis, IN, United States
| | - Anh Quynh Le
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana School of Medicine, Indianapolis, IN, United States
| | - Enze Liu
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, United States
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Annamaria Cesarano
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Francesco DiMeo
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Fabiana Perna
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Reuben Kapur
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana School of Medicine, Indianapolis, IN, United States
| | - Brian A. Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, United States
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Ngoc Tung Tran
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana School of Medicine, Indianapolis, IN, United States
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2
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Boyle EM, Blaney P, Stoeckle JH, Wang Y, Ghamlouch H, Gagler D, Braunstein M, Williams L, Tenenbaum A, Siegel A, Chen X, Varma G, Avigan J, Li A, Jinsi M, Kaminetzsky D, Arbini A, Montes L, Corre J, Rustad EH, Landgren O, Maura F, Walker BA, Bauer M, Bruno B, Tsirigos A, Davies FE, Morgan GJ. Multiomic Mapping of Acquired Chromosome 1 Copy-Number and Structural Variants to Identify Therapeutic Vulnerabilities in Multiple Myeloma. Clin Cancer Res 2023; 29:3901-3913. [PMID: 37449980 DOI: 10.1158/1078-0432.ccr-22-3209] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/27/2023] [Accepted: 07/12/2023] [Indexed: 07/18/2023]
Abstract
PURPOSE Chromosome 1 (chr1) copy-number abnormalities (CNA) and structural variants (SV) are frequent in newly diagnosed multiple myeloma (NDMM) and are associated with a heterogeneous impact on outcomes, the drivers of which are largely unknown. EXPERIMENTAL DESIGN A multiomic approach comprising CRISPR, gene mapping of CNAs and SVs, methylation, expression, and mutational analysis was used to document the extent of chr1 molecular variants and their impact on pathway utilization. RESULTS We identified two distinct groups of gain(1q): focal gains associated with limited gene-expression changes and a neutral prognosis, and whole-arm gains, which are associated with substantial gene-expression changes, complex genetics, and an adverse prognosis. CRISPR identified a number of dependencies on chr1 but only limited variants associated with acquired CNAs. We identified seven regions of deletion, nine of gain, three of chromothripsis (CT), and two of templated insertion (TI), which contain a number of potential drivers. An additional mechanism involving hypomethylation of genes at 1q may contribute to the aberrant gene expression of a number of genes. Expression changes associated with whole-arm gains were substantial and gene set enrichment analysis identified metabolic processes, apoptotic resistance, signaling via the MAPK pathway, and upregulation of transcription factors as being key drivers of the adverse prognosis associated with these variants. CONCLUSIONS Multiple layers of genetic complexity impact the phenotype associated with CNAs on chr1 to generate its associated clinical phenotype. Whole-arm gains of 1q are the critically important prognostic group that deregulate multiple pathways, which may offer therapeutic vulnerabilities.
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Affiliation(s)
- Eileen M Boyle
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Patrick Blaney
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
- Applied Bioinformatics Laboratories, NYU Langone Medical Center, New York, New York
| | - James H Stoeckle
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Yubao Wang
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Hussein Ghamlouch
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Dylan Gagler
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
- Applied Bioinformatics Laboratories, NYU Langone Medical Center, New York, New York
| | - Marc Braunstein
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Louis Williams
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
- Myeloma Group, Cleveland Clinic Foundation, Taussig Cancer Center, Cleveland, Ohio
| | - Avital Tenenbaum
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Ariel Siegel
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Xiaoyi Chen
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Gaurav Varma
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Jason Avigan
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Alexander Li
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Monica Jinsi
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - David Kaminetzsky
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Arnaldo Arbini
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | | | - Jill Corre
- Unit for Genomics in Myeloma, Institut Universitaire du Cancer de Toulouse-Oncopole, University Hospital, Toulouse; Centre de Recherche en Cancérologie de Toulouse, Institut National de la Santé et de la Recherche Médicale U1037, Toulouse, France
| | - Even H Rustad
- Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Ola Landgren
- Myeloma Service, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Francesco Maura
- Myeloma Service, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Department of Hematology Oncology, Indiana University, Indianapolis, Indiana
| | - Michael Bauer
- Department of Biomedical Informatics (DBMI), UAMS, Little-Rock, Arkansas
| | - Benedetto Bruno
- Department of Hematology, Azienda Ospedaliera Citta della Salute e della Scienza di Torino, Piemonte, Italy
| | - Aristotelis Tsirigos
- Applied Bioinformatics Laboratories, NYU Langone Medical Center, New York, New York
| | - Faith E Davies
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Gareth J Morgan
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
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Abstract
SIGNIFICANCE STATEMENT Acute febrile neutrophilic dermatosis (Sweet syndrome) is a rare idiopathic condition characterized by fever and whole-body rash of tender erythematous plaques of unknown etiology. Otorhinolaryngologic manifestations of the disease can be severe, yet they are sparsely reported in the literature. We present the first documented case of laryngeal involvement of Sweet syndrome.
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Affiliation(s)
- Brian A Walker
- Department of Otorhinolaryngology, The Mayo Clinic Arizona, Phoenix, AZ, USA
| | - Lindsey B Stull
- Department of Otorhinolaryngology, The Mayo Clinic Arizona, Phoenix, AZ, USA
| | - J Peyton Hines
- Department of Otorhinolaryngology, The Mayo Clinic Arizona, Phoenix, AZ, USA
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Liu E, Sudha P, Becker N, Jaouadi O, Suvannasankha A, Lee K, Abonour R, Abu Zaid M, Walker BA. Identifying novel mechanisms of biallelic TP53 loss refines poor outcome for patients with multiple myeloma. Blood Cancer J 2023; 13:144. [PMID: 37696786 PMCID: PMC10495448 DOI: 10.1038/s41408-023-00919-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2023] [Revised: 08/27/2023] [Accepted: 08/30/2023] [Indexed: 09/13/2023] Open
Abstract
Biallelic TP53 inactivation is the most important high-risk factor associated with poor survival in multiple myeloma. Classical biallelic TP53 inactivation has been defined as simultaneous mutation and copy number loss in most studies; however, numerous studies have demonstrated that other factors could lead to the inactivation of TP53. Here, we hypothesized that novel biallelic TP53 inactivated samples existed in the multiple myeloma population. A random forest regression model that exploited an expression signature of 16 differentially expressed genes between classical biallelic TP53 and TP53 wild-type samples was subsequently established and used to identify novel biallelic TP53 samples from monoallelic TP53 groups. The model reflected high accuracy and robust performance in newly diagnosed relapsed and refractory populations. Patient survival of classical and novel biallelic TP53 samples was consistently much worse than those with mono-allelic or wild-type TP53 status. We also demonstrated that some predicted biallelic TP53 samples simultaneously had copy number loss and aberrant splicing, resulting in overexpression of high-risk transcript variants, leading to biallelic inactivation. We discovered that splice site mutation and overexpression of the splicing factor MED18 were reasons for aberrant splicing. Taken together, our study unveiled the complex transcriptome of TP53, some of which might benefit future studies targeting abnormal TP53.
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Affiliation(s)
- Enze Liu
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Parvathi Sudha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Nathan Becker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Oumaima Jaouadi
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Attaya Suvannasankha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Kelvin Lee
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Rafat Abonour
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Mohammad Abu Zaid
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA.
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA.
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5
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Johnson TS, Sudha P, Liu E, Blaney P, Morgan G, Chopra VS, Santos CD, Nixon M, Huang K, Suvannasankha A, Zaid MA, Abonour R, Walker BA. Identifying 1q amplification and PHF19 expressing high-risk cells associated with relapsed/refractory multiple myeloma. Res Sq 2023:rs.3.rs-3221549. [PMID: 37645789 PMCID: PMC10462227 DOI: 10.21203/rs.3.rs-3221549/v1] [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: 08/31/2023]
Abstract
Multiple Myeloma is an incurable plasma cell malignancy with a poor survival rate that is usually treated with immunomodulatory drugs (iMiDs) and proteosome inhibitors (PIs). The malignant plasma cells quickly become resistant to these agents causing relapse and uncontrolled growth of resistant clones. From whole genome sequencing (WGS) and RNA sequencing (RNA-seq) studies, different high-risk translocation, copy number, mutational, and transcriptional markers have been identified. One of these markers, PHF19, epigenetically regulates cell cycle and other processes and has already been studied using RNA-seq. In this study a massive (325,025 cells and 49 patients) single cell multiomic dataset was generated with jointly quantified ATAC- and RNA-seq for each cell and matched genomic profiles for each patient. We identified an association between one plasma cell subtype with myeloma progression that we have called relapsed/refractory plasma cells (RRPCs). These cells are associated with 1q alterations, TP53 mutations, and higher expression of PHF19. We also identified downstream regulation of cell cycle inhibitors in these cells, possible regulation of the transcription factor (TF) PBX1 on 1q, and determined that PHF19 may be acting primarily through this subset of cells.
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Affiliation(s)
- Travis S. Johnson
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Indiana Biosciences Research Institute, Indianapolis, IN, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Experimental and Developmental Therapeutics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Parvathi Sudha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Enze Liu
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Patrick Blaney
- Perlmutter Cancer Center, Langone Health, New York University, New York, NY, USA
| | - Gareth Morgan
- Perlmutter Cancer Center, Langone Health, New York University, New York, NY, USA
| | | | | | | | - Kun Huang
- Department of Biostatistics and Health Data Science, School of Medicine, Indiana University, Indianapolis, IN, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Experimental and Developmental Therapeutics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Attaya Suvannasankha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
- Roudebush VAMC, Indianapolis, IN, USA
| | - Mohammad Abu Zaid
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Rafat Abonour
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Brian A. Walker
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
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6
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Nguyen HP, Le AQ, Liu E, Cesarano A, DiMeo F, Perna F, Kapur R, Walker BA, Tran NT. Protein arginine methyltransferase 1 is a therapeutic vulnerability in multiple myeloma. Front Immunol 2023; 14:1239614. [PMID: 37600810 PMCID: PMC10436492 DOI: 10.3389/fimmu.2023.1239614] [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: 06/13/2023] [Accepted: 07/11/2023] [Indexed: 08/22/2023] Open
Abstract
Multiple myeloma (MM) is a devastating plasma cell malignancy characterized by the expansion of aberrant monoclonal plasma cells in the bone marrow, leading to severe clinical manifestations and poor prognosis, particularly in relapsed/refractory cases. Identifying novel therapeutic targets is crucial to improve treatment outcomes in these patients. In this study, we investigated the role of the protein arginine methyltransferase 1 (PRMT1) in MM pathogenesis and explored its potential as a therapeutic target. We observed that PRMT1, responsible for most asymmetric di-methylation in cells, exhibited the highest expression among PRMT family members in MM cell lines and primary MM cells. Importantly, PRMT1 expression was significantly elevated in relapsed/refractory patients compared to newly diagnosed patients. High expression of PRMT1 expression was strongly associated with poor prognosis. We found that genetic or enzymatic inhibition of PRMT1 impaired MM cell growth, induced cell cycle arrest, and triggered cell death. Treatment with MS023, a potent PRMT type I inhibitor, demonstrated a robust inhibitory effect on the viability of primary cells isolated from newly diagnosed and proteasome inhibitor-relapsed/refractory patients in a dose-dependent manner. Suppression of PRMT1 downregulated genes related to cell division and upregulated genes associated with apoptosis pathway. We also found that genes related to immune response and lymphocyte activation were significantly upregulated in PRMT1-suppressed cells. Notably, the activation status of T cells was strikingly enhanced upon co-culturing with PRMT1-KO MM cells. In vivo studies using a xenograft model revealed that targeting PRMT1 by either CRISPR/Cas9-mediated knockout or MS023 treatment significantly attenuated MM tumor growth and prolonged the survival of tumor-bearing mice. Histological analysis further confirmed increased apoptotic cell death in MS023-treated tumors. Collectively, our findings establish PRMT1 as an indispensable and novel therapeutic vulnerability in MM. The elevated expression of PRMT1 in relapsed/refractory patients underscores its potential as a target for overcoming treatment resistance. Moreover, our results highlight the efficacy of MS023 as a promising therapeutic agent against MM, offering new avenues for therapeutic approaches in relapsed/refractory MM.
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Affiliation(s)
- Hong Phuong Nguyen
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana School of Medicine, Indianapolis, IN, United States
| | - Anh Quynh Le
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana School of Medicine, Indianapolis, IN, United States
| | - Enze Liu
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, United States
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Annamaria Cesarano
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Francesco DiMeo
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Fabiana Perna
- Division of Hematology/Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Reuben Kapur
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana School of Medicine, Indianapolis, IN, United States
| | - Brian A. Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, United States
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, United States
| | - Ngoc Tung Tran
- Herman B Wells Center for Pediatric Research, Department of Pediatrics, Indiana School of Medicine, Indianapolis, IN, United States
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7
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Bomken S, Enshaei A, Schwalbe EC, Mikulasova A, Dai Y, Zaka M, Fung KTM, Bashton M, Lim H, Jones L, Karataraki N, Winterman E, Ashby C, Attarbaschi A, Bertrand Y, Bradtke J, Buldini B, Burke GAA, Cazzaniga G, Gohring G, De Groot-Kruseman HA, Haferlach C, Nigro LL, Parihar M, Plesa A, Seaford E, Sonneveld E, Strehl S, Van der Velden VHJ, Rand V, Hunger SP, Harrison CJ, Bacon CM, Van Delft FW, Loh ML, Moppett J, Vormoor J, Walker BA, Moorman AV, Russell LJ. Molecular characterization and clinical outcome of B-cell precursor acute lymphoblastic leukemia with IG-MYC rearrangement. Haematologica 2023; 108:717-731. [PMID: 35484682 PMCID: PMC9973471 DOI: 10.3324/haematol.2021.280557] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2022] [Accepted: 03/31/2022] [Indexed: 11/09/2022] Open
Abstract
Rarely, immunophenotypically immature B-cell precursor acute lymphoblastic leukemia (BCP-ALL) carries an immunoglobulin- MYC rearrangement (IG-MYC-r). This can result in diagnostic confusion with Burkitt lymphoma/leukemia and use of individualized treatment schedules of unproven efficacy. Here we compare the molecular characteristics of these conditions and investigate historic clinical outcome data. We identified 90 cases registered in a national BCP-ALL clinical trial/registry. When present, diagnostic material underwent cytogenetic, exome, methylome and transcriptome analyses. The outcomes analyzed were 3-year event-free survival and overall survival. IG-MYC-r was identified in diverse cytogenetic backgrounds, co-existing with either established BCP-ALL-specific abnormalities (high hyperdiploidy, n=3; KMT2A-rearrangement, n=6; iAMP21, n=1; BCR-ABL1, n=1); BCL2/BCL6-rearrangements (n=15); or, most commonly, as the only defining feature (n=64). Within this final group, precursor-like V(D)J breakpoints predominated (8/9) and KRAS mutations were common (5/11). DNA methylation identified a cluster of V(D)J-rearranged cases, clearly distinct from Burkitt leukemia/lymphoma. Children with IG-MYC-r within that subgroup had a 3-year event-free survival of 47% and overall survival of 60%, representing a high-risk BCP-ALL. To develop effective management strategies this group of patients must be allowed access to contemporary, minimal residual disease-adapted, prospective clinical trial protocols.
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Affiliation(s)
- Simon Bomken
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne.
| | - Amir Enshaei
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Edward C Schwalbe
- Department of Applied Sciences, Northumbria University, Newcastle upon Tyne
| | - Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne
| | - Yunfeng Dai
- Department of Biostatistics, Colleges of Medicine, Public Health and Health Professions, University of Florida, Gainesville, Florida
| | - Masood Zaka
- School of Health and Life Sciences, Teesside University, Middlesbrough, UK; National Horizons Centre, Teesside University, Darlington
| | - Kent T M Fung
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Matthew Bashton
- The Hub for Biotechnology in the Built Environment, Faculty of Health and Life Sciences, Northumbria University, Newcastle upon Tyne
| | - Huezin Lim
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Lisa Jones
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Nefeli Karataraki
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Emily Winterman
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Cody Ashby
- Department of Biomedical Informatics / Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Yves Bertrand
- Department of Institute of Hematology Oncology Pediatric (IHOP), Hospices Civils de Lyon, Lyon
| | - Jutta Bradtke
- Institute of Pathology, Department Cytogenetics, University Hospital Giessen and Marburg
| | | | - G A Amos Burke
- Department of Paediatric Haematology, Oncology, and Palliative Care, Cambridge University Hospitals NHS Foundation Trust, Addenbrooke's Hospital, Cambridge
| | - Giovanni Cazzaniga
- School of Medicine and Surgery, University of Milano-Bicocca, Monza, Italy; Centro Ricerca Tettamanti, University of Milano-Bicocca, Monza
| | - Gudrun Gohring
- Department of Human Genetics, Hannover Medical School, Hannover
| | - Hesta A De Groot-Kruseman
- Dutch Childhood Oncology Group (DCOG), Utrecht, The Netherlands; Princess Maxima Center for Pediatric Oncology, Utrecht
| | | | - Luca Lo Nigro
- Head of Cytogenetic-Cytofluorimetric-Molecular Biology Laboratory, Center of Pediatric Hematology Oncology, Azienda Policlinico "G. Rodolico - San Marco", Catania
| | - Mayur Parihar
- Department of Cytogenetics and Laboratory Haematology, Tata Medical Centre, Kolkata, India
| | - Adriana Plesa
- Hematology and Flow cytometry Laboratory, Lyon Sud University Hospital, Hospices Civils de Lyon, Lyon
| | - Emma Seaford
- Department of Paediatric Oncology, Bristol Royal Hospital for Children, Bristol
| | | | - Sabine Strehl
- St. Anna Children's Cancer Research Institute, Vienna
| | | | - Vikki Rand
- School of Health and Life Sciences, Teesside University, Middlesbrough, UK; National Horizons Centre, Teesside University, Darlington
| | - Stephen P Hunger
- Department of Pediatrics and the Center for Childhood Cancer Research, Children's Hospital of Philadelphia and the Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA
| | - Christine J Harrison
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Chris M Bacon
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne
| | - Frederik W Van Delft
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; The Newcastle upon Tyne Hospitals NHS Foundation Trust, Newcastle upon Tyne
| | - Mignon L Loh
- Department of Pediatrics, Benioff Children's Hospital and the Helen Diller Family Comprehensive Cancer Center, University of California, San Francisco, CA
| | - John Moppett
- Department of Paediatric Oncology, Bristol Royal Hospital for Children, Bristol
| | - Josef Vormoor
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne, United Kingdom; Princess Maxima Center for Pediatric Oncology, Utrecht
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, IN
| | - Anthony V Moorman
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne
| | - Lisa J Russell
- Wolfson Childhood Cancer Centre, Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne.
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8
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Liu E, Becker N, Sudha P, Dong C, Liu Y, Keats J, Morgan G, Walker BA. Alternative splicing in multiple myeloma is associated with the non-homologous end joining pathway. Blood Cancer J 2023; 13:16. [PMID: 36670103 PMCID: PMC9859791 DOI: 10.1038/s41408-023-00783-0] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2022] [Revised: 12/27/2022] [Accepted: 01/05/2023] [Indexed: 01/21/2023] Open
Abstract
Alternative splicing plays a pivotal role in tumorigenesis and proliferation. However, its pattern and pathogenic role has not been systematically analyzed in multiple myeloma or its subtypes. Alternative splicing profiles for 598 newly diagnosed myeloma patients with comprehensive genomic annotation identified primary translocations, 1q amplification, and DIS3 events to have more differentially spliced events than those without. Splicing levels were correlated with expression of splicing factors. Moreover, the non-homologous end joining pathway was an independent factor that was highly associated with splicing frequency as well as an increased number of structural variants. We therefore identify an axis of high-risk disease encompassing expression of the non-homologous end joining pathway, increase structural variants, and increased alternative splicing that are linked together. This indicates a joint pathogenic role for DNA damage response and alternative RNA processing in myeloma.
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Affiliation(s)
- Enze Liu
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Nathan Becker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Parvathi Sudha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Chuanpeng Dong
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
- Department of Genetics, School of Medicine, Yale University, New Haven, CT, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA
| | - Jonathan Keats
- Translational Genomics Research Institute (TGen), Integrated Cancer Genomics Division, Phoenix, AZ, USA
| | - Gareth Morgan
- NYU Langone Medical Center, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology and Oncology, School of Medicine, Indiana University, Indianapolis, IN, USA.
- Center for Computational Biology and Bioinformatics, School of Medicine, Indiana University, Indianapolis, IN, USA.
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9
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Rasche L, Schinke C, Maura F, Bauer MA, Ashby C, Deshpande S, Poos AM, Zangari M, Thanendrarajan S, Davies FE, Walker BA, Barlogie B, Landgren O, Morgan GJ, van Rhee F, Weinhold N. The spatio-temporal evolution of multiple myeloma from baseline to relapse-refractory states. Nat Commun 2022; 13:4517. [PMID: 35922426 PMCID: PMC9349320 DOI: 10.1038/s41467-022-32145-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Accepted: 07/19/2022] [Indexed: 11/18/2022] Open
Abstract
Deciphering Multiple Myeloma evolution in the whole bone marrow is key to inform curative strategies. Here, we perform spatial-longitudinal whole-exome sequencing, including 140 samples collected from 24 Multiple Myeloma patients during up to 14 years. Applying imaging-guided sampling we observe three evolutionary patterns, including relapse driven by a single-cell expansion, competing/co-existing sub-clones, and unique sub-clones at distinct locations. While we do not find the unique relapse sub-clone in the baseline focal lesion(s), we show a close phylogenetic relationship between baseline focal lesions and relapse disease, highlighting focal lesions as hotspots of tumor evolution. In patients with ≥3 focal lesions on positron-emission-tomography at diagnosis, relapse is driven by multiple distinct sub-clones, whereas in other patients, a single-cell expansion is typically seen (p < 0.01). Notably, we observe resistant sub-clones that can be hidden over years, suggesting that a prerequisite for curative therapies would be to overcome not only tumor heterogeneity but also dormancy.
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Affiliation(s)
- Leo Rasche
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
- Mildred Scheel Early Career Center (MSNZ), University Hospital of Würzburg, Würzburg, Germany
| | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Francesco Maura
- Myeloma Program, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Michael A Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Shayu Deshpande
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Alexandra M Poos
- Department of Internal Medicine V, University Hospital of Heidelberg, Heidelberg, Germany
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Faith E Davies
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
| | - Bart Barlogie
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ola Landgren
- Myeloma Program, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Gareth J Morgan
- Perlmutter Cancer Center, New York University Langone Health, New York, NY, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Niels Weinhold
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
- Department of Internal Medicine V, University Hospital of Heidelberg, Heidelberg, Germany.
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10
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Rico D, Kent D, Karataraki N, Mikulasova A, Berlinguer-Palmini R, Walker BA, Javierre BM, Russell LJ, Brackley CA. High-resolution simulations of chromatin folding at genomic rearrangements in malignant B cells provide mechanistic insights into proto-oncogene deregulation. Genome Res 2022; 32:gr.276028.121. [PMID: 35863900 PMCID: PMC9341513 DOI: 10.1101/gr.276028.121] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 05/26/2022] [Indexed: 11/30/2022]
Abstract
Genomic rearrangements are known to result in proto-oncogene deregulation in many cancers, but the link to 3D genome structure remains poorly understood. Here, we used the highly predictive heteromorphic polymer (HiP-HoP) model to predict chromatin conformations at the proto-oncogene CCND1 in healthy and malignant B cells. After confirming that the model gives good predictions of Hi-C data for the nonmalignant human B cell-derived cell line GM12878, we generated predictions for two cancer cell lines, U266 and Z-138. These possess genome rearrangements involving CCND1 and the immunoglobulin heavy locus (IGH), which we mapped using targeted genome sequencing. Our simulations showed that a rearrangement in U266 cells where a single IGH super-enhancer is inserted next to CCND1 leaves the local topologically associated domain (TAD) structure intact. We also observed extensive changes in enhancer-promoter interactions within the TAD, suggesting that it is the downstream chromatin remodeling which gives rise to the oncogene activation, rather than the presence of the inserted super-enhancer DNA sequence per se. Simulations of the IGH-CCND1 reciprocal translocation in Z-138 cells revealed that an oncogenic fusion TAD is created, encompassing CCND1 and the IGH super-enhancers. We predicted how the structure and expression of CCND1 changes in these different cell lines, validating this using qPCR and fluorescence in situ hybridization microscopy. Our work demonstrates the power of polymer simulations to predict differences in chromatin interactions and gene expression for different translocation breakpoints.
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Affiliation(s)
- Daniel Rico
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Daniel Kent
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Nefeli Karataraki
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | | | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, Indiana 46202, USA
| | - Biola M Javierre
- Josep Carreras Leukaemia Research Institute (IJC), IJC Building, Campus ICO-Germans Trias i Pujol, Ctra de Can Ruti, 08916 Badalona, Barcelona, Spain
| | - Lisa J Russell
- Biosciences Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
- Translational and Clinical Research Institute, Newcastle University, Newcastle upon Tyne NE2 4HH, United Kingdom
| | - Chris A Brackley
- SUPA, School of Physics and Astronomy, University of Edinburgh, Edinburgh EH9 3FD, United Kingdom
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11
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Davies FE, Pawlyn C, Usmani SZ, San-Miguel JF, Einsele H, Boyle EM, Corre J, Auclair D, Cho HJ, Lonial S, Sonneveld P, Stewart AK, Bergsagel PL, Kaiser MF, Weisel K, Keats JJ, Mikhael JR, Morgan KE, Ghobrial IM, Orlowski RZ, Landgren CO, Gay F, Caers J, Chng WJ, Chari A, Walker BA, Kumar SK, Costa LJ, Anderson KC, Morgan GJ. Perspectives on the Risk-Stratified Treatment of Multiple Myeloma. Blood Cancer Discov 2022; 3:273-284. [PMID: 35653112 PMCID: PMC9894570 DOI: 10.1158/2643-3230.bcd-21-0205] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
The multiple myeloma treatment landscape has changed dramatically. This change, paralleled by an increase in scientific knowledge, has resulted in significant improvement in survival. However, heterogeneity remains in clinical outcomes, with a proportion of patients not benefiting from current approaches and continuing to have a poor prognosis. A significant proportion of the variability in outcome can be predicted on the basis of clinical and biochemical parameters and tumor-acquired genetic variants, allowing for risk stratification and a more personalized approach to therapy. This article discusses the principles that can enable the rational and effective development of therapeutic approaches for high-risk multiple myeloma.
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Affiliation(s)
| | - Charlotte Pawlyn
- Division of Cancer Therapeutics, The Institute of Cancer Research, London, United Kingdom
- The Royal Marsden Hospital, Department of Haematology, London, United Kingdom
| | - Saad Z. Usmani
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, New York
| | | | - Hermann Einsele
- Department of Internal Medicine II, University Hospital Würzburg, Würzburg, Germany
| | | | - Jill Corre
- Unité de Génomique du Myélome, Institut Universitaire du Cancer, Toulouse France. Institut National de la Santé et de la Recherche Médicale, Paris, France
| | - Daniel Auclair
- The Multiple Myeloma Research Foundation, Norwalk, Connecticut
| | - Hearn Jay Cho
- The Multiple Myeloma Research Foundation, Norwalk, Connecticut
- Multiple Myeloma Center of Excellence, Icahn School of Medicine at Mt. Sinai, New York, New York
| | - Sagar Lonial
- Department of Hematology and Medical Oncology, Winship Cancer Institute, Emory University, Atlanta, Georgia
| | - Pieter Sonneveld
- Erasmus MC Cancer Institute, Department of Hematology, Rotterdam, the Netherlands
| | - A. Keith Stewart
- University Health Network and the Princess Margaret Cancer Centre, Toronto, Ontario, Canada
| | | | - Martin F. Kaiser
- The Royal Marsden Hospital, Department of Haematology, London, United Kingdom
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, United Kingdom
| | - Katja Weisel
- Department of Oncology, Hematology and Bone Marrow Transplantation with Section of Pneumology, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Jonathan J. Keats
- Integrated Cancer Genomics, Translational Genomics Research Institute, Phoenix, Arizona
| | - Joseph R. Mikhael
- Translational Genomics Research Institute, City of Hope Cancer Center, Phoenix, Arizona
| | | | - Irene M. Ghobrial
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
| | - Robert Z. Orlowski
- Department of Lymphoma/Myeloma, The University of Texas MD Anderson Cancer Center, Houston, Texas
| | - C. Ola Landgren
- Myeloma Program, Sylvester Comprehensive Cancer Center, University of Miami, Miami, Florida
| | - Francesca Gay
- Division of Hematology, University of Torino, Torino, Italy
| | - Joseph Caers
- Department of Hematology, Centre Hospitalier Universitaire (CHU) de Liège, Liège, Belgium
| | - Wee Joo Chng
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, Indiana
- Department of Hematology, Mayo Clinic, Rochester, Minnesota
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Ajai Chari
- Multiple Myeloma Center of Excellence, Icahn School of Medicine at Mt. Sinai, New York, New York
| | - Brian A. Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, Indiana
| | - Shaji K. Kumar
- Department of Hematology, Mayo Clinic, Rochester, Minnesota
| | - Luciano J. Costa
- Division of Hematology and Oncology, Department of Medicine, University of Alabama at Birmingham, Birmingham, Alabama
| | - Kenneth C. Anderson
- Department of Medical Oncology, Dana Farber Cancer Institute, Harvard Medical School, Boston, Massachusetts
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12
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Sudha P, Ahsan A, Ashby C, Kausar T, Khera A, Kazeroun MH, Hsu CC, Wang L, Fitzsimons E, Salminen O, Blaney P, Czader M, Williams J, Abu Zaid MI, Ansari-Pour N, Yong KL, van Rhee F, Pierceall WE, Morgan GJ, Flynt E, Gooding S, Abonour R, Ramasamy K, Thakurta A, Walker BA. Myeloma Genome Project Panel is a Comprehensive Targeted Genomics Panel for Molecular Profiling of Patients with Multiple Myeloma. Clin Cancer Res 2022; 28:2854-2864. [PMID: 35522533 PMCID: PMC9250632 DOI: 10.1158/1078-0432.ccr-21-3695] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Revised: 01/11/2022] [Accepted: 05/03/2022] [Indexed: 11/16/2022]
Abstract
PURPOSE We designed a comprehensive multiple myeloma targeted sequencing panel to identify common genomic abnormalities in a single assay and validated it against known standards. EXPERIMENTAL DESIGN The panel comprised 228 genes/exons for mutations, 6 regions for translocations, and 56 regions for copy number abnormalities (CNA). Toward panel validation, targeted sequencing was conducted on 233 patient samples and further validated using clinical FISH (translocations), multiplex ligation probe analysis (MLPA; CNAs), whole-genome sequencing (WGS; CNAs, mutations, translocations), or droplet digital PCR (ddPCR) of known standards (mutations). RESULTS Canonical immunoglobulin heavy chain translocations were detected in 43.2% of patients by sequencing, and aligned with FISH except for 1 patient. CNAs determined by sequencing and MLPA for 22 regions were comparable in 103 samples and concordance between platforms was R2 = 0.969. Variant allele frequency (VAF) for 74 mutations were compared between sequencing and ddPCR with concordance of R2 = 0.9849. CONCLUSIONS In summary, we have developed a targeted sequencing panel that is as robust or superior to FISH and WGS. This molecular panel is cost-effective, comprehensive, clinically actionable, and can be routinely deployed to assist risk stratification at diagnosis or posttreatment to guide sequencing of therapies.
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Affiliation(s)
- Parvathi Sudha
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Aarif Ahsan
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Cody Ashby
- Department of Biomedical Informatics, College of Medicine, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | - Tasneem Kausar
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Akhil Khera
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Mohammad H. Kazeroun
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Chih-Chao Hsu
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Lin Wang
- Department of Pathology and Laboratory Research, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | | | - Outi Salminen
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Patrick Blaney
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Magdalena Czader
- Department of Pathology and Laboratory Research, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Jonathan Williams
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
| | - Mohammad I. Abu Zaid
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Naser Ansari-Pour
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
| | - Kwee L. Yong
- Cancer Institute, University College London, London, United Kingdom
| | - Frits van Rhee
- Myeloma Center, Winthrop P. Rockefeller Cancer institute, University of Arkansas for Medical Sciences, Little Rock, Arkansas
| | | | - Gareth J. Morgan
- Perlmutter Cancer Center, NYU Langone Medical Center, New York, New York
| | - Erin Flynt
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
| | - Sarah Gooding
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- MRC Molecular Haematology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, United Kingdom
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
| | - Rafat Abonour
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
| | - Karthik Ramasamy
- Oxford University Hospitals NHS Foundation Trust, Oxford, United Kingdom
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Anjan Thakurta
- Translational Medicine, Bristol Myers Squibb, Summit, New Jersey
- Oxford Center for Translational Myeloma Research, University of Oxford, Oxford, United Kingdom
- Radcliffe Department of Medicine, Medical Sciences Division, University of Oxford, Oxford, United Kingdom
| | - Brian A. Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University School of Medicine, Indiana University, Indianapolis, Indiana
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13
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Mikulasova A, Morgan GJ, Walker BA. Chromosomal abnormalities in multiple myeloma. Nat Rev Dis Primers 2022; 8:42. [PMID: 35710551 DOI: 10.1038/s41572-022-00374-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Aneta Mikulasova
- Biosciences Institute, Newcastle University, Newcastle upon Tyne, UK.
| | - Gareth J Morgan
- NYU Langone Medical Center, Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA.
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14
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Bustoros M, Anand S, Sklavenitis-Pistofidis R, Redd R, Boyle EM, Zhitomirsky B, Dunford AJ, Tai YT, Chavda SJ, Boehner C, Neuse CJ, Rahmat M, Dutta A, Casneuf T, Verona R, Kastritis E, Trippa L, Stewart C, Walker BA, Davies FE, Dimopoulos MA, Bergsagel PL, Yong K, Morgan GJ, Aguet F, Getz G, Ghobrial IM. Genetic subtypes of smoldering multiple myeloma are associated with distinct pathogenic phenotypes and clinical outcomes. Nat Commun 2022; 13:3449. [PMID: 35705541 PMCID: PMC9200804 DOI: 10.1038/s41467-022-30694-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2021] [Accepted: 05/13/2022] [Indexed: 12/12/2022] Open
Abstract
Smoldering multiple myeloma (SMM) is a precursor condition of multiple myeloma (MM) with significant heterogeneity in disease progression. Existing clinical models of progression risk do not fully capture this heterogeneity. Here we integrate 42 genetic alterations from 214 SMM patients using unsupervised binary matrix factorization (BMF) clustering and identify six distinct genetic subtypes. These subtypes are differentially associated with established MM-related RNA signatures, oncogenic and immune transcriptional profiles, and evolving clinical biomarkers. Three genetic subtypes are associated with increased risk of progression to active MM in both the primary and validation cohorts, indicating they can be used to better predict high and low-risk patients within the currently used clinical risk stratification models.
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Affiliation(s)
- Mark Bustoros
- Medical Oncology, Dana-Farber Cancer Center, Boston, MA, USA
- Division of Hematology & Medical Oncology, Meyer Cancer Center, Weill Cornell Medicine, New York, NY, USA
| | - Shankara Anand
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
- Boston University School of Medicine, Boston, MA, USA
| | | | - Robert Redd
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Eileen M Boyle
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | | | - Yu-Tzu Tai
- Medical Oncology, Dana-Farber Cancer Center, Boston, MA, USA
| | - Selina J Chavda
- Division of Hematology, University College London, London, UK
| | - Cody Boehner
- Medical Oncology, Dana-Farber Cancer Center, Boston, MA, USA
| | - Carl Jannes Neuse
- Medical Oncology, Dana-Farber Cancer Center, Boston, MA, USA
- University of Münster Medical School, Münster, Germany
| | - Mahshid Rahmat
- Medical Oncology, Dana-Farber Cancer Center, Boston, MA, USA
| | - Ankit Dutta
- Medical Oncology, Dana-Farber Cancer Center, Boston, MA, USA
| | | | - Raluca Verona
- Janssen Research and Development, Spring House, PA, USA
| | - Efstathis Kastritis
- Department of Clinical Therapeutics, National and Kapodistrian University of Athens, Athens, Greece
| | - Lorenzo Trippa
- Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Chip Stewart
- Broad Institute of MIT & Harvard, Cambridge, MA, USA
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN, USA
| | - Faith E Davies
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | | | - Kwee Yong
- Division of Hematology, University College London, London, UK
| | - Gareth J Morgan
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | - Gad Getz
- Broad Institute of MIT & Harvard, Cambridge, MA, USA.
- Department of Pathology, Massachusetts General Hospital Cancer Center, Boston, MA, USA.
| | - Irene M Ghobrial
- Medical Oncology, Dana-Farber Cancer Center, Boston, MA, USA.
- Broad Institute of MIT & Harvard, Cambridge, MA, USA.
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15
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Walker BA, Thorwarth RM, Stull LL, Hoxworth JM, Deep NL, Weisskopf PA. Incidence of Concomitant Semicircular Canal Dehiscence With Otosclerosis. Otol Neurotol Open 2022; 2:e012. [PMID: 38516327 PMCID: PMC10950147 DOI: 10.1097/ono.0000000000000012] [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] [Figures] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Accepted: 04/07/2022] [Indexed: 03/23/2024]
Abstract
Objective The concurrence of otosclerosis and superior semicircular canal dehiscence (SSCD) presents a diagnostic challenge and failure to differentiate between these 2 diagnoses results in mischaracterization and unsuccessful surgery. The objective of this study is to identify the incidence of SSCD in patients who have computed tomography (CT) evidence of otosclerosis. Study Design Retrospective chart review. Setting Tertiary referral hospital. Patients Adults with CT scan of the temporal bone diagnosed with radiological unilateral or bilateral fenestral otosclerosis from January 1995 to April 2018. Methods Retrospective review of patient imaging from a multi-center tertiary-referral health system from January 1995 to April 2018. Imaging was reviewed to quantify the incidence of SSCD among patients with CT-diagnosed bilateral fenestral otosclerosis. Poor quality imaging was excluded from review. Results One-thousand two-hundred eight patients (1214 CT scans) were identified with otosclerosis, of which 373 were diagnosed with fenestral otosclerosis (663 ears) with imaging of sufficient quality for review. This population was predominantly female (57.2%) with bilateral fenestral otosclerosis (78%). Of these, 23 ears (3.5%) had definitive evidence of SSCD, with an additional 15 ears (2.3%) with possible radiographic evidence of SSCD. There was no significant difference in laterality between the SSCD and otosclerosis. Conclusions Among 373 patients with fenestral otosclerosis per CT temporal bone imaging at a tertiary referral hospital, as many as 8.3% of patients had radiographic evidence of SSCD. Given this incidence, it continues to be important to consider SSCD when diagnosing and treating otosclerosis.
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Affiliation(s)
- Brian A. Walker
- Department of Otorhinolaryngology, The Mayo Clinic in Arizona, Phoenix, AZ
| | - Ryan M. Thorwarth
- Department of Otorhinolaryngology, The Mayo Clinic in Arizona, Phoenix, AZ
| | - Lindsey L. Stull
- Department of Otorhinolaryngology, The Mayo Clinic in Arizona, Phoenix, AZ
| | - Joseph M. Hoxworth
- Department of Radiology, Division of Neuroradiology, The Mayo Clinic in Arizona, Phoenix, AZ
| | - Nicholas L. Deep
- Department of Otorhinolaryngology, Division of Neurotology, The Mayo Clinic in Arizona, Phoenix, AZ
| | - Peter A. Weisskopf
- Department of Otorhinolaryngology, Division of Neurotology, The Mayo Clinic in Arizona, Phoenix, AZ
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16
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Ashby C, Boyle EM, Bauer MA, Mikulasova A, Wardell CP, Williams L, Siegel A, Blaney P, Braunstein M, Kaminetsky D, Keats J, Maura F, Landgren O, Walker BA, Davies FE, Morgan GJ. Structural variants shape the genomic landscape and clinical outcome of multiple myeloma. Blood Cancer J 2022; 12:85. [PMID: 35637217 PMCID: PMC9151656 DOI: 10.1038/s41408-022-00673-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 03/11/2022] [Accepted: 04/22/2022] [Indexed: 11/09/2022] Open
Abstract
Deciphering genomic architecture is key to identifying novel disease drivers and understanding the mechanisms underlying myeloma initiation and progression. In this work, using the CoMMpass dataset, we show that structural variants (SV) occur in a nonrandom fashion throughout the genome with an increased frequency in the t(4;14), RB1, or TP53 mutated cases and reduced frequency in t(11;14) cases. By mapping sites of chromosomal rearrangements to topologically associated domains and identifying significantly upregulated genes by RNAseq we identify both predicted and novel putative driver genes. These data highlight the heterogeneity of transcriptional dysregulation occurring as a consequence of both the canonical and novel structural variants. Further, it shows that the complex rearrangements chromoplexy, chromothripsis and templated insertions are common in MM with each variant having its own distinct frequency and impact on clinical outcome. Chromothripsis is associated with a significant independent negative impact on clinical outcome in newly diagnosed cases consistent with its use alongside other clinical and genetic risk factors to identify prognosis.
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Affiliation(s)
- Cody Ashby
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Eileen M Boyle
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| | - Michael A Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Aneta Mikulasova
- Institute of Cellular Medicine, University of Newcastle upon Tyne, Newcastle, UK
| | - Christopher P Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
- Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Louis Williams
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Ariel Siegel
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Patrick Blaney
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Marc Braunstein
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | - Jonathan Keats
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, USA
| | | | - Ola Landgren
- Sylvester Cancer Center University of Miami, Miami, FL, USA
| | - Brian A Walker
- Division of Hematology Oncology Indiana University, Indianapolis, IN, USA
| | - Faith E Davies
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gareth J Morgan
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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17
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Caro J, Cairns D, Menzies T, Boyle E, Pawlyn C, Cook G, Kaiser M, Walker BA, Owen R, Jackson GH, Morgan GJ, Heaney J, Drayson MT, Davies FE. Impact of Etiological Cytogenetic Abnormalities on the Depth of Immunoparesis and Survival in Newly Diagnosed Multiple Myeloma. Clin Lymphoma Myeloma Leuk 2022; 22:e279-e284. [PMID: 34876373 DOI: 10.1016/j.clml.2021.10.008] [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] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Accepted: 10/13/2021] [Indexed: 06/13/2023]
Abstract
INTRODUCTION/BACKGROUND Immunoparesis, or low polyclonal immunoglobulin levels, is commonly seen in multiple myeloma (MM), and is associated with poor clinical outcomes. MM can be divided into subgroups with distinct biology and outcomes based on etiologic cytogenetic abnormalities. These include hyperdiploidy and translocations of t(11;14), t(4;14), t(14;16), and t(14;20), with the latter 3 associated with high-risk disease. We hypothesized that the different etiologic cytogenetic abnormalities drive bone marrow microenvironmental changes, resulting in different degrees of immunoparesis, and subgroup-dependent effects on clinical outcomes. MATERIALS AND METHODS We performed a retrospective review of 985 newly diagnosed patients enrolled in the Myeloma IX and XI trials. Immunoglobulin levels, survival outcomes, and infection rates were evaluated for each cytogenetic subgroup. RESULTS A significant proportion of patients with high-risk t(4;14), t(14;16), or t(14;20) had suppressed polyclonal immunoglobulins compared to standard-risk patients with hyperdiploidy or t(11;14). The clinical impact of immunoparesis depended on the cytogenetic subgroup, with the degree of IgM suppression effecting progression-free and overall survival only in the hyperdiploid subgroup. There was no significant difference in infection rates amongst the etiologic subgroups. CONCLUSION These findings demonstrate that the etiologic cytogenetic subgroup influences the degree and clinical impact of immunoparesis. This suggests that the underlying cytogenetic abnormality affects remodeling of the bone marrow plasma cell niche, resulting in suppressed normal plasma cell function, and low immunoglobulin levels.
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Affiliation(s)
- Jessica Caro
- Perlmutter Cancer Center, NYU Langone Health, New York, NY.
| | - David Cairns
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, United Kingdom
| | - Tom Menzies
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, United Kingdom
| | - Eileen Boyle
- Perlmutter Cancer Center, NYU Langone Health, New York, NY
| | | | - Gordon Cook
- Leeds Institute of Clinical Trials Research, University of Leeds, Leeds, United Kingdom
| | - Martin Kaiser
- The Institute of Cancer Research, London, United Kingdom
| | | | - Roger Owen
- St James's University Hospital, Leeds, United Kingdom
| | - Graham H Jackson
- Department of Hematology, Newcastle University, Newcastle upon Tyne, United Kingdom
| | | | - Jennifer Heaney
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Mark T Drayson
- Institute of Immunology and Immunotherapy, University of Birmingham, Birmingham, United Kingdom
| | - Faith E Davies
- Perlmutter Cancer Center, NYU Langone Health, New York, NY
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18
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Walker BA, Gerber ME. Laryngeal Actinomycosis Presenting as Foreign Body. OTO Open 2022; 6:2473974X211073701. [PMID: 35174301 PMCID: PMC8841919 DOI: 10.1177/2473974x211073701] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022] Open
Affiliation(s)
- Brian A. Walker
- Department of Otorhinolaryngology, The Mayo Clinic in Arizona, Phoenix, Arizona, USA
| | - Mark E. Gerber
- Department of Otorhinolaryngology, Phoenix Children’s Hospital, Phoenix, Arizona, USA
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19
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Johnson TS, Yu CY, Huang Z, Xu S, Wang T, Dong C, Shao W, Zaid MA, Huang X, Wang Y, Bartlett C, Zhang Y, Walker BA, Liu Y, Huang K, Zhang J. Diagnostic Evidence GAuge of Single cells (DEGAS): a flexible deep transfer learning framework for prioritizing cells in relation to disease. Genome Med 2022; 14:11. [PMID: 35105355 PMCID: PMC8808996 DOI: 10.1186/s13073-022-01012-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2021] [Accepted: 01/07/2022] [Indexed: 12/13/2022] Open
Abstract
We propose DEGAS (Diagnostic Evidence GAuge of Single cells), a novel deep transfer learning framework, to transfer disease information from patients to cells. We call such transferrable information "impressions," which allow individual cells to be associated with disease attributes like diagnosis, prognosis, and response to therapy. Using simulated data and ten diverse single-cell and patient bulk tissue transcriptomic datasets from glioblastoma multiforme (GBM), Alzheimer's disease (AD), and multiple myeloma (MM), we demonstrate the feasibility, flexibility, and broad applications of the DEGAS framework. DEGAS analysis on myeloma single-cell transcriptomics identified PHF19high myeloma cells associated with progression. Availability: https://github.com/tsteelejohnson91/DEGAS .
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Affiliation(s)
- Travis S Johnson
- Department of Medicine, Indiana University School of Medicine, 535 Barnhill Dr, Indianapolis, IN, 46202, USA
- Department of Biomedical Informatics, The Ohio State University College of Medicine, 370 W 9th Ave, Columbus, OH, 43210, USA
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, 410 W 10th St, Suite 3000, Indianapolis, IN, 46202, USA
| | - Christina Y Yu
- Department of Medicine, Indiana University School of Medicine, 535 Barnhill Dr, Indianapolis, IN, 46202, USA
- Department of Biomedical Informatics, The Ohio State University College of Medicine, 370 W 9th Ave, Columbus, OH, 43210, USA
| | - Zhi Huang
- School of Electrical and Computer Engineering, Purdue University, 465 Northwestern Ave, West Lafayette, IN, 47907, USA
| | - Siwen Xu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W. 10th St, Suite 5000, Indianapolis, IN, 46202, USA
| | - Tongxin Wang
- Department of Computer Science, Indiana University, 150 S Woodlawn Ave, Bloomington, IN, 47405, USA
| | - Chuanpeng Dong
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W. 10th St, Suite 5000, Indianapolis, IN, 46202, USA
| | - Wei Shao
- Department of Medicine, Indiana University School of Medicine, 535 Barnhill Dr, Indianapolis, IN, 46202, USA
| | - Mohammad Abu Zaid
- Department of Medicine, Indiana University School of Medicine, 535 Barnhill Dr, Indianapolis, IN, 46202, USA
| | - Xiaoqing Huang
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, 410 W 10th St, Suite 3000, Indianapolis, IN, 46202, USA
| | - Yijie Wang
- Department of Computer Science, Indiana University, 150 S Woodlawn Ave, Bloomington, IN, 47405, USA
| | - Christopher Bartlett
- Battelle Center for Mathematical Medicine, Nationwide Children's Hospital, 575 Children's Crossroad, Columbus, OH, 43215, USA
| | - Yan Zhang
- Department of Biomedical Informatics, The Ohio State University College of Medicine, 370 W 9th Ave, Columbus, OH, 43210, USA
- The Ohio State University Comprehensive Cancer Center (OSUCCC - James), Starling-Loving Hall, 320 W 10th Ave, Columbus, OH, 43210, USA
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University Melvin and Bren Simon Comprehensive Cancer Center, 535 Barnhill Dr, Indianapolis, IN, 46202, USA
| | - Yunlong Liu
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, 410 W. 10th St, Suite 5000, Indianapolis, IN, 46202, USA
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th St, Suite 4000, Indianapolis, IN, 46202, USA
| | - Kun Huang
- Department of Medicine, Indiana University School of Medicine, 535 Barnhill Dr, Indianapolis, IN, 46202, USA.
- Department of Biostatistics and Health Data Science, Indiana University School of Medicine, 410 W 10th St, Suite 3000, Indianapolis, IN, 46202, USA.
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th St, Suite 4000, Indianapolis, IN, 46202, USA.
- Regenstrief Institute, 1101 W 10th St, Indianapolis, IN, 46202, USA.
| | - Jie Zhang
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, 410 W 10th St, Suite 4000, Indianapolis, IN, 46202, USA.
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20
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Mikulasova A, Kent D, Trevisan-Herraz M, Karataraki N, Fung KTM, Ashby C, Cieslak A, Yaccoby S, van Rhee F, Zangari M, Thanendrarajan S, Schinke C, Morgan GJ, Asnafi V, Spicuglia S, Brackley CA, Corcoran AE, Hambleton S, Walker BA, Rico D, Russell LJ. Epigenomic translocation of H3K4me3 broad domains over oncogenes following hijacking of super-enhancers. Genome Res 2021; 32:1343-1354. [PMID: 34933939 PMCID: PMC9341503 DOI: 10.1101/gr.276042.121] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 12/15/2021] [Indexed: 11/24/2022]
Abstract
Chromosomal translocations are important drivers of haematological malignancies whereby proto-oncogenes are activated by juxtaposition with enhancers, often called enhancer hijacking. We analyzed the epigenomic consequences of rearrangements between the super-enhancers of the immunoglobulin heavy locus (IGH) and proto-oncogene CCND1 that are common in B cell malignancies. By integrating BLUEPRINT epigenomic data with DNA breakpoint detection, we characterized the normal chromatin landscape of the human IGH locus and its dynamics after pathological genomic rearrangement. We detected an H3K4me3 broad domain (BD) within the IGH locus of healthy B cells that was absent in samples with IGH-CCND1 translocations. The appearance of H3K4me3-BD over CCND1 in the latter was associated with overexpression and extensive chromatin accessibility of its gene body. We observed similar cancer-specific H3K4me3-BDs associated with hijacking of super-enhancers of other common oncogenes in B cell (MAF, MYC, and FGFR3/NSD2) and T cell malignancies (LMO2, TLX3, and TAL1). Our analysis suggests that H3K4me3-BDs can be created by super-enhancers and supports the new concept of epigenomic translocation, in which the relocation of H3K4me3-BDs from cell identity genes to oncogenes accompanies the translocation of super-enhancers.
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Affiliation(s)
| | - Daniel Kent
- Newcastle University, Translational and Clinical Research Institute
| | | | | | - Kent T M Fung
- Newcastle University, Translational and Clinical Research Institute
| | - Cody Ashby
- University of Arkansas for Medical Sciences
| | - Agata Cieslak
- Université de Paris, Institut Necker Enfants Malades
| | | | | | | | | | | | | | - Vahid Asnafi
- Université de Paris, Institut Necker Enfants Malades
| | | | | | | | - Sophie Hambleton
- Newcastle University, Translational and Clinical Research Institute
| | - Brian A Walker
- Indiana University, Melvin and Bren Simon Comprehensive Cancer Center
| | | | - Lisa J Russell
- Newcastle University, Translational and Clinical Research Institute;
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21
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Ghamlouch H, Boyle EM, Blaney P, Wang Y, Choi J, Williams L, Bauer M, Auclair D, Bruno B, Walker BA, Davies FE, Morgan GJ. Insights into high-risk multiple myeloma from an analysis of the role of PHF19 in cancer. J Exp Clin Cancer Res 2021; 40:380. [PMID: 34857028 PMCID: PMC8638425 DOI: 10.1186/s13046-021-02185-1] [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] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 11/13/2021] [Indexed: 02/07/2023] Open
Abstract
Despite improvements in outcome, 15-25% of newly diagnosed multiple myeloma (MM) patients have treatment resistant high-risk (HR) disease with a poor survival. The lack of a genetic basis for HR has focused attention on the role played by epigenetic changes. Aberrant expression and somatic mutations affecting genes involved in the regulation of tri-methylation of the lysine (K) 27 on histone 3 H3 (H3K27me3) are common in cancer. H3K27me3 is catalyzed by EZH2, the catalytic subunit of the Polycomb Repressive Complex 2 (PRC2). The deregulation of H3K27me3 has been shown to be involved in oncogenic transformation and tumor progression in a variety of hematological malignancies including MM. Recently we have shown that aberrant overexpression of the PRC2 subunit PHD Finger Protein 19 (PHF19) is the most significant overall contributor to HR status further focusing attention on the role played by epigenetic change in MM. By modulating both the PRC2/EZH2 catalytic activity and recruitment, PHF19 regulates the expression of key genes involved in cell growth and differentiation. Here we review the expression, regulation and function of PHF19 both in normal and the pathological contexts of solid cancers and MM. We present evidence that strongly implicates PHF19 in the regulation of genes important in cell cycle and the genetic stability of MM cells making it highly relevant to HR MM behavior. A detailed understanding of the normal and pathological functions of PHF19 will allow us to design therapeutic strategies able to target aggressive subsets of MM.
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Affiliation(s)
- Hussein Ghamlouch
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA.
| | - Eileen M Boyle
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Patrick Blaney
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
- Applied Bioinformatics Laboratories (ABL), NYU Langone Medical Center, New York, NY, USA
| | - Yubao Wang
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Jinyoung Choi
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Louis Williams
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Daniel Auclair
- The Multiple Myeloma Research Foundation (MMRF), Norwalk, CT, USA
| | - Benedetto Bruno
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
| | - Faith E Davies
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA
| | - Gareth J Morgan
- Myeloma Research Program, NYU Langone Medical Center, Perlmutter Cancer Center, 522 1st Avenue, Manhattan, New York City, NY, 10016, USA.
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22
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Jones JR, Barber A, Le Bihan YV, Weinhold N, Ashby C, Walker BA, Wardell CP, Wang H, Kaiser MF, Jackson GH, Davies FE, Chopra R, Morgan GJ, Pawlyn C. Mutations in CRBN and other cereblon pathway genes are infrequently associated with acquired resistance to immunomodulatory drugs. Leukemia 2021; 35:3017-3020. [PMID: 34373585 PMCID: PMC8478640 DOI: 10.1038/s41375-021-01373-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 07/26/2021] [Accepted: 07/27/2021] [Indexed: 02/06/2023]
Affiliation(s)
- J R Jones
- The Institute of Cancer Research, London, UK.
- Brighton and Sussex Medical School, Brighton, UK.
- Kings College Hospital NHS Foundation Trust, London, UK.
| | - A Barber
- The Institute of Cancer Research, London, UK
| | | | - N Weinhold
- Department of Internal Medicine V, University Hospital of Heidelberg, Heidelberg, Germany
| | - C Ashby
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Arkansas, USA
| | - B A Walker
- Indiana University School of Medicine, Indiana, USA
| | - C P Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Arkansas, USA
| | - H Wang
- The Institute of Cancer Research, London, UK
| | - M F Kaiser
- The Institute of Cancer Research, London, UK
- The Royal Marsden Hospital, London, UK
| | - G H Jackson
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - F E Davies
- Perlmutter Cancer Center, NYU Langone Health, New York, USA
| | - R Chopra
- The Institute of Cancer Research, London, UK
- Apple Tree Partners, London, UK
| | - G J Morgan
- Perlmutter Cancer Center, NYU Langone Health, New York, USA
| | - C Pawlyn
- The Institute of Cancer Research, London, UK.
- The Royal Marsden Hospital, London, UK.
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23
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Boyle EM, Rosenthal A, Wang Y, Farmer P, Rutherford M, Ashby C, Bauer M, Johnson SK, Wardell CP, Hoering A, Schinke C, Thanendrarajan S, Zangari M, Barlogie B, Davies FE, Walker BA, van Rhee F, Morgan GJ. High-risk transcriptional profiles in multiple myeloma are an acquired feature that can occur in any subtype and more frequently with each subsequent relapse. Br J Haematol 2021; 195:283-286. [PMID: 34244996 DOI: 10.1111/bjh.17670] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Eileen M Boyle
- Perlmutter Cancer Center, NYU Langone Medical Center, Myeloma Research Program, New York, NY, USA
| | | | - Yan Wang
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Philip Farmer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Michael Rutherford
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Cody Ashby
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sarah K Johnson
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Christopher P Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Antje Hoering
- Cancer Research and Biostatistics - CRAB, Seattle, USA
| | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Bart Barlogie
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Faith E Davies
- Perlmutter Cancer Center, NYU Langone Medical Center, Myeloma Research Program, New York, NY, USA
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
| | - Frits van Rhee
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Gareth J Morgan
- Perlmutter Cancer Center, NYU Langone Medical Center, Myeloma Research Program, New York, NY, USA
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24
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Boyle EM, Williams L, Blaney P, Ashby C, Bauer M, Walker BA, Ghamlouch H, Choi J, Perrial E, Wang Y, Caro J, Stoeckle JH, Arbini A, Kaminetzky D, Braunstein M, Bruno B, Razzo B, Diamond B, Maclachlan K, Maura F, Landgren O, Litke R, Fegan CD, Keats J, Auclair D, Davies FE, Morgan GJ. Improving prognostic assignment in older adults with multiple myeloma using acquired genetic features, clonal hemopoiesis and telomere length. Leukemia 2021; 36:221-224. [PMID: 34148053 DOI: 10.1038/s41375-021-01320-3] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Revised: 05/17/2021] [Accepted: 06/03/2021] [Indexed: 11/09/2022]
Affiliation(s)
- Eileen M Boyle
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Louis Williams
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Patrick Blaney
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Cody Ashby
- Department of Biomedical Informatics, UAMS, Little Rock, AR, USA
| | - Michael Bauer
- Department of Biomedical Informatics, UAMS, Little Rock, AR, USA
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
| | - Hussein Ghamlouch
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Jinyoung Choi
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Emeline Perrial
- INSERM 1052/CNRS 5286 Cancer Research Center of Lyon, Lyon, France
| | - Yubao Wang
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Jessica Caro
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - James H Stoeckle
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Arnaldo Arbini
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - David Kaminetzky
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Marc Braunstein
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Benedetto Bruno
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Beatrice Razzo
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Benjamin Diamond
- Myeloma Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Kylee Maclachlan
- Myeloma Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Francesco Maura
- Myeloma Service, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ola Landgren
- Myeloma Program, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Rachel Litke
- Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | | | - Johnathan Keats
- Multiple Myeloma Research Laboratory, TGen, Phoenix, AZ, USA
| | | | - Faith E Davies
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA
| | - Gareth J Morgan
- Myeloma Research Program, Perlmutter Cancer Center, NYU Langone Medical Center, New-York, NY, USA.
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25
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Maura F, Boyle EM, Rustad EH, Ashby C, Kaminetzky D, Bruno B, Braunstein M, Bauer M, Blaney P, Wang Y, Ghamlouch H, Williams L, Stoeckle J, Davies FE, Walker BA, Maclachlan K, Diamond B, Landgren O, Morgan GJ. Chromothripsis as a pathogenic driver of multiple myeloma. Semin Cell Dev Biol 2021; 123:115-123. [PMID: 33958284 DOI: 10.1016/j.semcdb.2021.04.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [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: 03/09/2021] [Accepted: 04/16/2021] [Indexed: 12/29/2022]
Abstract
Analysis of the genetic basis for multiple myeloma (MM) has informed many of our current concepts of the biology that underlies disease initiation and progression. Studying these events in further detail is predicted to deliver important insights into its pathogenesis, prognosis and treatment. Information from whole genome sequencing of structural variation is revealing the role of these events as drivers of MM. In particular, we discuss how the insights we have gained from studying chromothripsis suggest that it can be used to provide information on disease initiation and that, as a consequence, it can be used for the clinical classification of myeloma precursor diseases allowing for early intervention and prognostic determination. For newly diagnosed MM, the integration of information on the presence of chromothripsis has the potential to significantly enhance current risk prediction strategies and to better characterize patients with high-risk disease biology. In this article we summarize the genetic basis for MM and the role played by chromothripsis as a critical pathogenic factor active at early disease phases.
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Affiliation(s)
- Francesco Maura
- Myeloma Program, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Eileen M Boyle
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Even H Rustad
- Institute for Cancer Research, Oslo University Hospital Radiumhospitalet, Oslo, Norway
| | - Cody Ashby
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Benedetto Bruno
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Marc Braunstein
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Michael Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Patrick Blaney
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Yubao Wang
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | | | - Louis Williams
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - James Stoeckle
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Faith E Davies
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Brian A Walker
- Melvin and Bren Simon Comprehensive Cancer Center, Division of Hematology Oncology Indiana University, Indianapolis, IN, USA
| | - Kylee Maclachlan
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ben Diamond
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ola Landgren
- Myeloma Program, Division of Hematology, Sylvester Comprehensive Cancer Center, University of Miami, Miami, FL, USA
| | - Gareth J Morgan
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
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26
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Schinke CD, Bird JT, Qu P, Yaccoby S, Lyzogubov VV, Shelton R, Ling W, Boyle EM, Deshpande S, Byrum SD, Washam C, Mackintosh S, Stephens O, Thanendrarajan S, Zangari M, Shaughnessy J, Zhan F, Barlogie B, van Rhee F, Walker BA. PHF19 inhibition as a therapeutic target in multiple myeloma. Curr Res Transl Med 2021; 69:103290. [PMID: 33894670 DOI: 10.1016/j.retram.2021.103290] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Revised: 03/16/2021] [Accepted: 04/06/2021] [Indexed: 02/01/2023]
Abstract
Epigenetic deregulation is increasingly recognized as a contributing pathological factor in multiple myeloma (MM). In particular tri-methylation of H3 lysine 27 (H3K27me3), which is catalyzed by PHD finger protein 19 (PHF19), a subunit of the Polycomb Repressive Complex 2 (PRC2), has recently shown to be a crucial mediator of MM tumorigenicity. Overexpression of PHF19 in MM has been associated with worse clinical outcome. Yet, while there is mounting evidence that PHF19 overexpression plays a crucial role in MM carcinogenesis downstream mechanisms remain to be elucidated. In the current study we use a functional knock down (KD) of PHF19 to investigate the biological role of PHF19 and show that PHF19KD leads to decreased tumor growth in vitro and in vivo. Expression of major cancer players such as bcl2, myc and EGR1 were decreased upon PHF19KD further underscoring the role of PHF19 in MM biology. Additionally, our results highlighted the prognostic impact of PHF19 overexpression, which was significantly associated with worse survival. Overall, our study underscores the premise that targeting the PHF19-PRC2 complex would open up avenues for novel MM therapies.
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Affiliation(s)
- Carolina D Schinke
- Myeloma Center, Division of Hematology/Oncology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States.
| | - Jordan T Bird
- College of Medicine, Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Pingping Qu
- Cancer Research and Biostatistics, Seattle, WA, United States
| | - Shmuel Yaccoby
- Myeloma Center, Division of Hematology/Oncology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Valeriy V Lyzogubov
- Myeloma Center, Division of Hematology/Oncology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Randal Shelton
- Myeloma Center, Division of Hematology/Oncology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Wen Ling
- Myeloma Center, Division of Hematology/Oncology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Eileen M Boyle
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, United States
| | - Sharyu Deshpande
- Myeloma Center, Division of Hematology/Oncology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Stephanie D Byrum
- College of Medicine, Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Charity Washam
- College of Medicine, Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Samuel Mackintosh
- College of Medicine, Department of Biochemistry and Molecular Biology, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Owen Stephens
- The College of Medicine, Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Sharmilan Thanendrarajan
- Myeloma Center, Division of Hematology/Oncology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Maurizio Zangari
- Myeloma Center, Division of Hematology/Oncology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - John Shaughnessy
- Myeloma Center, Division of Hematology/Oncology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Fenghuang Zhan
- Myeloma Center, Division of Hematology/Oncology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Bart Barlogie
- Division of Hematology, The Mount Sinai Hospital, New York, NY, Sinai, USA
| | - Frits van Rhee
- Myeloma Center, Division of Hematology/Oncology, Winthrop P. Rockefeller Cancer Institute, University of Arkansas for Medical Sciences, Little Rock, AR, United States
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, United States
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27
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Chen D, Abu Zaid MI, Reiter JL, Czader M, Wang L, McGuire P, Xuei X, Gao H, Huang K, Abonour R, Walker BA, Liu Y. Cryopreservation Preserves Cell-Type Composition and Gene Expression Profiles in Bone Marrow Aspirates From Multiple Myeloma Patients. Front Genet 2021; 12:663487. [PMID: 33968139 PMCID: PMC8099152 DOI: 10.3389/fgene.2021.663487] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/29/2021] [Indexed: 12/19/2022] Open
Abstract
Single-cell RNA sequencing reveals gene expression differences between individual cells and also identifies different cell populations that are present in the bulk starting material. To obtain an accurate assessment of patient samples, single-cell suspensions need to be generated as soon as possible once the tissue or sample has been collected. However, this requirement poses logistical challenges for experimental designs involving multiple samples from the same subject since these samples would ideally be processed at the same time to minimize technical variation in data analysis. Although cryopreservation has been shown to largely preserve the transcriptome, it is unclear whether the freeze-thaw process might alter gene expression profiles in a cell-type specific manner or whether changes in cell-type proportions might also occur. To address these questions in the context of multiple myeloma clinical studies, we performed single-cell RNA sequencing (scRNA-seq) to compare fresh and frozen cells isolated from bone marrow aspirates of six multiple myeloma patients, analyzing both myeloma cells (CD138+) and cells constituting the microenvironment (CD138−). We found that cryopreservation using 90% fetal calf serum and 10% dimethyl sulfoxide resulted in highly consistent gene expression profiles when comparing fresh and frozen samples from the same patient for both CD138+ myeloma cells (R ≥ 0.96) and for CD138– cells (R ≥ 0.9). We also demonstrate that CD138– cell-type proportions showed minimal alterations, which were mainly related to small differences in immune cell subtype sensitivity to the freeze-thaw procedures. Therefore, when processing fresh multiple myeloma samples is not feasible, cryopreservation is a useful option in single-cell profiling studies.
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Affiliation(s)
- Duojiao Chen
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - Mohammad I Abu Zaid
- Division of Hematology and Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Bone Marrow and Blood Stem Cell Transplantation Program, Indiana University Health, Indianapolis, IN, United States
| | - Jill L Reiter
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Magdalena Czader
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Lin Wang
- Department of Pathology, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Patrick McGuire
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Xiaoling Xuei
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Hongyu Gao
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Kun Huang
- Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States.,Division of Hematology and Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Rafat Abonour
- Division of Hematology and Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States.,Bone Marrow and Blood Stem Cell Transplantation Program, Indiana University Health, Indianapolis, IN, United States
| | - Brian A Walker
- Division of Hematology and Oncology, Department of Medicine, Indiana University School of Medicine, Indianapolis, IN, United States
| | - Yunlong Liu
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, United States.,Center for Computational Biology and Bioinformatics, Indiana University School of Medicine, Indianapolis, IN, United States.,Department of BioHealth Informatics, School of Informatics and Computing, Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States.,Center for Medical Genomics, Indiana University School of Medicine, Indianapolis, IN, United States
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28
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Bauer MA, Ashby C, Wardell C, Boyle EM, Ortiz M, Flynt E, Thakurta A, Morgan G, Walker BA. Differential RNA splicing as a potentially important driver mechanism in multiple myeloma. Haematologica 2021; 106:736-745. [PMID: 32079689 PMCID: PMC7927887 DOI: 10.3324/haematol.2019.235424] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [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: 09/13/2019] [Indexed: 12/27/2022] Open
Abstract
Disruption of the normal splicing patterns of RNA is a major factor in the pathogenesis of a number of diseases. Increasingly research has shown the strong influence that splicing patterns can have on cancer progression. Multiple Myeloma is a molecularly heterogeneous disease classified by the presence of key translocations, gene expression profiles and mutations but the splicing patterns in MM remains largely unexplored. We take a multifaceted approach to define the extent and impact of alternative splicing in MM. We look at the spliceosome component, SF3B1, with hotspot mutations (K700E and K666T/Q) shown to result in an increase in alternative splicing in other cancers. We discovered a number of differentially spliced genes in comparison of the SF3B1 mutant and wild type samples that included, MZB1, DYNLL1, TMEM14C and splicing related genes DHX9, CLASRP, and SNRPE. We identified a broader role for abnormal splicing showing clear differences in the extent of novel splice variants in the different translocation groups. We show that a high number of novel splice loci is associated with adverse survival and an ultra-high risk group. The enumeration of patterns of alternative splicing has the potential to refine MM classification and to aid in the risk stratification of patients.
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Affiliation(s)
- Michael A Bauer
- University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Cody Ashby
- University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Eileen M Boyle
- University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Maria Ortiz
- Celgene Institute for Translational Research Europe, Sevilla, Spain
| | - Erin Flynt
- Translational Development and Diagnostics, Celgene Corporation, Summit, NJ, USA
| | - Anjan Thakurta
- Translational Development and Diagnostics, Celgene Corporation, Summit, NJ, USA
| | - Gareth Morgan
- NYULangone Medical Center, Perlmuter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
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29
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Boyle EM, Deshpande S, Tytarenko R, Ashby C, Wang Y, Bauer MA, Johnson SK, Wardell CP, Thanendrarajan S, Zangari M, Facon T, Dumontet C, Barlogie B, Arbini A, Rustad EH, Maura F, Landgren O, Zhan F, van Rhee F, Schinke C, Davies FE, Morgan GJ, Walker BA. The molecular make up of smoldering myeloma highlights the evolutionary pathways leading to multiple myeloma. Nat Commun 2021; 12:293. [PMID: 33436579 PMCID: PMC7804406 DOI: 10.1038/s41467-020-20524-2] [Citation(s) in RCA: 45] [Impact Index Per Article: 15.0] [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: 07/30/2020] [Accepted: 12/08/2020] [Indexed: 12/28/2022] Open
Abstract
Smoldering myeloma (SMM) is associated with a high-risk of progression to myeloma (MM). We report the results of a study of 82 patients with both targeted sequencing that included a capture of the immunoglobulin and MYC regions. By comparing these results to newly diagnosed myeloma (MM) we show fewer NRAS and FAM46C mutations together with fewer adverse translocations, del(1p), del(14q), del(16q), and del(17p) in SMM consistent with their role as drivers of the transition to MM. KRAS mutations are associated with a shorter time to progression (HR 3.5 (1.5–8.1), p = 0.001). In an analysis of change in clonal structure over time we studied 53 samples from nine patients at multiple time points. Branching evolutionary patterns, novel mutations, biallelic hits in crucial tumour suppressor genes, and segmental copy number changes are key mechanisms underlying the transition to MM, which can precede progression and be used to guide early intervention strategies. Progression from asymptomatic smoldering multiple myeloma (SMM) to symptomatic Multiple Myeloma occurs at different rates in different patients. Here, the authors report fewer NRAS and FAM46C mutations and adverse translocations in SMM compared to MM, while KRAS mutations are associated with a shorter time to progression.
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Affiliation(s)
- Eileen M Boyle
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,INSERM 1052/CNRS 5286 Cancer Research Center of Lyon, Lyon, France.,Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Shayu Deshpande
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ruslana Tytarenko
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yan Wang
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Michael A Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sarah K Johnson
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Christopher P Wardell
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Thierry Facon
- Service des maladies du sang. Hôpital Claude Huriez, Lille University Hospital, Lille, France
| | - Charles Dumontet
- INSERM 1052/CNRS 5286 Cancer Research Center of Lyon, Lyon, France
| | - Bart Barlogie
- Division of Hematology, The Mount Sinai Hospital, New York, NY, USA
| | - Arnaldo Arbini
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Even H Rustad
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Francesco Maura
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Ola Landgren
- Myeloma Service, Department of Medicine, Memorial Sloan Kettering Cancer Center, New York, NY, USA
| | - Fenghuang Zhan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Faith E Davies
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA
| | - Gareth J Morgan
- Perlmutter Cancer Center, NYU Langone Health, New York, NY, USA.
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA.
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30
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Deshpande S, Tytarenko RG, Wang Y, Boyle EM, Ashby C, Schinke CD, Thanendrarajan S, Zangari M, Zhan F, Davies FE, Morgan GJ, van Rhee F, Walker BA. Monitoring treatment response and disease progression in myeloma with circulating cell-free DNA. Eur J Haematol 2020; 106:230-240. [PMID: 33107092 DOI: 10.1111/ejh.13541] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [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: 08/04/2020] [Revised: 10/21/2020] [Accepted: 10/22/2020] [Indexed: 01/06/2023]
Abstract
Circulating cell-free DNA (cfDNA) has the potential to capture spatial genetic heterogeneity in myeloma (MM) patients. We assessed whether cfDNA levels vary according to risk status defined by the 70 gene expression profile (GEP70). cfDNA levels in 77 patients were significantly higher in the GEP70 high-risk (HR) group compared to the low-risk (LR) group and correlated weakly with clinical markers including lactate dehydrogenase, β2 -microglobulin, and ISS. Patients with high cfDNA levels were associated with a worse PFS (hazard ratio 6.4; 95% CI of ratio 1.9-22) and OS (hazard ratio 4.4; 95% CI of ratio 1.2-15.7). Circulating tumor DNA (ctDNA) was elevated in the HR group and ctDNA correlated strongly with GEP70 risk score (Spearman r = .69, P = .0027). cfDNA concentrations were significantly elevated between days 3-5 after chemotherapy before falling back to baseline levels. ctDNA in two patients showed a similar spike in levels between days 3 and 5 after chemotherapy with a concomitant increase in allele fraction of KRAS mutations. We assessed cfDNA levels in 25 patients with smoldering myeloma with serial samples and showed increased allele fraction of mutated KRAS at progression in cfDNA. Our study shows that cfDNA is a dynamic tool to capture genetic events in myeloma.
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Affiliation(s)
- Shayu Deshpande
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ruslana G Tytarenko
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yan Wang
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Eileen M Boyle
- Perlmutter Cancer Center, Myeloma Research Program, NYU Langone Health, New York, NY, USA
| | - Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Carolina D Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Fenghuang Zhan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Faith E Davies
- Perlmutter Cancer Center, Myeloma Research Program, NYU Langone Health, New York, NY, USA
| | - Gareth J Morgan
- Perlmutter Cancer Center, Myeloma Research Program, NYU Langone Health, New York, NY, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian A Walker
- Division of Hematology Oncology, Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN, USA
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31
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Danziger SA, McConnell M, Gockley J, Young MH, Rosenthal A, Schmitz F, Reiss DJ, Farmer P, Alapat DV, Singh A, Ashby C, Bauer M, Ren Y, Smith K, Couto SS, van Rhee F, Davies F, Zangari M, Petty N, Orlowski RZ, Dhodapkar MV, Copeland WB, Fox B, Hoering A, Fitch A, Newhall K, Barlogie B, Trotter MWB, Hershberg RM, Walker BA, Dervan AP, Ratushny AV, Morgan GJ. Bone marrow microenvironments that contribute to patient outcomes in newly diagnosed multiple myeloma: A cohort study of patients in the Total Therapy clinical trials. PLoS Med 2020; 17:e1003323. [PMID: 33147277 PMCID: PMC7641353 DOI: 10.1371/journal.pmed.1003323] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 09/18/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND The tumor microenvironment (TME) is increasingly appreciated as an important determinant of cancer outcome, including in multiple myeloma (MM). However, most myeloma microenvironment studies have been based on bone marrow (BM) aspirates, which often do not fully reflect the cellular content of BM tissue itself. To address this limitation in myeloma research, we systematically characterized the whole bone marrow (WBM) microenvironment during premalignant, baseline, on treatment, and post-treatment phases. METHODS AND FINDINGS Between 2004 and 2019, 998 BM samples were taken from 436 patients with newly diagnosed MM (NDMM) at the University of Arkansas for Medical Sciences in Little Rock, Arkansas, United States of America. These patients were 61% male and 39% female, 89% White, 8% Black, and 3% other/refused, with a mean age of 58 years. Using WBM and matched cluster of differentiation (CD)138-selected tumor gene expression to control for tumor burden, we identified a subgroup of patients with an adverse TME associated with 17 fewer months of progression-free survival (PFS) (95% confidence interval [CI] 5-29, 49-69 versus 70-82 months, χ2 p = 0.001) and 15 fewer months of overall survival (OS; 95% CI -1 to 31, 92-120 versus 113-129 months, χ2 p = 0.036). Using immunohistochemistry-validated computational tools that identify distinct cell types from bulk gene expression, we showed that the adverse outcome was correlated with elevated CD8+ T cell and reduced granulocytic cell proportions. This microenvironment develops during the progression of premalignant to malignant disease and becomes less prevalent after therapy, in which it is associated with improved outcomes. In patients with quantified International Staging System (ISS) stage and 70-gene Prognostic Risk Score (GEP-70) scores, taking the microenvironment into consideration would have identified an additional 40 out of 290 patients (14%, premutation p = 0.001) with significantly worse outcomes (PFS, 95% CI 6-36, 49-73 versus 74-90 months) who were not identified by existing clinical (ISS stage III) and tumor (GEP-70) criteria as high risk. The main limitations of this study are that it relies on computationally identified cell types and that patients were treated with thalidomide rather than current therapies. CONCLUSIONS In this study, we observe that granulocyte signatures in the MM TME contribute to a more accurate prognosis. This implies that future researchers and clinicians treating patients should quantify TME components, in particular monocytes and granulocytes, which are often ignored in microenvironment studies.
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Affiliation(s)
- Samuel A. Danziger
- Bristol Myers Squibb, Seattle, Washington, United States of America
- * E-mail: (SAD); (AVR); (GJM)
| | - Mark McConnell
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | - Jake Gockley
- Sage Bionetworks, Seattle, Washington, United States of America
| | - Mary H. Young
- Sage Bionetworks, Seattle, Washington, United States of America
| | - Adam Rosenthal
- Cancer Research and Biostatistics, Seattle, Washington, United States of America
| | - Frank Schmitz
- Sage Bionetworks, Seattle, Washington, United States of America
| | - David J. Reiss
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | - Phil Farmer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Daisy V. Alapat
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Amrit Singh
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Michael Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Yan Ren
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | - Kelsie Smith
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | | | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Faith Davies
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Nathan Petty
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | - Robert Z. Orlowski
- The University of Texas MD Anderson Cancer Center, Houston, Texas, United States of America
| | - Madhav V. Dhodapkar
- Winship Cancer Institute, Emory University, Atlanta, Georgia, United States of America
| | | | - Brian Fox
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | - Antje Hoering
- Cancer Research and Biostatistics, Seattle, Washington, United States of America
| | - Alison Fitch
- Bristol Myers Squibb, Seattle, Washington, United States of America
| | - Katie Newhall
- Sage Bionetworks, Seattle, Washington, United States of America
| | - Bart Barlogie
- Department of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, New York, United States of America
| | | | | | - Brian A. Walker
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
| | | | - Alexander V. Ratushny
- Bristol Myers Squibb, Seattle, Washington, United States of America
- * E-mail: (SAD); (AVR); (GJM)
| | - Gareth J. Morgan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, Arkansas, United States of America
- * E-mail: (SAD); (AVR); (GJM)
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32
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Choudhury SR, Ashby C, Tytarenko R, Bauer M, Wang Y, Deshpande S, Den J, Schinke C, Zangari M, Thanendrarajan S, Davies FE, van Rhee F, Morgan GJ, Walker BA. The functional epigenetic landscape of aberrant gene expression in molecular subgroups of newly diagnosed multiple myeloma. J Hematol Oncol 2020; 13:108. [PMID: 32762714 PMCID: PMC7409490 DOI: 10.1186/s13045-020-00933-y] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023] Open
Abstract
Background Multiple Myeloma (MM) is a hematological malignancy with genomic heterogeneity and poor survival outcome. Apart from the central role of genetic lesions, epigenetic anomalies have been identified as drivers in the development of the disease. Methods Alterations in the DNA methylome were mapped in 52 newly diagnosed MM (NDMM) patients of six molecular subgroups and matched with loci-specific chromatin marks to define their impact on gene expression. Differential DNA methylation analysis was performed using DMAP with a ≥10% increase (hypermethylation) or decrease (hypomethylation) in NDMM subgroups, compared to control samples, considered significant for all the subsequent analyses with p<0.05 after adjusting for a false discovery rate. Results We identified differentially methylated regions (DMRs) within the etiological cytogenetic subgroups of myeloma, compared to control plasma cells. Using gene expression data we identified genes that are dysregulated and correlate with DNA methylation levels, indicating a role for DNA methylation in their transcriptional control. We demonstrated that 70% of DMRs in the MM epigenome were hypomethylated and overlapped with repressive H3K27me3. In contrast, differentially expressed genes containing hypermethylated DMRs within the gene body or hypomethylated DMRs at the promoters overlapped with H3K4me1, H3K4me3, or H3K36me3 marks. Additionally, enrichment of BRD4 or MED1 at the H3K27ac enriched DMRs functioned as super-enhancers (SE), controlling the overexpression of genes or gene-cassettes. Conclusions Therefore, this study presents the underlying epigenetic regulatory networks of gene expression dysregulation in NDMM patients and identifies potential targets for future therapies.
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Affiliation(s)
- Samrat Roy Choudhury
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Ruslana Tytarenko
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Michael Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Yan Wang
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Shayu Deshpande
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Judith Den
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | | | - Faith E Davies
- Department of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Gareth J Morgan
- Department of Medicine, NYU Langone Health, New York, NY, 10016, USA
| | - Brian A Walker
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA. .,Division of Hematology Oncology, Melvin and Bren Simon Comprehensive Cancer Center, Indiana University, Indianapolis, IN, 46202, USA.
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Parker NP, Weidenbecher MS, Friedman AD, Walker BA, Lott DG. KTP Laser Treatment of Early Glottic Cancer: A Multi-Institutional Retrospective Study. Ann Otol Rhinol Laryngol 2020; 130:47-55. [PMID: 32627613 DOI: 10.1177/0003489420938100] [Citation(s) in RCA: 3] [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: 11/15/2022]
Abstract
OBJECTIVES The primary objectives were to report oncologic outcomes of transoral laser microsurgery with potassium-titanyl-phosphate (KTP) laser (TLM-KTP) ablation of early glottic cancer (EGC). The secondary objectives were to report vocal outcomes and to analyze factors that might influence outcomes. METHODS A multi-institutional, retrospective analysis of consecutive patients treated for T1 or T2 glottic squamous cell carcinoma undergoing TLM-KTP ablation with at least 2 years of follow-up was performed. Patients with prior radiation or surgery for laryngeal disease were excluded. PRIMARY OUTCOME MEASURES INCLUDED surgical failures requiring radiation or laryngectomy, disease-specific survival (DSS), and overall survival (OS). Secondary outcome measures included: pre- and postoperative Voice Handicap Index-10 (VHI-10) scores. The effects of smoking status, stage, and anterior commissure involvement on outcomes were analyzed. RESULTS Overall 88 patients met inclusion criteria (83% male, 79.5% current or former smokers). Mean age was 68 (standard deviation (SD): 12). Mean follow-up was 39.5 months (SD: 15.3). Staging included 50 T1a, 21 T1b, and 20 T2 tumors, including three metachronous second primaries. Radiation and/or laryngectomy avoidance was achieved in 87/88 (98.9%) of patients, inclusive of 24 patients requiring KTP re-treatments. Two patients had biopsy-proven recurrence (2.3%), but only 21 of 24 re-treated patients received a formal biopsy. No patients died from laryngeal cancer. DSS and OS were 100% and 92.3%, respectively. The mean VHI-10 scores were 19.3 preoperatively, 3.8 at 6-months postop, and 3.8 at 2-years postop. Smokers had a longer interval to re-treatment (P = .03), patients with T2 lesions had a shorter interval to re-treatment (0.02), and patients with T2 lesions presented with worse initial VHI-10 scores (0.002). CONCLUSIONS A multi-institutional, retrospective case series of TLM-KTP ablation of EGC demonstrated excellent oncologic outcomes when close surveillance and proactive re-treatments were utilized. Disease-specific survival, overall survival, and vocal function were excellent. Additional studies are necessary to further analyze the merits and risks of this treatment approach.
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Affiliation(s)
- Noah P Parker
- Departments of Otolaryngology-Head and Neck Surgery and Speech and Hearing Sciences, Indiana University, Indianapolis, IN, USA
| | - Mark S Weidenbecher
- Department of Otolaryngology-Head and Neck Surgery, Case Western Reserve, Cleveland, OH, USA
| | - Aaron D Friedman
- Division of Otolaryngology-Head and Neck Surgery, NorthShore University Health System, Evanston, IL, USA
| | - Brian A Walker
- Department of Otorhinolaryngology-Head and Neck Surgery, Mayo Clinic Arizona, Phoenix, AZ, USA
| | - David G Lott
- Department of Otorhinolaryngology-Head and Neck Surgery, Mayo Clinic Arizona, Phoenix, AZ, USA
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Abstract
In this issue of Blood Cancer Discovery, Chesi and colleagues have performed a series of mouse experiments, combined with patient sample analysis, to delineate the role of del(13) in multiple myeloma. They identify loss of the miRNA cluster MIR15A/16-1 as critical for myelomagenesis and progression of disease. See related article by Chesi et al., p. 68.
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Affiliation(s)
- Brian A Walker
- Indiana University - Purdue University Indianapolis, Indianapolis, Indiana
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35
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Ashby C, Rutherford M, Bauer MA, Peterson EA, Wang Y, Boyle EM, Wardell CP, Walker BA. TarPan: an easily adaptable targeted sequencing panel viewer for research and clinical use. BMC Bioinformatics 2020; 21:144. [PMID: 32293247 PMCID: PMC7158102 DOI: 10.1186/s12859-020-3477-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Accepted: 03/31/2020] [Indexed: 02/01/2023] Open
Abstract
BACKGROUND The study of cancer genomics continually matures as the number of patient samples sequenced increases. As more data is generated, oncogenic drivers for specific cancer types are discovered along with their associated risks. This in turn leads to potential treatment strategies that pave the way to precision medicine. However, significant financial and analytical barriers make it infeasible to sequence the entire genome of every patient. In contrast, targeted sequencing panels give reliable information on relevant portions of the genome at a fiscally responsible cost. Therefore, we have created the Targeted Panel (TarPan) Viewer, a software tool, to investigate this type of data. RESULTS TarPan Viewer helps investigators understand data from targeted sequencing data by displaying the information through a web browser interface. Through this interface, investigators can easily observe copy number changes, mutations, and structural events in cancer samples. The viewer runs in R Shiny with a robust SQLite backend and its input is generated from bioinformatic algorithms reliably described in the literature. Here we show the results from using TarPan Viewer on publicly available follicular lymphoma, breast cancer, and multiple myeloma data. In addition, we have tested and utilized the viewer internally, and this data has been used in high-impact peer-reviewed publications. CONCLUSIONS We have designed a flexible, simple to setup viewer that is easily adaptable to any type of cancer targeted sequencing, and has already proven its use in a research laboratory environment. Further, we believe with deeper sequencing and/or more targeted application it could be of use in the clinic in conjunction with an appropriate targeted sequencing panel as a cost-effective diagnostic test, especially in cancers such as acute leukemia or diffuse large B-cell lymphoma that require rapid interventions.
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Affiliation(s)
- Cody Ashby
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA. .,Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Michael Rutherford
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Michael A Bauer
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Erich A Peterson
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yan Wang
- Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Eileen M Boyle
- Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Christopher P Wardell
- Department of Biomedical Informatics, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Cancer Institute: Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian A Walker
- Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
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36
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Boyle EM, Ashby C, Tytarenko RG, Deshpande S, Wang H, Wang Y, Rosenthal A, Sawyer J, Tian E, Flynt E, Hoering A, Johnson SK, Rutherford MW, Wardell CP, Bauer MA, Dumontet C, Facon T, Thanendrarajan S, Schinke CD, Zangari M, van Rhee F, Barlogie B, Cairns D, Jackson G, Thakurta A, Davies FE, Morgan GJ, Walker BA. BRAF and DIS3 Mutations Associate with Adverse Outcome in a Long-term Follow-up of Patients with Multiple Myeloma. Clin Cancer Res 2020; 26:2422-2432. [DOI: 10.1158/1078-0432.ccr-19-1507] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 10/11/2019] [Accepted: 01/22/2020] [Indexed: 11/16/2022]
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George SL, Izquierdo E, Campbell J, Koutroumanidou E, Proszek P, Jamal S, Hughes D, Yuan L, Marshall LV, Carceller F, Chisholm JC, Vaidya S, Mandeville H, Angelini P, Wasti A, Bexelius T, Thway K, Gatz SA, Clarke M, Al-Lazikani B, Barone G, Anderson J, Tweddle DA, Gonzalez D, Walker BA, Barton J, Depani S, Eze J, Ahmed SW, Moreno L, Pearson A, Shipley J, Jones C, Hargrave D, Jacques TS, Hubank M, Chesler L. A tailored molecular profiling programme for children with cancer to identify clinically actionable genetic alterations. Eur J Cancer 2019; 121:224-235. [PMID: 31543384 PMCID: PMC6839402 DOI: 10.1016/j.ejca.2019.07.027] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Revised: 06/27/2019] [Accepted: 07/23/2019] [Indexed: 11/10/2022]
Abstract
BACKGROUND For children with cancer, the clinical integration of precision medicine to enable predictive biomarker-based therapeutic stratification is urgently needed. METHODS We have developed a hybrid-capture next-generation sequencing (NGS) panel, specifically designed to detect genetic alterations in paediatric solid tumours, which gives reliable results from as little as 50 ng of DNA extracted from formalin-fixed paraffin-embedded (FFPE) tissue. In this study, we offered an NGS panel, with clinical reporting via a molecular tumour board for children with solid tumours. Furthermore, for a cohort of 12 patients, we used a circulating tumour DNA (ctDNA)-specific panel to sequence ctDNA from matched plasma samples and compared plasma and tumour findings. RESULTS A total of 255 samples were submitted from 223 patients for the NGS panel. Using FFPE tissue, 82% of all submitted samples passed quality control for clinical reporting. At least one genetic alteration was detected in 70% of sequenced samples. The overall detection rate of clinically actionable alterations, defined by modified OncoKB criteria, for all sequenced samples was 51%. A total of 8 patients were sequenced at different stages of treatment. In 6 of these, there were differences in the genetic alterations detected between time points. Sequencing of matched ctDNA in a cohort of extracranial paediatric solid tumours also identified a high detection rate of somatic alterations in plasma. CONCLUSION We demonstrate that tailored clinical molecular profiling of both tumour DNA and plasma-derived ctDNA is feasible for children with solid tumours. Furthermore, we show that a targeted NGS panel-based approach can identify actionable genetic alterations in a high proportion of patients.
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Affiliation(s)
- Sally L George
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK.
| | - Elisa Izquierdo
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK; Glioma Team, Division of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - James Campbell
- Bioinformatics Core Facility, The Institute of Cancer Research, London, UK
| | - Eleni Koutroumanidou
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Paula Proszek
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Sabri Jamal
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Deborah Hughes
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Lina Yuan
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Lynley V Marshall
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Fernando Carceller
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Julia C Chisholm
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Sucheta Vaidya
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Henry Mandeville
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Paola Angelini
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Ajla Wasti
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Tomas Bexelius
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Khin Thway
- Pathology Department, Royal Marsden NHS Foundation Trust, London, UK
| | - Susanne A Gatz
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK; Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK; Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK
| | - Matthew Clarke
- Glioma Team, Division of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Bissan Al-Lazikani
- Bioinformatics Core Facility, The Institute of Cancer Research, London, UK
| | - Giuseppe Barone
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - John Anderson
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, UK
| | - Deborah A Tweddle
- Northern Institute for Cancer Research, Newcastle University, Newcastle, UK
| | - David Gonzalez
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK; Centre for Cancer Research and Cell Biology, Queens University Belfast, Belfast, UK
| | - Brian A Walker
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK; Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jack Barton
- Developmental Biology and Cancer Programme, UCL GOS Institute of Child Health, London, UK
| | - Sarita Depani
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Jessica Eze
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Histology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Saira W Ahmed
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Histology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Lucas Moreno
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK; HNJ-CNIO Clinical Research Unit, Hospital Universitario Nino Jesus, Madrid, Spain; Paediatric Oncology & Haematology, Vall d'Hebron University Hospital, Barcelona, Spain
| | - Andrew Pearson
- Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
| | - Janet Shipley
- Sarcoma Molecular Pathology Team, Divisions of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Chris Jones
- Glioma Team, Division of Molecular Pathology and Cancer Therapeutics, The Institute of Cancer Research, London, UK
| | - Darren Hargrave
- Cancer Research UK Clinical Trials Unit, Institute of Cancer and Genomic Sciences, University of Birmingham, Birmingham, UK; Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Thomas S Jacques
- Department of Haematology and Oncology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK; Department of Histology, Great Ormond Street Hospital for Children NHS Foundation Trust, London, UK
| | - Michael Hubank
- Molecular Diagnostics Department, The Institute of Cancer Research and Clinical Genomics, The Royal Marsden NHS Foundation, London, UK
| | - Louis Chesler
- Paediatric Tumour Biology, Division of Clinical Studies, The Institute of Cancer Research, London, UK; Children and Young People's Unit, Royal Marsden NHS Foundation Trust, London, UK
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Pearson A, Proszek P, Pascual J, Fribbens C, Shamsher MK, Kingston B, O'Leary B, Herrera-Abreu MT, Cutts RJ, Garcia-Murillas I, Bye H, Walker BA, Gonzalez De Castro D, Yuan L, Jamal S, Hubank M, Lopez-Knowles E, Schuster EF, Dowsett M, Osin P, Nerurkar A, Parton M, Okines AF, Johnston SR, Ring A, Turner NC. Inactivating NF1 Mutations Are Enriched in Advanced Breast Cancer and Contribute to Endocrine Therapy Resistance. Clin Cancer Res 2019; 26:608-622. [DOI: 10.1158/1078-0432.ccr-18-4044] [Citation(s) in RCA: 37] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2018] [Revised: 07/23/2019] [Accepted: 10/02/2019] [Indexed: 11/16/2022]
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Went M, Kinnersley B, Sud A, Johnson DC, Weinhold N, Försti A, van Duin M, Orlando G, Mitchell JS, Kuiper R, Walker BA, Gregory WM, Hoffmann P, Jackson GH, Nöthen MM, da Silva Filho MI, Thomsen H, Broyl A, Davies FE, Thorsteinsdottir U, Hansson M, Kaiser M, Sonneveld P, Goldschmidt H, Stefansson K, Hemminki K, Nilsson B, Morgan GJ, Houlston RS. Transcriptome-wide association study of multiple myeloma identifies candidate susceptibility genes. Hum Genomics 2019; 13:37. [PMID: 31429796 PMCID: PMC6700979 DOI: 10.1186/s40246-019-0231-5] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2019] [Accepted: 08/12/2019] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND While genome-wide association studies (GWAS) of multiple myeloma (MM) have identified variants at 23 regions influencing risk, the genes underlying these associations are largely unknown. To identify candidate causal genes at these regions and search for novel risk regions, we performed a multi-tissue transcriptome-wide association study (TWAS). RESULTS GWAS data on 7319 MM cases and 234,385 controls was integrated with Genotype-Tissue Expression Project (GTEx) data assayed in 48 tissues (sample sizes, N = 80-491), including lymphocyte cell lines and whole blood, to predict gene expression. We identified 108 genes at 13 independent regions associated with MM risk, all of which were in 1 Mb of known MM GWAS risk variants. Of these, 94 genes, located in eight regions, had not previously been considered as a candidate gene for that locus. CONCLUSIONS Our findings highlight the value of leveraging expression data from multiple tissues to identify candidate genes responsible for GWAS associations which provide insight into MM tumorigenesis. Among the genes identified, a number have plausible roles in MM biology, notably APOBEC3C, APOBEC3H, APOBEC3D, APOBEC3F, APOBEC3G, or have been previously implicated in other malignancies. The genes identified in this TWAS can be explored for follow-up and validation to further understand their role in MM biology.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK.
| | - Ben Kinnersley
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - David C Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Niels Weinhold
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Asta Försti
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Mark van Duin
- Department of Hematology, Erasmus MC Cancer Institute, 3075, EA, Rotterdam, The Netherlands
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Jonathan S Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Rowan Kuiper
- Department of Hematology, Erasmus MC Cancer Institute, 3075, EA, Rotterdam, The Netherlands
| | - Brian A Walker
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Walter M Gregory
- Clinical Trials Research Unit, University of Leeds, Leeds, LS2 9PH, UK
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003, Basel, Switzerland
| | | | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, D-53127, Bonn, Germany
| | | | - Hauke Thomsen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Annemiek Broyl
- Department of Hematology, Erasmus MC Cancer Institute, 3075, EA, Rotterdam, The Netherlands
| | - Faith E Davies
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | | | - Markus Hansson
- Hematology Clinic, Skåne University Hospital, SE-221 85, Lund, Sweden
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84, Lund, Sweden
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
| | - Pieter Sonneveld
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
| | | | - Kari Hemminki
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84, Lund, Sweden
- Broad Institute, 7 Cambridge Center, Cambridge, MA, 02142, USA
| | - Gareth J Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, 15 Cotswold Road, Sutton, Surrey, SM2 5NG, UK
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40
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Sawyer JR, Tian E, Walker BA, Wardell C, Lukacs JL, Sammartino G, Bailey C, Schinke CD, Thanendrarajan S, Davies FE, Morgan GJ, Barlogie B, Zangari M, van Rhee F. An acquired high-risk chromosome instability phenotype in multiple myeloma: Jumping 1q Syndrome. Blood Cancer J 2019; 9:62. [PMID: 31399558 PMCID: PMC6689064 DOI: 10.1038/s41408-019-0226-4] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/01/2019] [Revised: 07/05/2019] [Accepted: 07/11/2019] [Indexed: 02/06/2023] Open
Abstract
Patients with multiple myeloma (MM) accumulate adverse copy number aberrations (CNAs), gains of 1q21, and 17p deletions during disease progression. A subset of these patients develops heightened 1q12 pericentromeric instability and jumping translocations of 1q12 (JT1q12), evidenced by increased copy CNAs of 1q21 and losses in receptor chromosomes (RC). To understand the progression of these aberrations we analyzed metaphase cells of 50 patients with ≥4 CNAs of 1q21 by G-banding, locus specific FISH, and spectral karyotyping. In eight patients with ≥5 CNAs of 1q21 we identified a chromosome instability phenotype similar to that found in ICF syndrome (immunodeficiency, centromeric instability, and facial anomalies). Strikingly, the acquired instability phenotype identified in these patients demonstrates the same transient structural aberrations of 1q12 as those found in ICF syndrome, suggesting similar underlying pathological mechanisms. Four types of clonal aberrations characterize this phenotype including JT1q12s, RC deletions, 1q12-21 breakage-fusion-bridge cycle amplifications, and RC insertions. In addition, recurring transient aberrations include 1q12 decondensation and breakage, triradials, and 1q micronuclei. The acquired self-propagating mobile property of 1q12 satellite DNA drives the continuous regeneration of 1q12 duplication/deletion events. For patients demonstrating this instability phenotype, we propose the term "Jumping 1q Syndrome."
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Affiliation(s)
- Jeffrey R Sawyer
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA. .,Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
| | - Erming Tian
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian A Walker
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Christopher Wardell
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Janet L Lukacs
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Gael Sammartino
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Clyde Bailey
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Carolina D Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Faith E Davies
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Gareth J Morgan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Bart Barlogie
- Department of Hematology and Medical Oncology, Tisch Cancer Institute, Icahn School of Medicine at Mount Sinai, New York, NY, USA
| | - Maurizio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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41
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Jones JR, Weinhold N, Ashby C, Walker BA, Wardell C, Pawlyn C, Rasche L, Melchor L, Cairns DA, Gregory WM, Johnson D, Begum DB, Ellis S, Sherborne AL, Cook G, Kaiser MF, Drayson MT, Owen RG, Jackson GH, Davies FE, Greaves M, Morgan GJ. Clonal evolution in myeloma: the impact of maintenance lenalidomide and depth of response on the genetics and sub-clonal structure of relapsed disease in uniformly treated newly diagnosed patients. Haematologica 2019; 104:1440-1450. [PMID: 30733268 PMCID: PMC6601103 DOI: 10.3324/haematol.2018.202200] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [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: 08/31/2018] [Accepted: 01/30/2019] [Indexed: 12/27/2022] Open
Abstract
The emergence of treatment resistant sub-clones is a key feature of relapse in multiple myeloma. Therapeutic attempts to extend remission and prevent relapse include maximizing response and the use of maintenance therapy. We used whole exome sequencing to study the genetics of paired samples taken at presentation and at relapse from 56 newly diagnosed patients, following induction therapy, randomized to receive either lenalidomide maintenance or observation as part of the Myeloma XI trial. Patients included were considered high risk, relapsing within 30 months of maintenance randomization. Patients achieving a complete response had predominantly branching evolutionary patterns leading to relapse, characterized by a greater mutational burden, an altered mutational profile, bi-allelic inactivation of tumor suppressor genes, and acquired structural aberrations. Conversely, in patients achieving a partial response, the evolutionary features were predominantly stable with a similar mutational and structural profile seen at both time points. There were no significant differences between patients relapsing after lenalidomide maintenance versus observation. This study shows that the depth of response is a key determinant of the evolutionary patterns seen at relapse. This trial is registered at clinicaltrials.gov identifier: 01554852.
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Affiliation(s)
- John R Jones
- Department of Haematology, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- The Institute of Cancer Research, London, UK
| | - Niels Weinhold
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Cody Ashby
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian A Walker
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Chris Wardell
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Charlotte Pawlyn
- Department of Haematology, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- The Institute of Cancer Research, London, UK
| | - Leo Rasche
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - David A Cairns
- Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research, University of Leeds, UK
| | - Walter M Gregory
- Clinical Trials Research Unit, Leeds Institute of Clinical Trials Research, University of Leeds, UK
| | | | - Dil B Begum
- The Institute of Cancer Research, London, UK
| | - Sidra Ellis
- The Institute of Cancer Research, London, UK
| | - Amy L Sherborne
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Gordon Cook
- Leeds Institute of Cancer and Pathology, University of Leeds, UK
| | - Martin F Kaiser
- Department of Haematology, The Royal Marsden Hospital NHS Foundation Trust, London, UK
- The Institute of Cancer Research, London, UK
| | - Mark T Drayson
- Clinical Immunology, School of Immunity and Infection, University of Birmingham, UK
| | - Roger G Owen
- Leeds Institute of Cancer and Pathology, University of Leeds, UK
| | - Graham H Jackson
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Faith E Davies
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Mel Greaves
- The Institute of Cancer Research, London, UK
| | - Gareth J Morgan
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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42
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Mikulasova A, Ashby C, Tytarenko RG, Qu P, Rosenthal A, Dent JA, Ryan KR, Bauer MA, Wardell CP, Hoering A, Mavrommatis K, Trotter M, Deshpande S, Yaccoby S, Tian E, Keats J, Auclair D, Jackson GH, Davies FE, Thakurta A, Morgan GJ, Walker BA. Microhomology-mediated end joining drives complex rearrangements and overexpression of MYC and PVT1 in multiple myeloma. Haematologica 2019; 105:1055-1066. [PMID: 31221783 PMCID: PMC7109748 DOI: 10.3324/haematol.2019.217927] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [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: 01/29/2019] [Accepted: 06/13/2019] [Indexed: 12/22/2022] Open
Abstract
MYC is a widely acting transcription factor and its deregulation is a crucial event in many human cancers. MYC is important biologically and clinically in multiple myeloma, but the mechanisms underlying its dysregulation are poorly understood. We show that MYC rearrangements are present in 36.0% of newly diagnosed myeloma patients, as detected in the largest set of next generation sequencing data to date (n=1,267). Rearrangements were complex and associated with increased expression of MYC and PVT1, but not other genes at 8q24. The highest effect on gene expression was detected in cases where the MYC locus is juxtaposed next to super-enhancers associated with genes such as IGH, IGK, IGL, TXNDC5/BMP6, FAM46C and FOXO3. We identified three hotspots of recombination at 8q24, one of which is enriched for IGH-MYC translocations. Breakpoint analysis indicates primary myeloma rearrangements involving the IGH locus occur through non-homologous end joining, whereas secondary MYC rearrangements occur through microhomology-mediated end joining. This mechanism is different to lymphomas, where non-homologous end joining generates MYC rearrangements. Rearrangements resulted in overexpression of key genes and chromatin immunoprecipitation-sequencing identified that HK2, a member of the glucose metabolism pathway, is directly over-expressed through binding of MYC at its promoter.
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Affiliation(s)
- Aneta Mikulasova
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Institute of Cellular Medicine, Newcastle University, Newcastle upon Tyne, UK
| | - Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ruslana G Tytarenko
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Pingping Qu
- Cancer Research and Biostatistics, Seattle, WA, USA
| | | | - Judith A Dent
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Katie R Ryan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Michael A Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | | | | | - Matthew Trotter
- Celgene Institute for Translational Research Europe, Seville, Spain
| | - Shayu Deshpande
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Shmuel Yaccoby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Erming Tian
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jonathan Keats
- Translational Genomics Research Institute, Phoenix, AZ, USA
| | | | - Graham H Jackson
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, UK
| | - Faith E Davies
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Gareth J Morgan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian A Walker
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA .,Division of Hematology Oncology, Indiana University, Indianapolis, IN, USA
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43
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Boyle EM, Leleu X, Petillon MO, Karlin L, Doyen C, Demarquette H, Royer B, Macro M, Moreau P, Fostier K, Marie-Lorraine C, Zarnitsky C, Perrot A, Herbaux C, Poulain S, Manier S, Beauvais D, Walker BA, Wardell CP, Vincent L, Frenzel L, Caillon H, Susanna S, Dejoie T, Avet-Loiseau H, Mohty M, Facon T. Daratumumab and dexamethasone is safe and effective for triple refractory myeloma patients: final results of the IFM 2014-04 (Etoile du Nord) trial. Br J Haematol 2019; 187:319-327. [PMID: 31218679 DOI: 10.1111/bjh.16059] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [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: 03/21/2019] [Accepted: 04/30/2019] [Indexed: 11/29/2022]
Abstract
Single agent daratumumab has shown clinical activity in relapsed, refractory multiple myeloma (RRMM). The Intergroupe Francophone du Myélome 2014-04 trial was designed to further investigate daratumumab in combination with dexamethasone in triple RRMM patients. Patients received daratumumab infusions in combination with weekly dexamethasone until disease progression or unacceptable toxicity. Fifty-seven patients were included in the trial and evaluable for response. The overall response rate and the clinical benefit rate were 33% (n = 19) and 48% (n = 27), respectively. Five (8·8%) patients achieved a very good partial response or better. The median time to response was 4 weeks. For responding patients, the median progression-free survival was 6·6 months, compared to 3·7 months (3·0-5·5) for those with a minimal or stable disease. The median overall survival (OS) for all patients was 16·7 months (11·2-24·0). For responding patients, the median OS was 23·23 months, whereas that of patients with progressive disease was 2·97 months. The incidence of infusion-related reactions was 37%; all cases were manageable and did not lead to dose reduction or permanent treatment discontinuation. These data demonstrate that treatment with daratumumab and dexamethasone results in a meaningful long-term benefit with an acceptable safety profile for patients with triple RRMM.
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Affiliation(s)
- Eileen M Boyle
- Department of Haematology, Hôpital Claude Huriez, Lille University Hospital, Lille, France
| | - Xavier Leleu
- Department of Haematology, Hôpital de la Miletrie, Poitiers University Hospital, Poitiers, France
| | - Marie-Odile Petillon
- Department of Haematology, Hôpital Claude Huriez, Lille University Hospital, Lille, France
| | - Lionel Karlin
- Department of Haematology, Hôpital Lyon Sud, Lyon University Hospital, Pierre-Bénite, France
| | - Chantal Doyen
- Department of Haematology, CHU Dinant Godinne, UCL Namur, Yvoir, Belgium
| | | | - Bruno Royer
- Department of Haematology, Hôpital St Louis, Paris, France
| | - Margaret Macro
- Department of Haematology, CHRU Cote de Nacre, Caen University Hospital, Caen, France
| | - Philippe Moreau
- Department of Haematology, CHRU Hôtel Dieu, Nantes, University Hospital, Nantes, France
| | - Karel Fostier
- Department of Haematology, UZ Brussel, Brussels, Belgium
| | | | - Charles Zarnitsky
- Department of Haematology, Centre Hospitalier J. Monod, CH du Havre, Le Havre, France
| | - Aurore Perrot
- Department of Haematology, Hôpitaux de Brabois, CHRU Nancy, Nancy, France
| | - Charles Herbaux
- Department of Haematology, Hôpital Claude Huriez, Lille University Hospital, Lille, France
| | - Stephanie Poulain
- Service d'Hématologie Cellulaire, Centre de Biologie Pathologie, Lille University Hospital, Lille, France.,INSERM UMRS 1172, Lille, France
| | - Salomon Manier
- Department of Haematology, Hôpital Claude Huriez, Lille University Hospital, Lille, France
| | - David Beauvais
- Department of Haematology, Hôpital Claude Huriez, Lille University Hospital, Lille, France
| | - Brian A Walker
- Myeloma Centre, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Laure Vincent
- Department of Haematology, CHU Montpellier, Montpellier, France
| | - Laurent Frenzel
- Department of Clinical Haematology, AP-HP, Necker Hospital, Paris, France
| | - Hélène Caillon
- Department of Biochemistry, University Hospital of Nantes, Nantes, France
| | - Schraen Susanna
- Department of Biochemistry, Biology Pathology Centre, Lille University Hospital, Lille, France
| | - Thomas Dejoie
- Department of Biochemistry, University Hospital of Nantes, Nantes, France
| | - Hervé Avet-Loiseau
- Genomics of Myeloma Unit, University Hospital of Toulouse, Toulouse, France
| | - Mohamad Mohty
- Department of Haematology, Hôpital Saint Antoine, APHP, Paris, France
| | - Thierry Facon
- Department of Haematology, Hôpital Claude Huriez, Lille University Hospital, Lille, France
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44
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Walker BA, Gerhards CM, Werner LA, Horn DL. Amplitude modulation detection and temporal modulation cutoff frequency in normal hearing infants. J Acoust Soc Am 2019; 145:3667. [PMID: 31255105 PMCID: PMC7112713 DOI: 10.1121/1.5111757] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2018] [Revised: 05/22/2019] [Accepted: 05/28/2019] [Indexed: 05/30/2023]
Abstract
The goal of this study was to determine if temporal modulation cutoff frequency was mature in three-month-old infants. Normal-hearing infants and young adults were tested in a single-interval forced-choice observer-based psychoacoustic procedure. Two parameters of the temporal modulation transfer function (TMTF) were estimated to separate temporal resolution from amplitude modulation sensitivity. The modulation detection threshold (MDT) of a broadband noise amplitude modulated at 10 Hz estimated the y-intercept of the TMTF. The cutoff frequency of the TMTF, measured at a modulation depth 4 dB greater than the MDT, provided an estimate of temporal resolution. MDT was obtained in 27 of 33 infants while both MDT and cutoff frequency was obtained in 15 infants and in 16 of 16 adults. Mean MDT was approximately 10 dB poorer in infants compared to adults. In contrast, mean temporal modulation cutoff frequency did not differ significantly between age groups. These results suggest that temporal resolution is mature, on average, by three months of age in normal hearing children despite immature sensitivity to amplitude modulation. The temporal modulation cutoff frequency approach used here may be a feasible way to examine development of temporal resolution in young listeners with markedly immature sensitivity to amplitude modulation.
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Affiliation(s)
- Brian A Walker
- University of Washington School of Medicine, Seattle, Washington 98195, USA
| | - Caitlin M Gerhards
- Department of Speech and Hearing Sciences, University of Washington, Seattle, Washington 98195, USA
| | - Lynne A Werner
- Department of Speech and Hearing Sciences, University of Washington, Seattle, Washington 98195, USA
| | - David L Horn
- Department of Otolaryngology-Head and Neck Surgery, Virginia Merrill Bloedel Hearing Research Center, University of Washington, Box 357923, Seattle, Washington 98195, USA
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45
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Ashby C, Tytarenko RG, Wang Y, Weinhold N, Johnson SK, Bauer M, Wardell CP, Schinke C, Thanendrarajan S, Zangari M, van Rhee F, Davies FE, Sawyer JR, Morgan GJ, Walker BA. Poor overall survival in hyperhaploid multiple myeloma is defined by double-hit bi-allelic inactivation of TP53. Oncotarget 2019; 10:732-737. [PMID: 30774775 PMCID: PMC6366829 DOI: 10.18632/oncotarget.26589] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [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: 11/22/2018] [Accepted: 12/29/2018] [Indexed: 11/25/2022] Open
Abstract
Hyperhaploid multiple myeloma is a rare numerical aberration group defined by a range of 24-34 chromosomes, which is associated with a poor prognosis with a 5-year survival rate of 23%. Hyperhaploid patient samples (n=8) were sequenced and copy number and mutations identified. Samples had a median of 13 monosomies (range 12-14), which in general were those not associated with trisomies in hyperdiploid samples. The chromosomes traditionally trisomic in hyperdiploid myeloma were disomic in hyperhaploid myeloma with retention of heterodisomy. We examined the hyperhaploid samples for frequently mutated genes and found that 8/8 (100%) hyperhaploid samples had a mutation in TP53, exceeding the overall rate of mutation in newly diagnosed patients (5.5%), indicating an oncogenic dependency in this group. All samples with TP53 mutation also had monosomy of chromosome 17, indicating bi-allelic inactivation of TP53. As such, this high risk group is part of double-hit myeloma.
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Affiliation(s)
- Cody Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Ruslana G Tytarenko
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Yan Wang
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Niels Weinhold
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Sarah K Johnson
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Michael Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Carolina Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | | | - Mauricio Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Frits van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Faith E Davies
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Jeffrey R Sawyer
- Department of Pathology, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Gareth J Morgan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Brian A Walker
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
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46
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Went M, Sud A, Försti A, Halvarsson BM, Weinhold N, Kimber S, van Duin M, Thorleifsson G, Holroyd A, Johnson DC, Li N, Orlando G, Law PJ, Ali M, Chen B, Mitchell JS, Gudbjartsson DF, Kuiper R, Stephens OW, Bertsch U, Broderick P, Campo C, Bandapalli OR, Einsele H, Gregory WA, Gullberg U, Hillengass J, Hoffmann P, Jackson GH, Jöckel KH, Johnsson E, Kristinsson SY, Mellqvist UH, Nahi H, Easton D, Pharoah P, Dunning A, Peto J, Canzian F, Swerdlow A, Eeles RA, Kote-Jarai Z, Muir K, Pashayan N, Nickel J, Nöthen MM, Rafnar T, Ross FM, da Silva Filho MI, Thomsen H, Turesson I, Vangsted A, Andersen NF, Waage A, Walker BA, Wihlborg AK, Broyl A, Davies FE, Thorsteinsdottir U, Langer C, Hansson M, Goldschmidt H, Kaiser M, Sonneveld P, Stefansson K, Morgan GJ, Hemminki K, Nilsson B, Houlston RS. Author Correction: Identification of multiple risk loci and regulatory mechanisms influencing susceptibility to multiple myeloma. Nat Commun 2019; 10:213. [PMID: 30631080 PMCID: PMC6328616 DOI: 10.1038/s41467-018-08107-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023] Open
Abstract
The original version of this Article contained an error in the spelling of a member of the PRACTICAL Consortium, Manuela Gago-Dominguez, which was incorrectly given as Manuela Gago Dominguez. This has now been corrected in both the PDF and HTML versions of the Article. Furthermore, in the original HTML version of this Article, the order of authors within the author list was incorrect. The PRACTICAL consortium was incorrectly listed after Richard S. Houlston and should have been listed after Nora Pashayan. This error has been corrected in the HTML version of the Article; the PDF version was correct at the time of publication.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Asta Försti
- German Cancer Research Center, 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden
| | - Britt-Marie Halvarsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Scott Kimber
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Mark van Duin
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | | | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - David C Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ni Li
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Mina Ali
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Bowang Chen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Jonathan S Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Daniel F Gudbjartsson
- deCODE Genetics, Sturlugata 8, IS-101, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, IS-101, Reykjavik, Iceland
| | - Rowan Kuiper
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Owen W Stephens
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Uta Bertsch
- German Cancer Research Center, 69120, Heidelberg, Germany
- National Centre of Tumor Diseases, 69120, Heidelberg, Germany
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Chiara Campo
- German Cancer Research Center, 69120, Heidelberg, Germany
| | | | | | - Walter A Gregory
- Clinical Trials Research Unit, University of Leeds, Leeds, LS2 9PH, UK
| | - Urban Gullberg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Jens Hillengass
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003, Basel, Switzerland
| | | | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, D-45147, Germany
| | - Ellinor Johnsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Sigurður Y Kristinsson
- Department of Hematology, Landspitali, National University Hospital of Iceland, IS-101, Reykjavik, Iceland
| | - Ulf-Henrik Mellqvist
- Section of Hematology, Sahlgrenska University Hospital, Gothenburg, 413 45, Sweden
| | - Hareth Nahi
- Center for Hematology and Regenerative Medicine, SE-171 77, Stockholm, Sweden
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Alison Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Jolanta Nickel
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, D-53127, Bonn, Germany
| | - Thorunn Rafnar
- deCODE Genetics, Sturlugata 8, IS-101, Reykjavik, Iceland
| | - Fiona M Ross
- Wessex Regional Genetics Laboratory, University of Southampton, Salisbury, SP2 8BJ, UK
| | | | - Hauke Thomsen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Ingemar Turesson
- Hematology Clinic, Skåne University Hospital, SE-221 85, Lund, Sweden
| | - Annette Vangsted
- Department of Haematology, University Hospital of Copenhagen at Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen, Denmark
| | - Niels Frost Andersen
- Department of Haematology, Aarhus University Hospital, Tage-Hansens Gade 2, DK-8000, Aarhus C, Denmark
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Box 8905, N-7491, Trondheim, Norway
| | - Brian A Walker
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Anna-Karin Wihlborg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Annemiek Broyl
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Faith E Davies
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Sturlugata 8, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Christian Langer
- Department of Internal Medicine III, University of Ulm, D-89081, Ulm, Germany
| | - Markus Hansson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
- Hematology Clinic, Skåne University Hospital, SE-221 85, Lund, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
- National Centre of Tumor Diseases, 69120, Heidelberg, Germany
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Pieter Sonneveld
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | | | - Gareth J Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Kari Hemminki
- German Cancer Research Center, 69120, Heidelberg, Germany.
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden.
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden.
- Broad Institute, 7 Cambridge Center, Cambridge, MA, 02142, USA.
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK.
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47
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Went M, Sud A, Speedy H, Sunter NJ, Försti A, Law PJ, Johnson DC, Mirabella F, Holroyd A, Li N, Orlando G, Weinhold N, van Duin M, Chen B, Mitchell JS, Mansouri L, Juliusson G, Smedby KE, Jayne S, Majid A, Dearden C, Allsup DJ, Bailey JR, Pratt G, Pepper C, Fegan C, Rosenquist R, Kuiper R, Stephens OW, Bertsch U, Broderick P, Einsele H, Gregory WM, Hillengass J, Hoffmann P, Jackson GH, Jöckel KH, Nickel J, Nöthen MM, da Silva Filho MI, Thomsen H, Walker BA, Broyl A, Davies FE, Hansson M, Goldschmidt H, Dyer MJS, Kaiser M, Sonneveld P, Morgan GJ, Hemminki K, Nilsson B, Catovsky D, Allan JM, Houlston RS. Genetic correlation between multiple myeloma and chronic lymphocytic leukaemia provides evidence for shared aetiology. Blood Cancer J 2018; 9:1. [PMID: 30602759 PMCID: PMC6315026 DOI: 10.1038/s41408-018-0162-8] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2018] [Accepted: 11/19/2018] [Indexed: 02/08/2023] Open
Abstract
The clustering of different types of B-cell malignancies in families raises the possibility of shared aetiology. To examine this, we performed cross-trait linkage disequilibrium (LD)-score regression of multiple myeloma (MM) and chronic lymphocytic leukaemia (CLL) genome-wide association study (GWAS) data sets, totalling 11,734 cases and 29,468 controls. A significant genetic correlation between these two B-cell malignancies was shown (Rg = 0.4, P = 0.0046). Furthermore, four of the 45 known CLL risk loci were shown to associate with MM risk and five of the 23 known MM risk loci associate with CLL risk. By integrating eQTL, Hi-C and ChIP-seq data, we show that these pleiotropic risk loci are enriched for B-cell regulatory elements and implicate B-cell developmental genes. These data identify shared biological pathways influencing the development of CLL and, MM and further our understanding of the aetiological basis of these B-cell malignancies.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Helen Speedy
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Nicola J Sunter
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Asta Försti
- German Cancer Research Center, 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - David C Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Fabio Mirabella
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ni Li
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Mark van Duin
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Bowang Chen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Jonathan S Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Larry Mansouri
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75105, Uppsala, Sweden
| | - Gunnar Juliusson
- Lund Strategic Research Center for Stem Cell Biology and Cell Therapy, Hematology and Transplantation, Lund University, Lund, Sweden
| | - Karin E Smedby
- Unit of Clinical Epidemiology, Department of Medicine, Karolinska Institutet, Stockholm, Sweden
| | - Sandrine Jayne
- Ernest and Helen Scott Haematological Research Institute, Leicester University, Leicester, UK
| | - Aneela Majid
- Ernest and Helen Scott Haematological Research Institute, Leicester University, Leicester, UK
| | - Claire Dearden
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - David J Allsup
- Department of Haematology, Hull Royal Infirmary, Hull, UK
| | - James R Bailey
- Hull York Medical School and University of Hull, Hull, UK
| | - Guy Pratt
- Department of Haematology, Birmingham Heartlands Hospital, Birmingham, UK
| | - Chris Pepper
- Department of Haematology, School of Medicine, Cardiff University, Cardiff, UK
| | - Chris Fegan
- Cardiff and Vale National Health Service Trust, Heath Park, Cardiff, UK
| | - Richard Rosenquist
- Department of Immunology, Genetics and Pathology, Science for Life Laboratory, Uppsala University, 75105, Uppsala, Sweden
| | - Rowan Kuiper
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Owen W Stephens
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Uta Bertsch
- German Cancer Research Center, 69120, Heidelberg, Germany
- National Centre of Tumor Diseases, 69120, Heidelberg, Germany
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | | | - Walter M Gregory
- Clinical Trials Research Unit, University of Leeds, Leeds, LS2 9PH, UK
| | - Jens Hillengass
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003, Basel, Switzerland
| | | | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, Germany
| | - Jolanta Nickel
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Department of Genomics, Life and Brain Center, University of Bonn, D-53127, Bonn, Germany
| | | | - Hauke Thomsen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Brian A Walker
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Annemiek Broyl
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Faith E Davies
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Markus Hansson
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund University, Lund, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
- National Centre of Tumor Diseases, 69120, Heidelberg, Germany
| | - Martin J S Dyer
- Ernest and Helen Scott Haematological Research Institute, Leicester University, Leicester, UK
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Pieter Sonneveld
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Gareth J Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Kari Hemminki
- German Cancer Research Center, 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, SE-221 84 Lund University, Lund, Sweden
- Broad Institute, 7 Cambridge Center, Cambridge, MA, 02142, USA
| | - Daniel Catovsky
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - James M Allan
- Northern Institute for Cancer Research, Newcastle University, Newcastle upon Tyne, NE2 4HH, UK
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
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48
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Rasche L, Alapat D, Kumar M, Gershner G, McDonald J, Wardell CP, Samant R, Van Hemert R, Epstein J, Williams AF, Thanendrarajan S, Schinke C, Bauer M, Ashby C, Tytarenko RG, van Rhee F, Walker BA, Zangari M, Barlogie B, Davies FE, Morgan GJ, Weinhold N. Combination of flow cytometry and functional imaging for monitoring of residual disease in myeloma. Leukemia 2018; 33:1713-1722. [PMID: 30573775 PMCID: PMC6586541 DOI: 10.1038/s41375-018-0329-0] [Citation(s) in RCA: 96] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Revised: 09/24/2018] [Accepted: 10/10/2018] [Indexed: 02/08/2023]
Abstract
The iliac crest is the sampling site for minimal residual disease (MRD) monitoring in multiple myeloma (MM). However, the disease distribution is often heterogeneous, and imaging can be used to complement MRD detection at a single site. We have investigated patients in complete remission (CR) during first-line or salvage therapy for whom MRD flow cytometry and the two imaging modalities positron emission tomography (PET) and diffusion-weighted magnetic resonance imaging (DW-MRI) were performed at the onset of CR. Residual focal lesions (FLs), detectable in 24% of first-line patients, were associated with short progression-free survival (PFS), with DW-MRI detecting disease in more patients. In some patients, FLs were only PET positive, indicating that the two approaches are complementary. Combining MRD and imaging improved prediction of outcome, with double-negative and double-positive features defining groups with excellent and dismal PFS, respectively. FLs were a rare event (12%) in first-line MRD-negative CR patients. In contrast, patients achieving an MRD-negative CR during salvage therapy frequently had FLs (50%). Multi-region sequencing and imaging in an MRD-negative patient showed persistence of spatially separated clones. In conclusion, we show that DW-MRI is a promising tool for monitoring residual disease that complements PET and should be combined with MRD.
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Affiliation(s)
- L Rasche
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.,Department of Internal Medicine 2, University Hospital of Würzburg, Würzburg, Germany
| | - D Alapat
- Pathology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - M Kumar
- Radiology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - G Gershner
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - J McDonald
- Radiology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C P Wardell
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - R Samant
- Radiology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - R Van Hemert
- Radiology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - J Epstein
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - A F Williams
- Pathology Department, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - S Thanendrarajan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Schinke
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - M Bauer
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - C Ashby
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - R G Tytarenko
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - F van Rhee
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - B A Walker
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - M Zangari
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - B Barlogie
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - F E Davies
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - G J Morgan
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - N Weinhold
- Myeloma Center, University of Arkansas for Medical Sciences, Little Rock, AR, USA.
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49
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Affiliation(s)
- Brian A Walker
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR
| | - Gareth J Morgan
- Myeloma Institute, University of Arkansas for Medical Sciences, Little Rock, AR
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50
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Went M, Sud A, Försti A, Halvarsson BM, Weinhold N, Kimber S, van Duin M, Thorleifsson G, Holroyd A, Johnson DC, Li N, Orlando G, Law PJ, Ali M, Chen B, Mitchell JS, Gudbjartsson DF, Kuiper R, Stephens OW, Bertsch U, Broderick P, Campo C, Bandapalli OR, Einsele H, Gregory WA, Gullberg U, Hillengass J, Hoffmann P, Jackson GH, Jöckel KH, Johnsson E, Kristinsson SY, Mellqvist UH, Nahi H, Easton D, Pharoah P, Dunning A, Peto J, Canzian F, Swerdlow A, Eeles RA, Kote-Jarai ZS, Muir K, Pashayan N, Nickel J, Nöthen MM, Rafnar T, Ross FM, da Silva Filho MI, Thomsen H, Turesson I, Vangsted A, Andersen NF, Waage A, Walker BA, Wihlborg AK, Broyl A, Davies FE, Thorsteinsdottir U, Langer C, Hansson M, Goldschmidt H, Kaiser M, Sonneveld P, Stefansson K, Morgan GJ, Hemminki K, Nilsson B, Houlston RS. Identification of multiple risk loci and regulatory mechanisms influencing susceptibility to multiple myeloma. Nat Commun 2018; 9:3707. [PMID: 30213928 PMCID: PMC6137048 DOI: 10.1038/s41467-018-04989-w] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [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: 12/12/2017] [Accepted: 06/06/2018] [Indexed: 02/08/2023] Open
Abstract
Genome-wide association studies (GWAS) have transformed our understanding of susceptibility to multiple myeloma (MM), but much of the heritability remains unexplained. We report a new GWAS, a meta-analysis with previous GWAS and a replication series, totalling 9974 MM cases and 247,556 controls of European ancestry. Collectively, these data provide evidence for six new MM risk loci, bringing the total number to 23. Integration of information from gene expression, epigenetic profiling and in situ Hi-C data for the 23 risk loci implicate disruption of developmental transcriptional regulators as a basis of MM susceptibility, compatible with altered B-cell differentiation as a key mechanism. Dysregulation of autophagy/apoptosis and cell cycle signalling feature as recurrently perturbed pathways. Our findings provide further insight into the biological basis of MM.
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Affiliation(s)
- Molly Went
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Asta Försti
- German Cancer Research Center, 69120, Heidelberg, Germany
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden
| | - Britt-Marie Halvarsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Niels Weinhold
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Scott Kimber
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Mark van Duin
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | | | - Amy Holroyd
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - David C Johnson
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Ni Li
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Giulia Orlando
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Philip J Law
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Mina Ali
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Bowang Chen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Jonathan S Mitchell
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Daniel F Gudbjartsson
- deCODE Genetics, Sturlugata 8, IS-101, Reykjavik, Iceland
- School of Engineering and Natural Sciences, University of Iceland, IS-101, Reykjavik, Iceland
| | - Rowan Kuiper
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Owen W Stephens
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Uta Bertsch
- German Cancer Research Center, 69120, Heidelberg, Germany
- National Centre of Tumor Diseases, 69120, Heidelberg, Germany
| | - Peter Broderick
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Chiara Campo
- German Cancer Research Center, 69120, Heidelberg, Germany
| | | | | | - Walter A Gregory
- Clinical Trials Research Unit, University of Leeds, Leeds, LS2 9PH, UK
| | - Urban Gullberg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Jens Hillengass
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Per Hoffmann
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Division of Medical Genetics, Department of Biomedicine, University of Basel, 4003, Basel, Switzerland
| | | | - Karl-Heinz Jöckel
- Institute for Medical Informatics, Biometry and Epidemiology, University Hospital Essen, University of Duisburg-Essen, Essen, D-45147, Germany
| | - Ellinor Johnsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Sigurður Y Kristinsson
- Department of Hematology, Landspitali, National University Hospital of Iceland, IS-101, Reykjavik, Iceland
| | - Ulf-Henrik Mellqvist
- Section of Hematology, Sahlgrenska University Hospital, Gothenburg, 413 45, Sweden
| | - Hareth Nahi
- Center for Hematology and Regenerative Medicine, SE-171 77, Stockholm, Sweden
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Paul Pharoah
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Centre for Cancer Genetic Epidemiology, Department of Public Health and Primary Care, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Alison Dunning
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
| | - Julian Peto
- Department of Non-Communicable Disease Epidemiology, London School of Hygiene and Tropical Medicine, London, WC1E 7HT, UK
| | - Federico Canzian
- Genomic Epidemiology Group, German Cancer Research Center (DKFZ), Heidelberg, 69120, Germany
| | - Anthony Swerdlow
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Division of Breast Cancer Research, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
- Royal Marsden NHS Foundation Trust, Fulham Road, London, SW3 6JJ, UK
| | - ZSofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Kenneth Muir
- Institute of Population Health, University of Manchester, Manchester, M13 9PL, UK
- Warwick Medical School, University of Warwick, Coventry, CV4 7AL, UK
| | - Nora Pashayan
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB1 8RN, UK
- Department of Applied Health Research, University College London, London, WC1E 7HB, UK
| | - Jolanta Nickel
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
| | - Markus M Nöthen
- Institute of Human Genetics, University of Bonn, D-53127, Bonn, Germany
- Department of Genomics, Life & Brain Center, University of Bonn, D-53127, Bonn, Germany
| | - Thorunn Rafnar
- deCODE Genetics, Sturlugata 8, IS-101, Reykjavik, Iceland
| | - Fiona M Ross
- Wessex Regional Genetics Laboratory, University of Southampton, Salisbury, SP2 8BJ, UK
| | | | - Hauke Thomsen
- German Cancer Research Center, 69120, Heidelberg, Germany
| | - Ingemar Turesson
- Hematology Clinic, Skåne University Hospital, SE-221 85, Lund, Sweden
| | - Annette Vangsted
- Department of Haematology, University Hospital of Copenhagen at Rigshospitalet, Blegdamsvej 9, DK-2100, Copenhagen, Denmark
| | - Niels Frost Andersen
- Department of Haematology, Aarhus University Hospital, Tage-Hansens Gade 2, DK-8000, Aarhus C, Denmark
| | - Anders Waage
- Department of Cancer Research and Molecular Medicine, Norwegian University of Science and Technology, Box 8905, N-7491, Trondheim, Norway
| | - Brian A Walker
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Anna-Karin Wihlborg
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
| | - Annemiek Broyl
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | - Faith E Davies
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Unnur Thorsteinsdottir
- deCODE Genetics, Sturlugata 8, IS-101, Reykjavik, Iceland
- Faculty of Medicine, University of Iceland, IS-101, Reykjavik, Iceland
| | - Christian Langer
- Department of Internal Medicine III, University of Ulm, D-89081, Ulm, Germany
| | - Markus Hansson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden
- Hematology Clinic, Skåne University Hospital, SE-221 85, Lund, Sweden
| | - Hartmut Goldschmidt
- Department of Internal Medicine V, University of Heidelberg, 69117, Heidelberg, Germany
- National Centre of Tumor Diseases, 69120, Heidelberg, Germany
| | - Martin Kaiser
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK
| | - Pieter Sonneveld
- Department of Hematology, Erasmus MC Cancer Institute, 3075 EA, Rotterdam, The Netherlands
| | | | - Gareth J Morgan
- Myeloma Institute for Research and Therapy, University of Arkansas for Medical Sciences, Little Rock, AR, 72205, USA
| | - Kari Hemminki
- German Cancer Research Center, 69120, Heidelberg, Germany.
- Center for Primary Health Care Research, Lund University, SE-205 02, Malmo, Sweden.
| | - Björn Nilsson
- Hematology and Transfusion Medicine, Department of Laboratory Medicine, BMC B13, Lund University, SE-221 84, Lund, Sweden.
- Broad Institute, 7 Cambridge Center, Cambridge, MA, 02142, USA.
| | - Richard S Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, SW7 3RP, UK.
- Division of Molecular Pathology, The Institute of Cancer Research, London, SW7 3RP, UK.
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